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abstract:
- lang: eng
  text: How functional protein sequences are distributed in sequence space is fundamentally
    important for evolutionary theory and protein design, particularly if a large
    diversity of protein functions are hidden in evolutionarily unexplored areas of
    the sequence space. However, this question is understudied in part because experimental
    and computational studies use extant sequences as a starting point to study sequence
    space. Here, we study whether extant sequences are representative of the entire
    functional sequence space. Across thousands of protein families from vertebrates
    and bacteria we calculate the dimensionality and the volume of sequence space
    occupied by extant homologs. We find that the observed dimensionality and volume
    of extant sequence space are minuscule, many orders of magnitude smaller than
    what we estimated using a model of protein evolution. Simulating sequence evolution
    we then quantify the impact of phylogeny, selection, and epistasis on restricting
    the evolutionary exploration of sequence space. We find that sequence evolution
    from a single common ancestor, or a single point of origin in sequence space,
    is by far the largest limiting factor that reduces the dimensionality and volume
    of extant sequence space. These results indicate that there are vast areas of
    functional sequence space that have not been explored in evolution because of
    the excessive restrictions on natural exploration of the protein sequence space
    imposed by the point of origin effect. We suggest that protein design methods
    that rely on extant sequences may be limited in their ability to discover truly
    novel functions.
acknowledgement: We thank Olga Kalinina for feedback on our manuscript, Vsevolod Kuksin
  for fruitful discussions and Lev Tsarin for participation in the design of our models.
  This work was supported by Japan Science and Technology Agency as part of Adopting
  Sustainable Partnerships for Innovative Research Ecosystem, Grant No. JPMJAP24B2
  (F.A.K. and L.H.I.), and Fonds Zur Förderung der Wissenschaftlichen Forschung Grant
  ESP253-B (O.O.B.)
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Lada H.
  full_name: Isakova, Lada H.
  last_name: Isakova
- first_name: Elizaveta
  full_name: Streltsova, Elizaveta
  id: 57a170da-dc96-11ea-b7c8-ab3565071bf7
  last_name: Streltsova
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
- first_name: Peter K.
  full_name: Vlasov, Peter K.
  last_name: Vlasov
- first_name: Fyodor
  full_name: Kondrashov, Fyodor
  id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
  last_name: Kondrashov
  orcid: 0000-0001-8243-4694
citation:
  ama: Isakova LH, Streltsova E, Bochkareva O, Vlasov PK, Kondrashov F. Descent from
    a common ancestor restricts exploration of protein sequence space. <i>Proceedings
    of the National Academy of Sciences</i>. 2026;123(14):e2532018123. doi:<a href="https://doi.org/10.1073/pnas.2532018123">10.1073/pnas.2532018123</a>
  apa: Isakova, L. H., Streltsova, E., Bochkareva, O., Vlasov, P. K., &#38; Kondrashov,
    F. (2026). Descent from a common ancestor restricts exploration of protein sequence
    space. <i>Proceedings of the National Academy of Sciences</i>. National Academy
    of Sciences. <a href="https://doi.org/10.1073/pnas.2532018123">https://doi.org/10.1073/pnas.2532018123</a>
  chicago: Isakova, Lada H., Elizaveta Streltsova, Olga Bochkareva, Peter K. Vlasov,
    and Fyodor Kondrashov. “Descent from a Common Ancestor Restricts Exploration of
    Protein Sequence Space.” <i>Proceedings of the National Academy of Sciences</i>.
    National Academy of Sciences, 2026. <a href="https://doi.org/10.1073/pnas.2532018123">https://doi.org/10.1073/pnas.2532018123</a>.
  ieee: L. H. Isakova, E. Streltsova, O. Bochkareva, P. K. Vlasov, and F. Kondrashov,
    “Descent from a common ancestor restricts exploration of protein sequence space,”
    <i>Proceedings of the National Academy of Sciences</i>, vol. 123, no. 14. National
    Academy of Sciences, p. e2532018123, 2026.
  ista: Isakova LH, Streltsova E, Bochkareva O, Vlasov PK, Kondrashov F. 2026. Descent
    from a common ancestor restricts exploration of protein sequence space. Proceedings
    of the National Academy of Sciences. 123(14), e2532018123.
  mla: Isakova, Lada H., et al. “Descent from a Common Ancestor Restricts Exploration
    of Protein Sequence Space.” <i>Proceedings of the National Academy of Sciences</i>,
    vol. 123, no. 14, National Academy of Sciences, 2026, p. e2532018123, doi:<a href="https://doi.org/10.1073/pnas.2532018123">10.1073/pnas.2532018123</a>.
  short: L.H. Isakova, E. Streltsova, O. Bochkareva, P.K. Vlasov, F. Kondrashov, Proceedings
    of the National Academy of Sciences 123 (2026) e2532018123.
date_created: 2026-04-12T22:01:47Z
date_published: 2026-04-07T00:00:00Z
date_updated: 2026-05-04T06:57:31Z
day: '07'
ddc:
- '570'
department:
- _id: UlWa
doi: 10.1073/pnas.2532018123
external_id:
  pmid:
  - '41915737'
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page: e2532018123
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publication: Proceedings of the National Academy of Sciences
publication_identifier:
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publisher: National Academy of Sciences
quality_controlled: '1'
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title: Descent from a common ancestor restricts exploration of protein sequence space
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abstract:
- lang: eng
  text: Active regulation of gene expression, orchestrated by complex interactions
    of activators and repressors at promoters, controls the fate of organisms. In
    contrast, basal expression at uninduced promoters is considered to be a dynamically
    inert mode of non-functional “promoter leakiness”, merely a byproduct of transcriptional
    regulation. Here, we investigate the basal expression mode of the mar operon,
    the main regulator of intrinsic multiple antibiotic resistance in Escherichia
    coli, and link its dynamic properties to the non-canonical, yet highly conserved
    start codon of marR across Enterobacteriaceae. Real-time, single-cell measurements
    across tens of generations reveal that basal expression consists of rare stochastic
    gene expression pulses, which maximize variability in wildtype and, surprisingly,
    transiently accelerate cellular elongation rates. Competition experiments show
    that basal expression confers fitness advantages to wildtype across several transitions
    between exponential and stationary growth by shortening lag times. The dynamically
    rich basal expression of the mar operon has likely been evolutionarily maintained
    for its role in growth homeostasis of Enterobacteria within the gut environment,
    thereby allowing other ancillary gene regulatory roles to evolve, e.g. control
    of costly-to-induce multi-drug efflux pumps. Understanding the complex selection
    forces governing genetic systems involved in intrinsic multi-drug resistance is
    crucial for effective public health measures.
article_processing_charge: No
author:
- first_name: Kirti
  full_name: Jain, Kirti
  id: 330F0278-F248-11E8-B48F-1D18A9856A87
  last_name: Jain
  orcid: 0000-0002-3809-0449
- first_name: Robert
  full_name: Hauschild, Robert
  id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
  last_name: Hauschild
  orcid: 0000-0001-9843-3522
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
- first_name: Roderich
  full_name: Römhild, Roderich
  id: 68E56E44-62B0-11EA-B963-444F3DDC885E
  last_name: Römhild
  orcid: 0000-0001-9480-5261
- first_name: Gašper
  full_name: Tkačik, Gašper
  id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
  last_name: Tkačik
  orcid: 0000-0002-6699-1455
- first_name: Calin C
  full_name: Guet, Calin C
  id: 47F8433E-F248-11E8-B48F-1D18A9856A87
  last_name: Guet
  orcid: 0000-0001-6220-2052
citation:
  ama: Jain K, Hauschild R, Bochkareva O, Römhild R, Tkačik G, Guet CC. Data for “Pulsatile
    basal gene expression as a fitness determinant in bacteria.” 2025. doi:<a href="https://doi.org/10.15479/AT:ISTA:19294">10.15479/AT:ISTA:19294</a>
  apa: Jain, K., Hauschild, R., Bochkareva, O., Römhild, R., Tkačik, G., &#38; Guet,
    C. C. (2025). Data for “Pulsatile basal gene expression as a fitness determinant
    in bacteria.” Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/AT:ISTA:19294">https://doi.org/10.15479/AT:ISTA:19294</a>
  chicago: Jain, Kirti, Robert Hauschild, Olga Bochkareva, Roderich Römhild, Gašper
    Tkačik, and Calin C Guet. “Data for ‘Pulsatile Basal Gene Expression as a Fitness
    Determinant in Bacteria.’” Institute of Science and Technology Austria, 2025.
    <a href="https://doi.org/10.15479/AT:ISTA:19294">https://doi.org/10.15479/AT:ISTA:19294</a>.
  ieee: K. Jain, R. Hauschild, O. Bochkareva, R. Römhild, G. Tkačik, and C. C. Guet,
    “Data for ‘Pulsatile basal gene expression as a fitness determinant in bacteria.’”
    Institute of Science and Technology Austria, 2025.
  ista: Jain K, Hauschild R, Bochkareva O, Römhild R, Tkačik G, Guet CC. 2025. Data
    for ‘Pulsatile basal gene expression as a fitness determinant in bacteria’, Institute
    of Science and Technology Austria, <a href="https://doi.org/10.15479/AT:ISTA:19294">10.15479/AT:ISTA:19294</a>.
  mla: Jain, Kirti, et al. <i>Data for “Pulsatile Basal Gene Expression as a Fitness
    Determinant in Bacteria.”</i> Institute of Science and Technology Austria, 2025,
    doi:<a href="https://doi.org/10.15479/AT:ISTA:19294">10.15479/AT:ISTA:19294</a>.
  short: K. Jain, R. Hauschild, O. Bochkareva, R. Römhild, G. Tkačik, C.C. Guet, (2025).
corr_author: '1'
date_created: 2025-03-04T13:27:21Z
date_published: 2025-03-04T00:00:00Z
date_updated: 2026-05-20T08:33:07Z
day: '04'
ddc:
- '570'
department:
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- _id: Bio
- _id: FyKo
- _id: GaTk
doi: 10.15479/AT:ISTA:19294
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title: Data for "Pulsatile basal gene expression as a fitness determinant in bacteria"
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  short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
APC_amount: 5949 EUR
OA_place: publisher
OA_type: hybrid
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abstract:
- lang: eng
  text: Active regulation of gene expression, orchestrated by complex interactions
    of activators and repressors at promoters, controls the fate of organisms. In
    contrast, basal expression at uninduced promoters is considered to be a dynamically
    inert mode of nonfunctional “promoter leakiness,” merely a byproduct of transcriptional
    regulation. Here, we investigate the basal expression mode of the mar operon,
    the main regulator of intrinsic multiple antibiotic resistance in Escherichia
    coli, and link its dynamic properties to the noncanonical, yet highly conserved
    start codon of marR across Enterobacteriaceae. Real-time, single-cell measurements
    across tens of generations reveal that basal expression consists of rare stochastic
    gene expression pulses, which maximize variability in wildtype and, surprisingly,
    transiently accelerate cellular elongation rates. Competition experiments show
    that basal expression confers fitness advantages to wildtype across several transitions
    between exponential and stationary growth by shortening lag times. The dynamically
    rich basal expression of the mar operon has likely been evolutionarily maintained
    for its role in growth homeostasis of Enterobacteria within the gut environment,
    thereby allowing other ancillary gene regulatory roles to evolve, e.g., control
    of costly-to-induce multidrug efflux pumps. Understanding the complex selection
    forces governing genetic systems involved in intrinsic multidrug resistance is
    crucial for effective public health measures.
acknowledged_ssus:
- _id: Bio
acknowledgement: K.J. thanks B. Wu, I. Tomanek, K. Tomasek for detailed discussions
  on the manuscript, all other members from the Guet laboratory for valuable feedback,
  R. Chait, & Imaging and Optics Facility, Institute of Science and Technology Austria
  for helping with microscopy, Dr. Sudha Rao and Dr. Raja Mugasimangalam, Genotypic
  Technology India for allowing time off to address the revisions. K.J. acknowledges
  Institute of Science and Technology fellowship IC1006FELL02, R.H. was supported
  in part by Chan Zuckerberg Initiative and Donor Advised-Fund grant 2020-225401 (https://doi.org/10.37921/120055ratwvi),
  O.O.B. acknowledges Fonds Zur Förderung der Wissenschaftlichen Forschung (FWF) Grant
  ESP253-B, R.R. acknowledges FWF Grant 10.55776/ESP219, C.C.G. acknowledges FWF I5127-B.
article_number: e2413709122
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Kirti
  full_name: Jain, Kirti
  id: 330F0278-F248-11E8-B48F-1D18A9856A87
  last_name: Jain
  orcid: 0000-0002-3809-0449
- first_name: Robert
  full_name: Hauschild, Robert
  id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
  last_name: Hauschild
  orcid: 0000-0001-9843-3522
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
- first_name: Roderich
  full_name: Römhild, Roderich
  id: 68E56E44-62B0-11EA-B963-444F3DDC885E
  last_name: Römhild
  orcid: 0000-0001-9480-5261
- first_name: Gašper
  full_name: Tkačik, Gašper
  id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
  last_name: Tkačik
  orcid: 0000-0002-6699-1455
- first_name: Calin C
  full_name: Guet, Calin C
  id: 47F8433E-F248-11E8-B48F-1D18A9856A87
  last_name: Guet
  orcid: 0000-0001-6220-2052
citation:
  ama: Jain K, Hauschild R, Bochkareva O, Römhild R, Tkačik G, Guet CC. Pulsatile
    basal gene expression as a fitness determinant in bacteria. <i>Proceedings of
    the National Academy of Sciences</i>. 2025;122(15). doi:<a href="https://doi.org/10.1073/pnas.2413709122">10.1073/pnas.2413709122</a>
  apa: Jain, K., Hauschild, R., Bochkareva, O., Römhild, R., Tkačik, G., &#38; Guet,
    C. C. (2025). Pulsatile basal gene expression as a fitness determinant in bacteria.
    <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences.
    <a href="https://doi.org/10.1073/pnas.2413709122">https://doi.org/10.1073/pnas.2413709122</a>
  chicago: Jain, Kirti, Robert Hauschild, Olga Bochkareva, Roderich Römhild, Gašper
    Tkačik, and Calin C Guet. “Pulsatile Basal Gene Expression as a Fitness Determinant
    in Bacteria.” <i>Proceedings of the National Academy of Sciences</i>. National
    Academy of Sciences, 2025. <a href="https://doi.org/10.1073/pnas.2413709122">https://doi.org/10.1073/pnas.2413709122</a>.
  ieee: K. Jain, R. Hauschild, O. Bochkareva, R. Römhild, G. Tkačik, and C. C. Guet,
    “Pulsatile basal gene expression as a fitness determinant in bacteria,” <i>Proceedings
    of the National Academy of Sciences</i>, vol. 122, no. 15. National Academy of
    Sciences, 2025.
  ista: Jain K, Hauschild R, Bochkareva O, Römhild R, Tkačik G, Guet CC. 2025. Pulsatile
    basal gene expression as a fitness determinant in bacteria. Proceedings of the
    National Academy of Sciences. 122(15), e2413709122.
  mla: Jain, Kirti, et al. “Pulsatile Basal Gene Expression as a Fitness Determinant
    in Bacteria.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122,
    no. 15, e2413709122, National Academy of Sciences, 2025, doi:<a href="https://doi.org/10.1073/pnas.2413709122">10.1073/pnas.2413709122</a>.
  short: K. Jain, R. Hauschild, O. Bochkareva, R. Römhild, G. Tkačik, C.C. Guet, Proceedings
    of the National Academy of Sciences 122 (2025).
corr_author: '1'
date_created: 2025-04-27T22:02:13Z
date_published: 2025-04-15T00:00:00Z
date_updated: 2026-05-20T08:33:08Z
day: '15'
ddc:
- '570'
department:
- _id: CaGu
- _id: Bio
- _id: FyKo
- _id: GaTk
doi: 10.1073/pnas.2413709122
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pmid: 1
project:
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  grant_number: CZI01
  name: Tools for automation and feedback microscopy
- _id: bd6f94d1-d553-11ed-ba76-ae9f07250f74
  grant_number: E219
  name: Non-canonical antibiotic interactions
- _id: 34e076d6-11ca-11ed-8bc3-aec76c41a181
  grant_number: I05127
  name: Evolutionary analysis of gene regulation
publication: Proceedings of the National Academy of Sciences
publication_identifier:
  eissn:
  - 1091-6490
  issn:
  - 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
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title: Pulsatile basal gene expression as a fitness determinant in bacteria
tmp:
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  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 122
year: '2025'
...
---
_id: '14716'
abstract:
- lang: eng
  text: "Background: Antimicrobial resistance (AMR) poses a significant global health
    threat, and an accurate prediction of bacterial resistance patterns is critical
    for effective treatment and control strategies. In recent years, machine learning
    (ML) approaches have emerged as powerful tools for analyzing large-scale bacterial
    AMR data. However, ML methods often ignore evolutionary relationships among bacterial
    strains, which can greatly impact performance of the ML methods, especially if
    resistance-associated features are attempted to be detected. Genome-wide association
    studies (GWAS) methods like linear mixed models accounts for the evolutionary
    relationships in bacteria, but they uncover only highly significant variants which
    have already been reported in literature.\r\n\r\nResults: In this work, we introduce
    a novel phylogeny-related parallelism score (PRPS), which measures whether a certain
    feature is correlated with the population structure of a set of samples. We demonstrate
    that PRPS can be used, in combination with SVM- and random forest-based models,
    to reduce the number of features in the analysis, while simultaneously increasing
    models’ performance. We applied our pipeline to publicly available AMR data from
    PATRIC database for Mycobacterium tuberculosis against six common antibiotics.\r\n\r\nConclusions:
    Using our pipeline, we re-discovered known resistance-associated mutations as
    well as new candidate mutations which can be related to resistance and not previously
    reported in the literature. We demonstrated that taking into account phylogenetic
    relationships not only improves the model performance, but also yields more biologically
    relevant predicted most contributing resistance markers."
acknowledgement: Open Access funding enabled and organized by Projekt DEAL. A.Y. and
  O.V.K. acknowledge financial support from the Klaus Faber Foundation. A.A.A. was
  funded by the Helmholtz AI project AMR-XAI. The work of O.O.B. is funded by Fonds
  zur Förderung der Wissenschaftlichen Forschung (FWF), Grant ESP 253-B.
article_number: '404'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Alper
  full_name: Yurtseven, Alper
  last_name: Yurtseven
- first_name: Sofia
  full_name: Buyanova, Sofia
  id: 2F54A7BC-3902-11EA-AC87-BC9F3DDC885E
  last_name: Buyanova
- first_name: Amay Ajaykumar A.
  full_name: Agrawal, Amay Ajaykumar A.
  last_name: Agrawal
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
- first_name: Olga V V.
  full_name: Kalinina, Olga V V.
  last_name: Kalinina
citation:
  ama: Yurtseven A, Buyanova S, Agrawal AAA, Bochkareva O, Kalinina OVV. Machine learning
    and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis.
    <i>BMC Microbiology</i>. 2023;23(1). doi:<a href="https://doi.org/10.1186/s12866-023-03147-7">10.1186/s12866-023-03147-7</a>
  apa: Yurtseven, A., Buyanova, S., Agrawal, A. A. A., Bochkareva, O., &#38; Kalinina,
    O. V. V. (2023). Machine learning and phylogenetic analysis allow for predicting
    antibiotic resistance in M. tuberculosis. <i>BMC Microbiology</i>. Springer Nature.
    <a href="https://doi.org/10.1186/s12866-023-03147-7">https://doi.org/10.1186/s12866-023-03147-7</a>
  chicago: Yurtseven, Alper, Sofia Buyanova, Amay Ajaykumar A. Agrawal, Olga Bochkareva,
    and Olga V V. Kalinina. “Machine Learning and Phylogenetic Analysis Allow for
    Predicting Antibiotic Resistance in M. Tuberculosis.” <i>BMC Microbiology</i>.
    Springer Nature, 2023. <a href="https://doi.org/10.1186/s12866-023-03147-7">https://doi.org/10.1186/s12866-023-03147-7</a>.
  ieee: A. Yurtseven, S. Buyanova, A. A. A. Agrawal, O. Bochkareva, and O. V. V. Kalinina,
    “Machine learning and phylogenetic analysis allow for predicting antibiotic resistance
    in M. tuberculosis,” <i>BMC Microbiology</i>, vol. 23, no. 1. Springer Nature,
    2023.
  ista: Yurtseven A, Buyanova S, Agrawal AAA, Bochkareva O, Kalinina OVV. 2023. Machine
    learning and phylogenetic analysis allow for predicting antibiotic resistance
    in M. tuberculosis. BMC Microbiology. 23(1), 404.
  mla: Yurtseven, Alper, et al. “Machine Learning and Phylogenetic Analysis Allow
    for Predicting Antibiotic Resistance in M. Tuberculosis.” <i>BMC Microbiology</i>,
    vol. 23, no. 1, 404, Springer Nature, 2023, doi:<a href="https://doi.org/10.1186/s12866-023-03147-7">10.1186/s12866-023-03147-7</a>.
  short: A. Yurtseven, S. Buyanova, A.A.A. Agrawal, O. Bochkareva, O.V.V. Kalinina,
    BMC Microbiology 23 (2023).
date_created: 2023-12-31T23:01:02Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2025-09-09T14:06:03Z
day: '01'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1186/s12866-023-03147-7
external_id:
  isi:
  - '001128788700001'
  pmid:
  - '38124060'
file:
- access_level: open_access
  checksum: 7ff5e95f3496ff663301eb4a13a316d5
  content_type: application/pdf
  creator: dernst
  date_created: 2024-01-02T09:09:32Z
  date_updated: 2024-01-02T09:09:32Z
  file_id: '14723'
  file_name: 2023_BMCMicrobiology_Yurtseven.pdf
  file_size: 1979922
  relation: main_file
  success: 1
file_date_updated: 2024-01-02T09:09:32Z
has_accepted_license: '1'
intvolume: '        23'
isi: 1
issue: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: BMC Microbiology
publication_identifier:
  eissn:
  - 1471-2180
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Machine learning and phylogenetic analysis allow for predicting antibiotic
  resistance in M. tuberculosis
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 23
year: '2023'
...
---
_id: '10927'
abstract:
- lang: eng
  text: "Motivation\r\nHigh plasticity of bacterial genomes is provided by numerous
    mechanisms including horizontal gene transfer and recombination via numerous flanking
    repeats. Genome rearrangements such as inversions, deletions, insertions and duplications
    may independently occur in different strains, providing parallel adaptation or
    phenotypic diversity. Specifically, such rearrangements might be responsible for
    virulence, antibiotic resistance and antigenic variation. However, identification
    of such events requires laborious manual inspection and verification of phyletic
    pattern consistency.\r\nResults\r\nHere, we define the term ‘parallel rearrangements’
    as events that occur independently in phylogenetically distant bacterial strains
    and present a formalization of the problem of parallel rearrangements calling.
    We implement an algorithmic solution for the identification of parallel rearrangements
    in bacterial populations as a tool PaReBrick. The tool takes a collection of strains
    represented as a sequence of oriented synteny blocks and a phylogenetic tree as
    input data. It identifies rearrangements, tests them for consistency with a tree,
    and sorts the events by their parallelism score. The tool provides diagrams of
    the neighbors for each block of interest, allowing the detection of horizontally
    transferred blocks or their extra copies and the inversions in which copied blocks
    are involved. We demonstrated PaReBrick’s efficiency and accuracy and showed its
    potential to detect genome rearrangements responsible for pathogenicity and adaptation
    in bacterial genomes."
acknowledgement: "The authors thank the 2020 student class of the Bioinformatics Institute,
  who\r\nused the first versions of the tool and provided many valuable suggestions
  to\r\nimprove usability. They also thank Louisa Gonzalez Somermeyer for manuscript
  proofreading\r\nThis work was supported by the National Center for Cognitive Research
  of\r\nITMO University and JetBrains Research [to A.Z and N.A.]; and the European\r\nUnion’s
  Horizon 2020 Research and Innovation Programme under the Marie\r\nSkłodowska-Curie
  [754411 to O.B.].\r\nPaReBrick is written in Python and is available on GitHub:
  https://github.com/ctlab/parallel-rearrangements."
article_processing_charge: No
article_type: original
author:
- first_name: Alexey
  full_name: Zabelkin, Alexey
  last_name: Zabelkin
- first_name: Yulia
  full_name: Yakovleva, Yulia
  last_name: Yakovleva
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
- first_name: Nikita
  full_name: Alexeev, Nikita
  last_name: Alexeev
citation:
  ama: 'Zabelkin A, Yakovleva Y, Bochkareva O, Alexeev N. PaReBrick: PArallel REarrangements
    and BReaks identification toolkit. <i>Bioinformatics</i>. 2022;38(2):357-363.
    doi:<a href="https://doi.org/10.1093/bioinformatics/btab691">10.1093/bioinformatics/btab691</a>'
  apa: 'Zabelkin, A., Yakovleva, Y., Bochkareva, O., &#38; Alexeev, N. (2022). PaReBrick:
    PArallel REarrangements and BReaks identification toolkit. <i>Bioinformatics</i>.
    Oxford University Press. <a href="https://doi.org/10.1093/bioinformatics/btab691">https://doi.org/10.1093/bioinformatics/btab691</a>'
  chicago: 'Zabelkin, Alexey, Yulia Yakovleva, Olga Bochkareva, and Nikita Alexeev.
    “PaReBrick: PArallel REarrangements and BReaks Identification Toolkit.” <i>Bioinformatics</i>.
    Oxford University Press, 2022. <a href="https://doi.org/10.1093/bioinformatics/btab691">https://doi.org/10.1093/bioinformatics/btab691</a>.'
  ieee: 'A. Zabelkin, Y. Yakovleva, O. Bochkareva, and N. Alexeev, “PaReBrick: PArallel
    REarrangements and BReaks identification toolkit,” <i>Bioinformatics</i>, vol.
    38, no. 2. Oxford University Press, pp. 357–363, 2022.'
  ista: 'Zabelkin A, Yakovleva Y, Bochkareva O, Alexeev N. 2022. PaReBrick: PArallel
    REarrangements and BReaks identification toolkit. Bioinformatics. 38(2), 357–363.'
  mla: 'Zabelkin, Alexey, et al. “PaReBrick: PArallel REarrangements and BReaks Identification
    Toolkit.” <i>Bioinformatics</i>, vol. 38, no. 2, Oxford University Press, 2022,
    pp. 357–63, doi:<a href="https://doi.org/10.1093/bioinformatics/btab691">10.1093/bioinformatics/btab691</a>.'
  short: A. Zabelkin, Y. Yakovleva, O. Bochkareva, N. Alexeev, Bioinformatics 38 (2022)
    357–363.
corr_author: '1'
date_created: 2022-03-27T22:01:46Z
date_published: 2022-01-15T00:00:00Z
date_updated: 2025-05-14T11:05:09Z
day: '15'
ddc:
- '000'
department:
- _id: FyKo
doi: 10.1093/bioinformatics/btab691
ec_funded: 1
external_id:
  isi:
  - '000743380100008'
file:
- access_level: open_access
  checksum: 4b5688ff9ac86180ccdf7f82fa33d926
  content_type: application/pdf
  creator: dernst
  date_created: 2022-03-28T08:07:46Z
  date_updated: 2022-03-28T08:07:46Z
  file_id: '10930'
  file_name: 2022_Bioinformatics_Zabelkin.pdf
  file_size: 3425744
  relation: main_file
  success: 1
file_date_updated: 2022-03-28T08:07:46Z
has_accepted_license: '1'
intvolume: '        38'
isi: 1
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 357-363
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
publication: Bioinformatics
publication_identifier:
  eissn:
  - 1460-2059
  issn:
  - 1367-4803
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
  link:
  - relation: software
    url: https://github.com/ctlab/parallel-rearrangements
scopus_import: '1'
status: public
title: 'PaReBrick: PArallel REarrangements and BReaks identification toolkit'
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2022'
...
---
_id: '11344'
abstract:
- lang: eng
  text: Until recently, Shigella and enteroinvasive Escherichia coli were thought
    to be primate-restricted pathogens. The base of their pathogenicity is the type
    3 secretion system (T3SS) encoded by the pINV virulence plasmid, which facilitates
    host cell invasion and subsequent proliferation. A large family of T3SS effectors,
    E3 ubiquitin-ligases encoded by the ipaH genes, have a key role in the Shigella
    pathogenicity through the modulation of cellular ubiquitination that degrades
    host proteins. However, recent genomic studies identified ipaH genes in the genomes
    of Escherichia marmotae, a potential marmot pathogen, and an E. coli extracted
    from fecal samples of bovine calves, suggesting that non-human hosts may also
    be infected by these strains, potentially pathogenic to humans. We performed a
    comparative genomic study of the functional repertoires in the ipaH gene family
    in Shigella and enteroinvasive Escherichia from human and predicted non-human
    hosts. We found that fewer than half of Shigella genomes had a complete set of
    ipaH genes, with frequent gene losses and duplications that were not consistent
    with the species tree and nomenclature. Non-human host IpaH proteins had a diverse
    set of substrate-binding domains and, in contrast to the Shigella proteins, two
    variants of the NEL C-terminal domain. Inconsistencies between strains phylogeny
    and composition of effectors indicate horizontal gene transfer between E. coli
    adapted to different hosts. These results provide a framework for understanding
    of ipaH-mediated host-pathogens interactions and suggest a need for a genomic
    study of fecal samples from diseased animals.
acknowledgement: 'The project was initiated with Aygul Minnegalieva and Yulia Yakovleva
  at the Summer School of Molecular and Theoretical Biology (SMTB-2020), supported
  by the Zimin Foundation. We thank Inna Shapovalenko, Daria Abuzova, Elizaveta Kaminskaya,
  and Dmitriy Zvezdin for their contribution to the project during SMTB-2020. We also
  thank Peter Vlasov for fruitful discussions.This study was supported by the Russian
  Foundation for Basic Research (RFBR), Grant # 20-54-14005 and Fonds zur Förderung
  der wissenschaftlichen Forschung (FWF), Grant # I5127-B. The work of OB is supported
  by the European Union’s Horizon 2020 Research and Innovation Programme under the
  Marie Skłodowska-Curie Grant Agreement No. 754411. '
article_number: '6868'
article_processing_charge: No
article_type: original
author:
- first_name: NO
  full_name: Dranenko, NO
  last_name: Dranenko
- first_name: MN
  full_name: Tutukina, MN
  last_name: Tutukina
- first_name: MS
  full_name: Gelfand, MS
  last_name: Gelfand
- first_name: Fyodor
  full_name: Kondrashov, Fyodor
  id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
  last_name: Kondrashov
  orcid: 0000-0001-8243-4694
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
citation:
  ama: Dranenko N, Tutukina M, Gelfand M, Kondrashov F, Bochkareva O. Chromosome-encoded
    IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. <i>Scientific
    Reports</i>. 2022;12. doi:<a href="https://doi.org/10.1038/s41598-022-10827-3">10.1038/s41598-022-10827-3</a>
  apa: Dranenko, N., Tutukina, M., Gelfand, M., Kondrashov, F., &#38; Bochkareva,
    O. (2022). Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive
    Escherichia. <i>Scientific Reports</i>. Springer Nature. <a href="https://doi.org/10.1038/s41598-022-10827-3">https://doi.org/10.1038/s41598-022-10827-3</a>
  chicago: Dranenko, NO, MN Tutukina, MS Gelfand, Fyodor Kondrashov, and Olga Bochkareva.
    “Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human Enteroinvasive Escherichia.”
    <i>Scientific Reports</i>. Springer Nature, 2022. <a href="https://doi.org/10.1038/s41598-022-10827-3">https://doi.org/10.1038/s41598-022-10827-3</a>.
  ieee: N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, and O. Bochkareva, “Chromosome-encoded
    IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia,” <i>Scientific
    Reports</i>, vol. 12. Springer Nature, 2022.
  ista: Dranenko N, Tutukina M, Gelfand M, Kondrashov F, Bochkareva O. 2022. Chromosome-encoded
    IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Scientific
    Reports. 12, 6868.
  mla: Dranenko, NO, et al. “Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human
    Enteroinvasive Escherichia.” <i>Scientific Reports</i>, vol. 12, 6868, Springer
    Nature, 2022, doi:<a href="https://doi.org/10.1038/s41598-022-10827-3">10.1038/s41598-022-10827-3</a>.
  short: N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, O. Bochkareva, Scientific
    Reports 12 (2022).
corr_author: '1'
date_created: 2022-05-02T07:08:42Z
date_published: 2022-04-27T00:00:00Z
date_updated: 2026-04-15T08:51:09Z
day: '27'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1038/s41598-022-10827-3
ec_funded: 1
external_id:
  isi:
  - '000788639400032'
  pmid:
  - '35477739'
file:
- access_level: open_access
  checksum: 12601b8a5c6b83bb618f92bcb963ecc9
  content_type: application/pdf
  creator: dernst
  date_created: 2022-05-02T09:05:20Z
  date_updated: 2022-05-02T09:05:20Z
  file_id: '11349'
  file_name: 2022_ScientificReports_Dranenko.pdf
  file_size: 3564155
  relation: main_file
  success: 1
file_date_updated: 2022-05-02T09:05:20Z
has_accepted_license: '1'
intvolume: '        12'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
- _id: 34e076d6-11ca-11ed-8bc3-aec76c41a181
  grant_number: I05127
  name: Evolutionary analysis of gene regulation
publication: Scientific Reports
publication_identifier:
  issn:
  - 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive
  Escherichia
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2022'
...
---
_id: '9380'
abstract:
- lang: eng
  text: Shigella are pathogens originating within the Escherichia lineage but frequently
    classified as a separate genus. Shigella genomes contain numerous insertion sequences
    (ISs) that lead to pseudogenisation of affected genes and an increase of non-homologous
    recombination. Here, we study 414 genomes of E. coli and Shigella strains to assess
    the contribution of genomic rearrangements to Shigella evolution. We found that
    Shigella experienced exceptionally high rates of intragenomic rearrangements and
    had a decreased rate of homologous recombination compared to pathogenic and non-pathogenic
    E. coli. The high rearrangement rate resulted in independent disruption of syntenic
    regions and parallel rearrangements in different Shigella lineages. Specifically,
    we identified two types of chromosomally encoded E3 ubiquitin-protein ligases
    acquired independently by all Shigella strains that also showed a high level of
    sequence conservation in the promoter and further in the 5′-intergenic region.
    In the only available enteroinvasive E. coli (EIEC) strain, which is a pathogenic
    E. coli with a phenotype intermediate between Shigella and non-pathogenic E. coli,
    we found a rate of genome rearrangements comparable to those in other E. coli
    and no functional copies of the two Shigella-specific E3 ubiquitin ligases. These
    data indicate that the accumulation of ISs influenced many aspects of genome evolution
    and played an important role in the evolution of intracellular pathogens. Our
    research demonstrates the power of comparative genomics-based on synteny block
    composition and an important role of non-coding regions in the evolution of genomic
    islands.
acknowledgement: We thank Fyodor Kondrashov for valuable advice and manuscript proofreading.
  We also thank Alla Mikheenko for assistance with Circos.
article_number: '628622'
article_processing_charge: No
article_type: original
author:
- first_name: Zaira
  full_name: Seferbekova, Zaira
  last_name: Seferbekova
- first_name: Alexey
  full_name: Zabelkin, Alexey
  last_name: Zabelkin
- first_name: Yulia
  full_name: Yakovleva, Yulia
  last_name: Yakovleva
- first_name: Robert
  full_name: Afasizhev, Robert
  last_name: Afasizhev
- first_name: Natalia O.
  full_name: Dranenko, Natalia O.
  last_name: Dranenko
- first_name: Nikita
  full_name: Alexeev, Nikita
  last_name: Alexeev
- first_name: Mikhail S.
  full_name: Gelfand, Mikhail S.
  last_name: Gelfand
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
citation:
  ama: Seferbekova Z, Zabelkin A, Yakovleva Y, et al. High rates of genome rearrangements
    and pathogenicity of Shigella spp. <i>Frontiers in Microbiology</i>. 2021;12.
    doi:<a href="https://doi.org/10.3389/fmicb.2021.628622">10.3389/fmicb.2021.628622</a>
  apa: Seferbekova, Z., Zabelkin, A., Yakovleva, Y., Afasizhev, R., Dranenko, N. O.,
    Alexeev, N., … Bochkareva, O. (2021). High rates of genome rearrangements and
    pathogenicity of Shigella spp. <i>Frontiers in Microbiology</i>. Frontiers. <a
    href="https://doi.org/10.3389/fmicb.2021.628622">https://doi.org/10.3389/fmicb.2021.628622</a>
  chicago: Seferbekova, Zaira, Alexey Zabelkin, Yulia Yakovleva, Robert Afasizhev,
    Natalia O. Dranenko, Nikita Alexeev, Mikhail S. Gelfand, and Olga Bochkareva.
    “High Rates of Genome Rearrangements and Pathogenicity of Shigella Spp.” <i>Frontiers
    in Microbiology</i>. Frontiers, 2021. <a href="https://doi.org/10.3389/fmicb.2021.628622">https://doi.org/10.3389/fmicb.2021.628622</a>.
  ieee: Z. Seferbekova <i>et al.</i>, “High rates of genome rearrangements and pathogenicity
    of Shigella spp,” <i>Frontiers in Microbiology</i>, vol. 12. Frontiers, 2021.
  ista: Seferbekova Z, Zabelkin A, Yakovleva Y, Afasizhev R, Dranenko NO, Alexeev
    N, Gelfand MS, Bochkareva O. 2021. High rates of genome rearrangements and pathogenicity
    of Shigella spp. Frontiers in Microbiology. 12, 628622.
  mla: Seferbekova, Zaira, et al. “High Rates of Genome Rearrangements and Pathogenicity
    of Shigella Spp.” <i>Frontiers in Microbiology</i>, vol. 12, 628622, Frontiers,
    2021, doi:<a href="https://doi.org/10.3389/fmicb.2021.628622">10.3389/fmicb.2021.628622</a>.
  short: Z. Seferbekova, A. Zabelkin, Y. Yakovleva, R. Afasizhev, N.O. Dranenko, N.
    Alexeev, M.S. Gelfand, O. Bochkareva, Frontiers in Microbiology 12 (2021).
corr_author: '1'
date_created: 2021-05-09T22:01:38Z
date_published: 2021-04-12T00:00:00Z
date_updated: 2025-04-14T07:43:52Z
day: '12'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.3389/fmicb.2021.628622
ec_funded: 1
external_id:
  isi:
  - '000643713300001'
file:
- access_level: open_access
  checksum: 2f856543add59273a482a7f326fc0400
  content_type: application/pdf
  creator: kschuh
  date_created: 2021-05-11T13:05:52Z
  date_updated: 2021-05-11T13:05:52Z
  file_id: '9384'
  file_name: 2021_Frontiers_Microbiology_Seferbekova.pdf
  file_size: 14362316
  relation: main_file
  success: 1
file_date_updated: 2021-05-11T13:05:52Z
has_accepted_license: '1'
intvolume: '        12'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
publication: Frontiers in Microbiology
publication_identifier:
  eissn:
  - 1664-302X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: High rates of genome rearrangements and pathogenicity of Shigella spp
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '15071'
abstract:
- lang: eng
  text: "A mesophilic methanogenic culture, designated JL01, was isolated from Holocene
    permafrost in the Russian Arctic [1]. After long-term extensive cultivation at
    15°C it turned out to be a tied binary culture of archaeal (JL01) and bacterial
    (Sphaerochaeta associata GLS2) strains.\r\nStrain JL01 was a strict anaerobe and
    grew on methanol, acetate and methylamines as energy and carbon sources. Cells
    were irregular coccoid, non-motile, non-spore-forming, and Gram-stainpositive.
    Optimum conditions for growth were 24-28 oC, pH 6.8–7.3 and 0.075-0.1 M NaCl.\r\nPhylogenetic
    tree reconstructions based on 16S rRNA and concatenated alignment of broadly\r\nconserved
    protein-coding genes revealed its close relation to Methanosarcina mazei S-6\r\nT
    (similarity 99.5%). The comparison of whole genomic sequences (ANI) of the isolate
    and the type strain of M.mazei was 98.5%, which is higher than the values recommended
    for new species. Thus strain JL01 (=VKM B-2370=JCM 31898) represents the first
    M. mazei isolated from permanently subzero Arcticsediments. The long-term co-cultivation
    of JL01 with S. associata GLS2T showed the methane production without any additional
    carbon and energy sources. Genome analysis of S. associata GLS2T revealed putative
    genes involved in methanochondroithin catabolism."
acknowledgement: "The work was supported by of Russian Foundation of Basic Research:
  grant № 19-04-00831 for Viktoria Shcherbakova and Olga Troshina, grant № 18-34-00334
  for Viktoriia Oshurkova and Vladimir Trubitsyn. \r\nWe thank Dr Natalia Suzina (IBPM
  RAS, Federal Research Center Pushchino Center for\r\nBiological Research RAS) for
  the help with the microscopic studies, respectively; Dr. Margarita Meyer (Division
  of Genetics, Department of Medicine, BWH and HMS, USA) and Dr Fedor Kondrashov (IST,
  Austria) for their help in obtaining the genomic sequence of strain JL01. "
article_processing_charge: Yes
author:
- first_name: Viktoriia
  full_name: Oshurkova, Viktoriia
  last_name: Oshurkova
- first_name: Olga
  full_name: Troshina, Olga
  last_name: Troshina
- first_name: Vladimir
  full_name: Trubitsyn, Vladimir
  last_name: Trubitsyn
- first_name: Yana
  full_name: Ryzhmanova, Yana
  last_name: Ryzhmanova
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
- first_name: Viktoria
  full_name: Shcherbakova, Viktoria
  last_name: Shcherbakova
citation:
  ama: 'Oshurkova V, Troshina O, Trubitsyn V, Ryzhmanova Y, Bochkareva O, Shcherbakova
    V. Characterization of methanosarcina mazei JL01 isolated from holocene arctic
    permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta
    associata GLS2T. In: <i>Proceedings of 1st International Electronic Conference
    on Microbiology</i>. MDPI; 2020. doi:<a href="https://doi.org/10.3390/ecm2020-07116">10.3390/ecm2020-07116</a>'
  apa: 'Oshurkova, V., Troshina, O., Trubitsyn, V., Ryzhmanova, Y., Bochkareva, O.,
    &#38; Shcherbakova, V. (2020). Characterization of methanosarcina mazei JL01 isolated
    from holocene arctic permafrost and study of the archaeon cooperation with bacterium
    Sphaerochaeta associata GLS2T. In <i>Proceedings of 1st International Electronic
    Conference on Microbiology</i>. Virtual: MDPI. <a href="https://doi.org/10.3390/ecm2020-07116">https://doi.org/10.3390/ecm2020-07116</a>'
  chicago: Oshurkova, Viktoriia, Olga Troshina, Vladimir Trubitsyn, Yana Ryzhmanova,
    Olga Bochkareva, and Viktoria Shcherbakova. “Characterization of Methanosarcina
    Mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon
    Cooperation with Bacterium Sphaerochaeta Associata GLS2T.” In <i>Proceedings of
    1st International Electronic Conference on Microbiology</i>. MDPI, 2020. <a href="https://doi.org/10.3390/ecm2020-07116">https://doi.org/10.3390/ecm2020-07116</a>.
  ieee: V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, and
    V. Shcherbakova, “Characterization of methanosarcina mazei JL01 isolated from
    holocene arctic permafrost and study of the archaeon cooperation with bacterium
    Sphaerochaeta associata GLS2T,” in <i>Proceedings of 1st International Electronic
    Conference on Microbiology</i>, Virtual, 2020.
  ista: 'Oshurkova V, Troshina O, Trubitsyn V, Ryzhmanova Y, Bochkareva O, Shcherbakova
    V. 2020. Characterization of methanosarcina mazei JL01 isolated from holocene
    arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta
    associata GLS2T. Proceedings of 1st International Electronic Conference on Microbiology.
    ECM: Electronic Conference on Microbiology.'
  mla: Oshurkova, Viktoriia, et al. “Characterization of Methanosarcina Mazei JL01
    Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation
    with Bacterium Sphaerochaeta Associata GLS2T.” <i>Proceedings of 1st International
    Electronic Conference on Microbiology</i>, MDPI, 2020, doi:<a href="https://doi.org/10.3390/ecm2020-07116">10.3390/ecm2020-07116</a>.
  short: V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, V.
    Shcherbakova, in:, Proceedings of 1st International Electronic Conference on Microbiology,
    MDPI, 2020.
conference:
  end_date: 2020-11-30
  location: Virtual
  name: 'ECM: Electronic Conference on Microbiology'
  start_date: 2020-11-02
date_created: 2024-03-04T11:41:31Z
date_published: 2020-11-02T00:00:00Z
date_updated: 2024-03-20T08:06:22Z
day: '02'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.3390/ecm2020-07116
file:
- access_level: open_access
  checksum: d1914af7811a21a4b2744eb51b5834e3
  content_type: application/pdf
  creator: dernst
  date_created: 2024-03-20T08:05:46Z
  date_updated: 2024-03-20T08:05:46Z
  file_id: '15127'
  file_name: 2020_ECM_Oshurkova.pdf
  file_size: 595543
  relation: main_file
  success: 1
file_date_updated: 2024-03-20T08:05:46Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Proceedings of 1st International Electronic Conference on Microbiology
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: Characterization of methanosarcina mazei JL01 isolated from holocene arctic
  permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata
  GLS2T
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8263'
abstract:
- lang: eng
  text: "Background: The genus Streptococcus comprises pathogens that strongly influence
    the health of humans and animals. Genome sequencing of multiple Streptococcus
    strains demonstrated high variability in gene content and order even in closely
    related strains of the same species and created a newly emerged object for genomic
    analysis, the pan-genome. Here we analysed the genome evolution of 25 strains
    of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of
    Streptococcus pneumoniae.\r\n\r\nResults: Fractions of the pan-genome, unique,
    periphery, and universal genes differ in size, functional composition, the level
    of nucleotide substitutions, and predisposition to horizontal gene transfer and
    genomic rearrangements. The density of substitutions in intergenic regions appears
    to be correlated with selection acting on adjacent genes, implying that more conserved
    genes tend to have more conserved regulatory regions.\r\nThe total pan-genome
    of the genus is open, but only due to strain-specific genes, whereas other pan-genome
    fractions reach saturation. We have identified the set of genes with phylogenies
    inconsistent with species and non-conserved location in the chromosome; these
    genes are rare in at least one species and have likely experienced recent horizontal
    transfer between species. The strain-specific fraction is enriched with mobile
    elements and hypothetical proteins, but also contains a number of candidate virulence-related
    genes, so it may have a strong impact on adaptability and pathogenicity.\r\nMapping
    the rearrangements to the phylogenetic tree revealed large parallel inversions
    in all species. A parallel inversion of length 15 kB with breakpoints formed by
    genes encoding surface antigen proteins PhtD and PhtB in S. pneumoniae leads to
    replacement of gene fragments that likely indicates the action of an antigen variation
    mechanism.\r\n\r\nConclusions: Members of genus Streptococcus have a highly dynamic,
    open pan-genome, that potentially confers them with the ability to adapt to changing
    environmental conditions, i.e. antibiotic resistance or transmission between different
    hosts. Hence, integrated analysis of all aspects of genome evolution is important
    for the identification of potential pathogens and design of drugs and vaccines."
article_number: '83'
article_processing_charge: No
article_type: original
author:
- first_name: Pavel V.
  full_name: Shelyakin, Pavel V.
  last_name: Shelyakin
  orcid: 0000-0003-0120-9319
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
- first_name: Anna A.
  full_name: Karan, Anna A.
  last_name: Karan
- first_name: Mikhail S.
  full_name: Gelfand, Mikhail S.
  last_name: Gelfand
citation:
  ama: 'Shelyakin PV, Bochkareva O, Karan AA, Gelfand MS. Micro-evolution of three
    Streptococcus species: Selection, antigenic variation, and horizontal gene inflow.
    <i>BMC Evolutionary Biology</i>. 2019;19. doi:<a href="https://doi.org/10.1186/s12862-019-1403-6">10.1186/s12862-019-1403-6</a>'
  apa: 'Shelyakin, P. V., Bochkareva, O., Karan, A. A., &#38; Gelfand, M. S. (2019).
    Micro-evolution of three Streptococcus species: Selection, antigenic variation,
    and horizontal gene inflow. <i>BMC Evolutionary Biology</i>. Springer Nature.
    <a href="https://doi.org/10.1186/s12862-019-1403-6">https://doi.org/10.1186/s12862-019-1403-6</a>'
  chicago: 'Shelyakin, Pavel V., Olga Bochkareva, Anna A. Karan, and Mikhail S. Gelfand.
    “Micro-Evolution of Three Streptococcus Species: Selection, Antigenic Variation,
    and Horizontal Gene Inflow.” <i>BMC Evolutionary Biology</i>. Springer Nature,
    2019. <a href="https://doi.org/10.1186/s12862-019-1403-6">https://doi.org/10.1186/s12862-019-1403-6</a>.'
  ieee: 'P. V. Shelyakin, O. Bochkareva, A. A. Karan, and M. S. Gelfand, “Micro-evolution
    of three Streptococcus species: Selection, antigenic variation, and horizontal
    gene inflow,” <i>BMC Evolutionary Biology</i>, vol. 19. Springer Nature, 2019.'
  ista: 'Shelyakin PV, Bochkareva O, Karan AA, Gelfand MS. 2019. Micro-evolution of
    three Streptococcus species: Selection, antigenic variation, and horizontal gene
    inflow. BMC Evolutionary Biology. 19, 83.'
  mla: 'Shelyakin, Pavel V., et al. “Micro-Evolution of Three Streptococcus Species:
    Selection, Antigenic Variation, and Horizontal Gene Inflow.” <i>BMC Evolutionary
    Biology</i>, vol. 19, 83, Springer Nature, 2019, doi:<a href="https://doi.org/10.1186/s12862-019-1403-6">10.1186/s12862-019-1403-6</a>.'
  short: P.V. Shelyakin, O. Bochkareva, A.A. Karan, M.S. Gelfand, BMC Evolutionary
    Biology 19 (2019).
date_created: 2020-08-15T11:04:07Z
date_published: 2019-03-27T00:00:00Z
date_updated: 2023-02-23T13:28:54Z
day: '27'
doi: 10.1186/s12862-019-1403-6
extern: '1'
intvolume: '        19'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1186/s12862-019-1403-6
month: '03'
oa: 1
oa_version: Published Version
publication: BMC Evolutionary Biology
publication_identifier:
  issn:
  - 1471-2148
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'Micro-evolution of three Streptococcus species: Selection, antigenic variation,
  and horizontal gene inflow'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2019'
...
---
_id: '9731'
abstract:
- lang: eng
  text: OGs with putative pseudogenes by the number of affected genomes in different
    chlamydial species. Frameshift and nonsense mutations located less than 60 bp
    upstreamof the gene end or present in a single genome from the corresponding OG
    were excluded. (CSV 31 kb)
article_processing_charge: No
author:
- first_name: Olga
  full_name: Sigalova, Olga
  last_name: Sigalova
- first_name: Andrei
  full_name: Chaplin, Andrei
  last_name: Chaplin
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
- first_name: Pavel
  full_name: Shelyakin, Pavel
  last_name: Shelyakin
- first_name: Vsevolod
  full_name: Filaretov, Vsevolod
  last_name: Filaretov
- first_name: Evgeny
  full_name: Akkuratov, Evgeny
  last_name: Akkuratov
- first_name: Valentina
  full_name: Burskaia, Valentina
  last_name: Burskaia
- first_name: Mikhail S.
  full_name: Gelfand, Mikhail S.
  last_name: Gelfand
citation:
  ama: Sigalova O, Chaplin A, Bochkareva O, et al. Additional file 11 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. 2019. doi:<a href="https://doi.org/10.6084/m9.figshare.9808772.v1">10.6084/m9.figshare.9808772.v1</a>
  apa: Sigalova, O., Chaplin, A., Bochkareva, O., Shelyakin, P., Filaretov, V., Akkuratov,
    E., … Gelfand, M. S. (2019). Additional file 11 of Chlamydia pan-genomic analysis
    reveals balance between host adaptation and selective pressure to genome reduction.
    Springer Nature. <a href="https://doi.org/10.6084/m9.figshare.9808772.v1">https://doi.org/10.6084/m9.figshare.9808772.v1</a>
  chicago: Sigalova, Olga, Andrei Chaplin, Olga Bochkareva, Pavel Shelyakin, Vsevolod
    Filaretov, Evgeny Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional
    File 11 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation
    and Selective Pressure to Genome Reduction.” Springer Nature, 2019. <a href="https://doi.org/10.6084/m9.figshare.9808772.v1">https://doi.org/10.6084/m9.figshare.9808772.v1</a>.
  ieee: O. Sigalova <i>et al.</i>, “Additional file 11 of Chlamydia pan-genomic analysis
    reveals balance between host adaptation and selective pressure to genome reduction.”
    Springer Nature, 2019.
  ista: Sigalova O, Chaplin A, Bochkareva O, Shelyakin P, Filaretov V, Akkuratov E,
    Burskaia V, Gelfand MS. 2019. Additional file 11 of Chlamydia pan-genomic analysis
    reveals balance between host adaptation and selective pressure to genome reduction,
    Springer Nature, <a href="https://doi.org/10.6084/m9.figshare.9808772.v1">10.6084/m9.figshare.9808772.v1</a>.
  mla: Sigalova, Olga, et al. <i>Additional File 11 of Chlamydia Pan-Genomic Analysis
    Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>.
    Springer Nature, 2019, doi:<a href="https://doi.org/10.6084/m9.figshare.9808772.v1">10.6084/m9.figshare.9808772.v1</a>.
  short: O. Sigalova, A. Chaplin, O. Bochkareva, P. Shelyakin, V. Filaretov, E. Akkuratov,
    V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-07-27T14:09:11Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-04-03T09:39:40Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808772.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.9808772.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
  record:
  - id: '6898'
    relation: used_in_publication
    status: public
status: public
title: Additional file 11 of Chlamydia pan-genomic analysis reveals balance between
  host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9783'
abstract:
- lang: eng
  text: Predicted frameshift and nonsense mutations in Chlamydial pan-genome. For
    the analysis of putative pseudogenes, events located less than 60 bp. away from
    gene end or present in a single genome from the corresponding OG were excluded.
    (CSV 600 kb)
article_processing_charge: No
author:
- first_name: Olga M.
  full_name: Sigalova, Olga M.
  last_name: Sigalova
- first_name: Andrei V.
  full_name: Chaplin, Andrei V.
  last_name: Chaplin
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
- first_name: Pavel V.
  full_name: Shelyakin, Pavel V.
  last_name: Shelyakin
- first_name: Vsevolod A.
  full_name: Filaretov, Vsevolod A.
  last_name: Filaretov
- first_name: Evgeny E.
  full_name: Akkuratov, Evgeny E.
  last_name: Akkuratov
- first_name: Valentina
  full_name: Burskaia, Valentina
  last_name: Burskaia
- first_name: Mikhail S.
  full_name: Gelfand, Mikhail S.
  last_name: Gelfand
citation:
  ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 10 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. 2019. doi:<a href="https://doi.org/10.6084/m9.figshare.9808760.v1">10.6084/m9.figshare.9808760.v1</a>
  apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
    V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 10 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. Springer Nature. <a href="https://doi.org/10.6084/m9.figshare.9808760.v1">https://doi.org/10.6084/m9.figshare.9808760.v1</a>
  chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
    Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
    Gelfand. “Additional File 10 of Chlamydia Pan-Genomic Analysis Reveals Balance
    between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
    Nature, 2019. <a href="https://doi.org/10.6084/m9.figshare.9808760.v1">https://doi.org/10.6084/m9.figshare.9808760.v1</a>.
  ieee: O. M. Sigalova <i>et al.</i>, “Additional file 10 of Chlamydia pan-genomic
    analysis reveals balance between host adaptation and selective pressure to genome
    reduction.” Springer Nature, 2019.
  ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
    EE, Burskaia V, Gelfand MS. 2019. Additional file 10 of Chlamydia pan-genomic
    analysis reveals balance between host adaptation and selective pressure to genome
    reduction, Springer Nature, <a href="https://doi.org/10.6084/m9.figshare.9808760.v1">10.6084/m9.figshare.9808760.v1</a>.
  mla: Sigalova, Olga M., et al. <i>Additional File 10 of Chlamydia Pan-Genomic Analysis
    Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>.
    Springer Nature, 2019, doi:<a href="https://doi.org/10.6084/m9.figshare.9808760.v1">10.6084/m9.figshare.9808760.v1</a>.
  short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
    E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-06T07:59:56Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-04-03T09:39:40Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808760.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.9808760.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
  record:
  - id: '6898'
    relation: used_in_publication
    status: public
status: public
title: Additional file 10 of Chlamydia pan-genomic analysis reveals balance between
  host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '6898'
abstract:
- lang: eng
  text: "Background\r\n\r\nChlamydia are ancient intracellular pathogens with reduced,
    though strikingly conserved genome. Despite their parasitic lifestyle and isolated
    intracellular environment, these bacteria managed to avoid accumulation of deleterious
    mutations leading to subsequent genome degradation characteristic for many parasitic
    bacteria.\r\nResults\r\n\r\nWe report pan-genomic analysis of sixteen species
    from genus Chlamydia including identification and functional annotation of orthologous
    genes, and characterization of gene gains, losses, and rearrangements. We demonstrate
    the overall genome stability of these bacteria as indicated by a large fraction
    of common genes with conserved genomic locations. On the other hand, extreme evolvability
    is confined to several paralogous gene families such as polymorphic membrane proteins
    and phospholipase D, and likely is caused by the pressure from the host immune
    system.\r\nConclusions\r\n\r\nThis combination of a large, conserved core genome
    and a small, evolvable periphery likely reflect the balance between the selective
    pressure towards genome reduction and the need to adapt to escape from the host
    immunity."
article_number: '710'
article_processing_charge: No
author:
- first_name: Olga M.
  full_name: Sigalova, Olga M.
  last_name: Sigalova
- first_name: Andrei V.
  full_name: Chaplin, Andrei V.
  last_name: Chaplin
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
- first_name: Pavel V.
  full_name: Shelyakin, Pavel V.
  last_name: Shelyakin
- first_name: Vsevolod A.
  full_name: Filaretov, Vsevolod A.
  last_name: Filaretov
- first_name: Evgeny E.
  full_name: Akkuratov, Evgeny E.
  last_name: Akkuratov
- first_name: Valentina
  full_name: Burskaia, Valentina
  last_name: Burskaia
- first_name: Mikhail S.
  full_name: Gelfand, Mikhail S.
  last_name: Gelfand
citation:
  ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Chlamydia pan-genomic analysis
    reveals balance between host adaptation and selective pressure to genome reduction.
    <i>BMC Genomics</i>. 2019;20(1). doi:<a href="https://doi.org/10.1186/s12864-019-6059-5">10.1186/s12864-019-6059-5</a>
  apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
    V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Chlamydia pan-genomic analysis
    reveals balance between host adaptation and selective pressure to genome reduction.
    <i>BMC Genomics</i>. BioMed Central. <a href="https://doi.org/10.1186/s12864-019-6059-5">https://doi.org/10.1186/s12864-019-6059-5</a>
  chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
    Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
    Gelfand. “Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation
    and Selective Pressure to Genome Reduction.” <i>BMC Genomics</i>. BioMed Central,
    2019. <a href="https://doi.org/10.1186/s12864-019-6059-5">https://doi.org/10.1186/s12864-019-6059-5</a>.
  ieee: O. M. Sigalova <i>et al.</i>, “Chlamydia pan-genomic analysis reveals balance
    between host adaptation and selective pressure to genome reduction,” <i>BMC Genomics</i>,
    vol. 20, no. 1. BioMed Central, 2019.
  ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
    EE, Burskaia V, Gelfand MS. 2019. Chlamydia pan-genomic analysis reveals balance
    between host adaptation and selective pressure to genome reduction. BMC Genomics.
    20(1), 710.
  mla: Sigalova, Olga M., et al. “Chlamydia Pan-Genomic Analysis Reveals Balance between
    Host Adaptation and Selective Pressure to Genome Reduction.” <i>BMC Genomics</i>,
    vol. 20, no. 1, 710, BioMed Central, 2019, doi:<a href="https://doi.org/10.1186/s12864-019-6059-5">10.1186/s12864-019-6059-5</a>.
  short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
    E.E. Akkuratov, V. Burskaia, M.S. Gelfand, BMC Genomics 20 (2019).
date_created: 2019-09-22T22:00:36Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-04-03T09:39:42Z
day: '12'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1186/s12864-019-6059-5
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title: Chlamydia pan-genomic analysis reveals balance between host adaptation and
  selective pressure to genome reduction
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
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abstract:
- lang: eng
  text: Distribution of OGs with mosaic phyletic patterns across species (complete
    genomes only). (CSV 7 kb)
article_processing_charge: No
author:
- first_name: Olga M.
  full_name: Sigalova, Olga M.
  last_name: Sigalova
- first_name: Andrei V.
  full_name: Chaplin, Andrei V.
  last_name: Chaplin
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
- first_name: Pavel V.
  full_name: Shelyakin, Pavel V.
  last_name: Shelyakin
- first_name: Vsevolod A.
  full_name: Filaretov, Vsevolod A.
  last_name: Filaretov
- first_name: Evgeny E.
  full_name: Akkuratov, Evgeny E.
  last_name: Akkuratov
- first_name: Valentina
  full_name: Burskaia, Valentina
  last_name: Burskaia
- first_name: Mikhail S.
  full_name: Gelfand, Mikhail S.
  last_name: Gelfand
citation:
  ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 15 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. 2019. doi:<a href="https://doi.org/10.6084/m9.figshare.9808802.v1">10.6084/m9.figshare.9808802.v1</a>
  apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
    V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 15 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. Springer Nature. <a href="https://doi.org/10.6084/m9.figshare.9808802.v1">https://doi.org/10.6084/m9.figshare.9808802.v1</a>
  chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
    Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
    Gelfand. “Additional File 15 of Chlamydia Pan-Genomic Analysis Reveals Balance
    between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
    Nature, 2019. <a href="https://doi.org/10.6084/m9.figshare.9808802.v1">https://doi.org/10.6084/m9.figshare.9808802.v1</a>.
  ieee: O. M. Sigalova <i>et al.</i>, “Additional file 15 of Chlamydia pan-genomic
    analysis reveals balance between host adaptation and selective pressure to genome
    reduction.” Springer Nature, 2019.
  ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
    EE, Burskaia V, Gelfand MS. 2019. Additional file 15 of Chlamydia pan-genomic
    analysis reveals balance between host adaptation and selective pressure to genome
    reduction, Springer Nature, <a href="https://doi.org/10.6084/m9.figshare.9808802.v1">10.6084/m9.figshare.9808802.v1</a>.
  mla: Sigalova, Olga M., et al. <i>Additional File 15 of Chlamydia Pan-Genomic Analysis
    Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>.
    Springer Nature, 2019, doi:<a href="https://doi.org/10.6084/m9.figshare.9808802.v1">10.6084/m9.figshare.9808802.v1</a>.
  short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
    E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-11T14:26:40Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-04-03T09:39:40Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808802.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.9808802.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
  record:
  - id: '6898'
    relation: used_in_publication
    status: public
status: public
title: Additional file 15 of Chlamydia pan-genomic analysis reveals balance between
  host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9892'
abstract:
- lang: eng
  text: Distribution of OGs with mosaic phyletic patterns across species (all genomes).
    (CSV 10 kb)
article_processing_charge: No
author:
- first_name: Olga M.
  full_name: Sigalova, Olga M.
  last_name: Sigalova
- first_name: Andrei V
  full_name: Chaplin, Andrei V
  last_name: Chaplin
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
- first_name: Pavel V.
  full_name: Shelyakin, Pavel V.
  last_name: Shelyakin
- first_name: Vsevolod A.
  full_name: Filaretov, Vsevolod A.
  last_name: Filaretov
- first_name: Evgeny E.
  full_name: Akkuratov, Evgeny E.
  last_name: Akkuratov
- first_name: Valentina
  full_name: Burskaia, Valentina
  last_name: Burskaia
- first_name: Mikhail S.
  full_name: Gelfand, Mikhail S.
  last_name: Gelfand
citation:
  ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 16 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. 2019. doi:<a href="https://doi.org/10.6084/m9.figshare.9808814.v1">10.6084/m9.figshare.9808814.v1</a>
  apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
    V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 16 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. Springer Nature. <a href="https://doi.org/10.6084/m9.figshare.9808814.v1">https://doi.org/10.6084/m9.figshare.9808814.v1</a>
  chicago: Sigalova, Olga M., Andrei V Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
    Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
    Gelfand. “Additional File 16 of Chlamydia Pan-Genomic Analysis Reveals Balance
    between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
    Nature, 2019. <a href="https://doi.org/10.6084/m9.figshare.9808814.v1">https://doi.org/10.6084/m9.figshare.9808814.v1</a>.
  ieee: O. M. Sigalova <i>et al.</i>, “Additional file 16 of Chlamydia pan-genomic
    analysis reveals balance between host adaptation and selective pressure to genome
    reduction.” Springer Nature, 2019.
  ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
    EE, Burskaia V, Gelfand MS. 2019. Additional file 16 of Chlamydia pan-genomic
    analysis reveals balance between host adaptation and selective pressure to genome
    reduction, Springer Nature, <a href="https://doi.org/10.6084/m9.figshare.9808814.v1">10.6084/m9.figshare.9808814.v1</a>.
  mla: Sigalova, Olga M., et al. <i>Additional File 16 of Chlamydia Pan-Genomic Analysis
    Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>.
    Springer Nature, 2019, doi:<a href="https://doi.org/10.6084/m9.figshare.9808814.v1">10.6084/m9.figshare.9808814.v1</a>.
  short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
    E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T07:11:53Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-04-03T09:39:40Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808814.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.9808814.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
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  - id: '6898'
    relation: used_in_publication
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status: public
title: Additional file 16 of Chlamydia pan-genomic analysis reveals balance between
  host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9893'
abstract:
- lang: eng
  text: Summary of peripheral genesa phyletic patterns and tree concordance. (CSV
    26 kb)
article_processing_charge: No
author:
- first_name: Olga M.
  full_name: Sigalova, Olga M.
  last_name: Sigalova
- first_name: Andrei V.
  full_name: Chaplin, Andrei V.
  last_name: Chaplin
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
- first_name: Pavel V.
  full_name: Shelyakin, Pavel V.
  last_name: Shelyakin
- first_name: Vsevolod A.
  full_name: Filaretov, Vsevolod A.
  last_name: Filaretov
- first_name: Evgeny E.
  full_name: Akkuratov, Evgeny E.
  last_name: Akkuratov
- first_name: Valentina
  full_name: Burskaia, Valentina
  last_name: Burskaia
- first_name: Mikhail S.
  full_name: Gelfand, Mikhail S.
  last_name: Gelfand
citation:
  ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 17 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. 2019. doi:<a href="https://doi.org/10.6084/m9.figshare.9808820.v1">10.6084/m9.figshare.9808820.v1</a>
  apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
    V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 17 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. Springer Nature. <a href="https://doi.org/10.6084/m9.figshare.9808820.v1">https://doi.org/10.6084/m9.figshare.9808820.v1</a>
  chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
    Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
    Gelfand. “Additional File 17 of Chlamydia Pan-Genomic Analysis Reveals Balance
    between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
    Nature, 2019. <a href="https://doi.org/10.6084/m9.figshare.9808820.v1">https://doi.org/10.6084/m9.figshare.9808820.v1</a>.
  ieee: O. M. Sigalova <i>et al.</i>, “Additional file 17 of Chlamydia pan-genomic
    analysis reveals balance between host adaptation and selective pressure to genome
    reduction.” Springer Nature, 2019.
  ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
    EE, Burskaia V, Gelfand MS. 2019. Additional file 17 of Chlamydia pan-genomic
    analysis reveals balance between host adaptation and selective pressure to genome
    reduction, Springer Nature, <a href="https://doi.org/10.6084/m9.figshare.9808820.v1">10.6084/m9.figshare.9808820.v1</a>.
  mla: Sigalova, Olga M., et al. <i>Additional File 17 of Chlamydia Pan-Genomic Analysis
    Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>.
    Springer Nature, 2019, doi:<a href="https://doi.org/10.6084/m9.figshare.9808820.v1">10.6084/m9.figshare.9808820.v1</a>.
  short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
    E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T07:20:10Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-04-03T09:39:41Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808820.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.9808820.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
  record:
  - id: '6898'
    relation: used_in_publication
    status: public
status: public
title: Additional file 17 of Chlamydia pan-genomic analysis reveals balance between
  host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9894'
abstract:
- lang: eng
  text: Orthologous families (OFs) derived by MCL clustering of OGs. (CSV 189 kb)
article_processing_charge: No
author:
- first_name: Olga M.
  full_name: Sigalova, Olga M.
  last_name: Sigalova
- first_name: Andrei V.
  full_name: Chaplin, Andrei V.
  last_name: Chaplin
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
- first_name: Pavel V.
  full_name: Shelyakin, Pavel V.
  last_name: Shelyakin
- first_name: Vsevolod A.
  full_name: Filaretov, Vsevolod A.
  last_name: Filaretov
- first_name: Evgeny E.
  full_name: Akkuratov, Evgeny E.
  last_name: Akkuratov
- first_name: Valentina
  full_name: Burskaia, Valentina
  last_name: Burskaia
- first_name: Mikhail S.
  full_name: Gelfand, Mikhail S.
  last_name: Gelfand
citation:
  ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 18 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. 2019. doi:<a href="https://doi.org/10.6084/m9.figshare.9808826.v1">10.6084/m9.figshare.9808826.v1</a>
  apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
    V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 18 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. Springer Nature. <a href="https://doi.org/10.6084/m9.figshare.9808826.v1">https://doi.org/10.6084/m9.figshare.9808826.v1</a>
  chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
    Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
    Gelfand. “Additional File 18 of Chlamydia Pan-Genomic Analysis Reveals Balance
    between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
    Nature, 2019. <a href="https://doi.org/10.6084/m9.figshare.9808826.v1">https://doi.org/10.6084/m9.figshare.9808826.v1</a>.
  ieee: O. M. Sigalova <i>et al.</i>, “Additional file 18 of Chlamydia pan-genomic
    analysis reveals balance between host adaptation and selective pressure to genome
    reduction.” Springer Nature, 2019.
  ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
    EE, Burskaia V, Gelfand MS. 2019. Additional file 18 of Chlamydia pan-genomic
    analysis reveals balance between host adaptation and selective pressure to genome
    reduction, Springer Nature, <a href="https://doi.org/10.6084/m9.figshare.9808826.v1">10.6084/m9.figshare.9808826.v1</a>.
  mla: Sigalova, Olga M., et al. <i>Additional File 18 of Chlamydia Pan-Genomic Analysis
    Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>.
    Springer Nature, 2019, doi:<a href="https://doi.org/10.6084/m9.figshare.9808826.v1">10.6084/m9.figshare.9808826.v1</a>.
  short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
    E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T07:25:07Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-04-03T09:39:41Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808826.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.9808826.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
  record:
  - id: '6898'
    relation: used_in_publication
    status: public
status: public
title: Additional file 18 of Chlamydia pan-genomic analysis reveals balance between
  host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9895'
abstract:
- lang: eng
  text: Additional information on proteins from OG1. (CSV 30 kb)
article_processing_charge: No
author:
- first_name: Olga M.
  full_name: Sigalova, Olga M.
  last_name: Sigalova
- first_name: Andrei V.
  full_name: Chaplin, Andrei V.
  last_name: Chaplin
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
- first_name: Pavel V.
  full_name: Shelyakin, Pavel V.
  last_name: Shelyakin
- first_name: Vsevolod A.
  full_name: Filaretov, Vsevolod A.
  last_name: Filaretov
- first_name: Evgeny E.
  full_name: Akkuratov, Evgeny E.
  last_name: Akkuratov
- first_name: Valentina
  full_name: Burskaia, Valentina
  last_name: Burskaia
- first_name: Mikhail S.
  full_name: Gelfand, Mikhail S.
  last_name: Gelfand
citation:
  ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 19 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. 2019. doi:<a href="https://doi.org/10.6084/m9.figshare.9808835.v1">10.6084/m9.figshare.9808835.v1</a>
  apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
    V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 19 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. Springer Nature. <a href="https://doi.org/10.6084/m9.figshare.9808835.v1">https://doi.org/10.6084/m9.figshare.9808835.v1</a>
  chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
    Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
    Gelfand. “Additional File 19 of Chlamydia Pan-Genomic Analysis Reveals Balance
    between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
    Nature, 2019. <a href="https://doi.org/10.6084/m9.figshare.9808835.v1">https://doi.org/10.6084/m9.figshare.9808835.v1</a>.
  ieee: O. M. Sigalova <i>et al.</i>, “Additional file 19 of Chlamydia pan-genomic
    analysis reveals balance between host adaptation and selective pressure to genome
    reduction.” Springer Nature, 2019.
  ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
    EE, Burskaia V, Gelfand MS. 2019. Additional file 19 of Chlamydia pan-genomic
    analysis reveals balance between host adaptation and selective pressure to genome
    reduction, Springer Nature, <a href="https://doi.org/10.6084/m9.figshare.9808835.v1">10.6084/m9.figshare.9808835.v1</a>.
  mla: Sigalova, Olga M., et al. <i>Additional File 19 of Chlamydia Pan-Genomic Analysis
    Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>.
    Springer Nature, 2019, doi:<a href="https://doi.org/10.6084/m9.figshare.9808835.v1">10.6084/m9.figshare.9808835.v1</a>.
  short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
    E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T07:44:52Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-04-03T09:39:41Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808835.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.9808835.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
  record:
  - id: '6898'
    relation: used_in_publication
    status: public
status: public
title: Additional file 19 of Chlamydia pan-genomic analysis reveals balance between
  host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9896'
abstract:
- lang: eng
  text: Summary of the analysed genomes. (CSV 24 kb)
article_processing_charge: No
author:
- first_name: Olga M.
  full_name: Sigalova, Olga M.
  last_name: Sigalova
- first_name: Andrei V.
  full_name: Chaplin, Andrei V.
  last_name: Chaplin
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
- first_name: Pavel V.
  full_name: Shelyakin, Pavel V.
  last_name: Shelyakin
- first_name: Vsevolod A.
  full_name: Filaretov, Vsevolod A.
  last_name: Filaretov
- first_name: Evgeny E.
  full_name: Akkuratov, Evgeny E.
  last_name: Akkuratov
- first_name: Valentina
  full_name: Burskaia, Valentina
  last_name: Burskaia
- first_name: Mikhail S.
  full_name: Gelfand, Mikhail S.
  last_name: Gelfand
citation:
  ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 1 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. 2019. doi:<a href="https://doi.org/10.6084/m9.figshare.9808841.v1">10.6084/m9.figshare.9808841.v1</a>
  apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
    V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 1 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. Springer Nature. <a href="https://doi.org/10.6084/m9.figshare.9808841.v1">https://doi.org/10.6084/m9.figshare.9808841.v1</a>
  chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
    Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
    Gelfand. “Additional File 1 of Chlamydia Pan-Genomic Analysis Reveals Balance
    between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
    Nature, 2019. <a href="https://doi.org/10.6084/m9.figshare.9808841.v1">https://doi.org/10.6084/m9.figshare.9808841.v1</a>.
  ieee: O. M. Sigalova <i>et al.</i>, “Additional file 1 of Chlamydia pan-genomic
    analysis reveals balance between host adaptation and selective pressure to genome
    reduction.” Springer Nature, 2019.
  ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
    EE, Burskaia V, Gelfand MS. 2019. Additional file 1 of Chlamydia pan-genomic analysis
    reveals balance between host adaptation and selective pressure to genome reduction,
    Springer Nature, <a href="https://doi.org/10.6084/m9.figshare.9808841.v1">10.6084/m9.figshare.9808841.v1</a>.
  mla: Sigalova, Olga M., et al. <i>Additional File 1 of Chlamydia Pan-Genomic Analysis
    Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>.
    Springer Nature, 2019, doi:<a href="https://doi.org/10.6084/m9.figshare.9808841.v1">10.6084/m9.figshare.9808841.v1</a>.
  short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
    E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T07:50:53Z
date_published: 2019-09-02T00:00:00Z
date_updated: 2026-04-03T09:39:41Z
day: '02'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808841.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.9808841.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
  record:
  - id: '6898'
    relation: used_in_publication
    status: public
status: public
title: Additional file 1 of Chlamydia pan-genomic analysis reveals balance between
  host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9897'
abstract:
- lang: eng
  text: Frameshift and nonsense mutations near homopolymeric tracts of OG1 genes.
    Only 374 genes with typical length and domain composition were considered. (CSV
    6 kb)
article_processing_charge: No
author:
- first_name: Olga M.
  full_name: Sigalova, Olga M.
  last_name: Sigalova
- first_name: Andrei V.
  full_name: Chaplin, Andrei V.
  last_name: Chaplin
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
- first_name: Pavel V.
  full_name: Shelyakin, Pavel V.
  last_name: Shelyakin
- first_name: Vsevolod A.
  full_name: Filaretov, Vsevolod A.
  last_name: Filaretov
- first_name: Evgeny E.
  full_name: Akkuratov, Evgeny E.
  last_name: Akkuratov
- first_name: Valentina
  full_name: Burskaia, Valentina
  last_name: Burskaia
- first_name: Mikhail S.
  full_name: Gelfand, Mikhail S.
  last_name: Gelfand
citation:
  ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 20 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. 2019. doi:<a href="https://doi.org/10.6084/m9.figshare.9808850.v1">10.6084/m9.figshare.9808850.v1</a>
  apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
    V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 20 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. Springer Nature. <a href="https://doi.org/10.6084/m9.figshare.9808850.v1">https://doi.org/10.6084/m9.figshare.9808850.v1</a>
  chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
    Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
    Gelfand. “Additional File 20 of Chlamydia Pan-Genomic Analysis Reveals Balance
    between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
    Nature, 2019. <a href="https://doi.org/10.6084/m9.figshare.9808850.v1">https://doi.org/10.6084/m9.figshare.9808850.v1</a>.
  ieee: O. M. Sigalova <i>et al.</i>, “Additional file 20 of Chlamydia pan-genomic
    analysis reveals balance between host adaptation and selective pressure to genome
    reduction.” Springer Nature, 2019.
  ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
    EE, Burskaia V, Gelfand MS. 2019. Additional file 20 of Chlamydia pan-genomic
    analysis reveals balance between host adaptation and selective pressure to genome
    reduction, Springer Nature, <a href="https://doi.org/10.6084/m9.figshare.9808850.v1">10.6084/m9.figshare.9808850.v1</a>.
  mla: Sigalova, Olga M., et al. <i>Additional File 20 of Chlamydia Pan-Genomic Analysis
    Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>.
    Springer Nature, 2019, doi:<a href="https://doi.org/10.6084/m9.figshare.9808850.v1">10.6084/m9.figshare.9808850.v1</a>.
  short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
    E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T07:58:15Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-04-03T09:39:41Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808850.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.9808850.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
  record:
  - id: '6898'
    relation: used_in_publication
    status: public
status: public
title: Additional file 20 of Chlamydia pan-genomic analysis reveals balance between
  host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9898'
abstract:
- lang: eng
  text: All polyN tracts of length 5 or more nucleotides in sequences of genes from
    OG1. Sequences were extracted and scanned prior to automatic correction for frameshifts
    implemented in the RAST pipeline. (CSV 133 kb)
article_processing_charge: No
author:
- first_name: Olga M.
  full_name: Sigalova, Olga M.
  last_name: Sigalova
- first_name: Andrei V.
  full_name: Chaplin, Andrei V.
  last_name: Chaplin
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
- first_name: Pavel V.
  full_name: Shelyakin, Pavel V.
  last_name: Shelyakin
- first_name: Vsevolod A.
  full_name: Filaretov, Vsevolod A.
  last_name: Filaretov
- first_name: Evgeny E.
  full_name: Akkuratov, Evgeny E.
  last_name: Akkuratov
- first_name: Valentina
  full_name: Burskaia, Valentina
  last_name: Burskaia
- first_name: Mikhail S.
  full_name: Gelfand, Mikhail S.
  last_name: Gelfand
citation:
  ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 21 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. 2019. doi:<a href="https://doi.org/10.6084/m9.figshare.9808859.v1">10.6084/m9.figshare.9808859.v1</a>
  apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
    V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 21 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. Springer Nature. <a href="https://doi.org/10.6084/m9.figshare.9808859.v1">https://doi.org/10.6084/m9.figshare.9808859.v1</a>
  chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
    Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
    Gelfand. “Additional File 21 of Chlamydia Pan-Genomic Analysis Reveals Balance
    between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
    Nature, 2019. <a href="https://doi.org/10.6084/m9.figshare.9808859.v1">https://doi.org/10.6084/m9.figshare.9808859.v1</a>.
  ieee: O. M. Sigalova <i>et al.</i>, “Additional file 21 of Chlamydia pan-genomic
    analysis reveals balance between host adaptation and selective pressure to genome
    reduction.” Springer Nature, 2019.
  ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
    EE, Burskaia V, Gelfand MS. 2019. Additional file 21 of Chlamydia pan-genomic
    analysis reveals balance between host adaptation and selective pressure to genome
    reduction, Springer Nature, <a href="https://doi.org/10.6084/m9.figshare.9808859.v1">10.6084/m9.figshare.9808859.v1</a>.
  mla: Sigalova, Olga M., et al. <i>Additional File 21 of Chlamydia Pan-Genomic Analysis
    Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>.
    Springer Nature, 2019, doi:<a href="https://doi.org/10.6084/m9.figshare.9808859.v1">10.6084/m9.figshare.9808859.v1</a>.
  short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
    E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T08:10:23Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-04-03T09:39:41Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808859.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.9808859.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
  record:
  - id: '6898'
    relation: used_in_publication
    status: public
status: public
title: Additional file 21 of Chlamydia pan-genomic analysis reveals balance between
  host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...