[{"abstract":[{"text":"Collagens are fundamental components of extracellular matrices, requiring precise intracellular post-translational modifications for proper function. Among the modifications, prolyl 4-hydroxylation is critical to stabilise the collagen triple helix. In humans, this reaction is mediated by collagen prolyl 4-hydroxylases (P4Hs). While humans possess three genes encoding these enzymes (P4H⍺s), Drosophila melanogaster harbour at least 26 candidates for collagen P4H⍺s despite its simple genome, and it is poorly understood which of them are actually working on collagen in the fly. In this study, we addressed this question by carrying out thorough bioinformatic and biochemical analyses. We demonstrate that among the 26 potential collagen P4H⍺s, PH4⍺EFB shares the highest homology with vertebrate collagen P4H⍺s. Furthermore, while collagen P4Hs and their substrates must exist in the same cells, our transcriptomic analyses at the tissue and single cell levels showed a global co-expression of PH4⍺EFB but not the other P4H⍺-related genes with the collagen IV genes. Moreover, expression of PH4⍺EFB during embryogenesis was found to precede that of collagen IV, presumably enabling efficient collagen modification by PH4⍺EFB. Finally, biochemical assays confirm that PH4⍺EFB binds collagen, supporting its direct role in collagen IV modification. Collectively, we identify PH4⍺EFB as the primary and potentially constitutive prolyl 4-hydroxylase responsible for collagen IV biosynthesis in Drosophila. Our findings highlight the remarkably simple nature of Drosophila collagen IV biosynthesis, which may serve as a blueprint for defining the minimal requirements for collagen engineering.","lang":"eng"}],"file_date_updated":"2026-01-05T13:09:01Z","language":[{"iso":"eng"}],"page":"101-113","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":141,"intvolume":"       141","status":"public","type":"journal_article","scopus_import":"1","isi":1,"department":[{"_id":"BeVi"}],"date_published":"2025-11-01T00:00:00Z","acknowledgement":"This project was supported by the All May See Foundation 7031,182 to YI, the Louisiana Board of Regents Support Fund: Research Competitiveness Subprogram to MAT, Austrian science fund (FWF) as part of the SFB Meiosis consortium FWF SFB F88-10 to Beatriz Vicoso (supported ME), American Heart Association 16POST2726018 and American Cancer Society 132,123-PF-18–025–01-CSM postdoctoral fellowships to ALZ, National Institutes of Health R01 GM136961 and R35 GM148485 to SH-B, and the Academy of Medical Sciences/the Wellcome Trust/ the Government Department of Business, Energy and Industrial Strategy/the British Heart Foundation/Diabetes UK Springboard Award SBF008\\1115 to YM. \r\nComputational analyses of single-nucleus transcriptome data were performed on the high performance computer (HPC) at Bournemouth University, the HPC at Institute of Science and Technology Austria, and the high-performance computational resources provided by the Louisiana Optical Network Infrastructure (http://www.loni.org). The authors are grateful to the researchers who published the transcriptome datasets [48,49,52,55] that became the essential bases for this study, to FlyBase for curating the datasets in an easily accessible format, and the Drosophila Genomics Resource Center (DGRC), supported by NIH grant 2P40OD010949, for providing the D17 cell line used in this research. The authors thank Kristian Koski (University of Oulu, Finland) for crucial advice on the domain structure of collagen P4H⍺s, and Ryusuke Niwa and Ryo Hoshino (University of Tsukuba, Japan) for helpful discussions on SP.","has_accepted_license":"1","project":[{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810"}],"OA_place":"publisher","pmid":1,"oa":1,"ddc":["570"],"date_created":"2025-09-28T22:01:26Z","_id":"20404","day":"01","OA_type":"hybrid","publication_status":"published","issue":"11","file":[{"file_size":5844254,"relation":"main_file","date_created":"2026-01-05T13:09:01Z","access_level":"open_access","checksum":"764257db41865d19daec1935788f72d7","creator":"dernst","content_type":"application/pdf","date_updated":"2026-01-05T13:09:01Z","success":1,"file_name":"2025_MatrixBiology_Ishikawa.pdf","file_id":"20948"}],"doi":"10.1016/j.matbio.2025.09.002","author":[{"first_name":"Yoshihiro","last_name":"Ishikawa","full_name":"Ishikawa, Yoshihiro"},{"first_name":"Melissa A","orcid":"0000-0002-9752-7380","last_name":"Toups","full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi"},{"first_name":"Allison L.","last_name":"Zajac","full_name":"Zajac, Allison L."},{"full_name":"Horne-Badovinac, Sally","last_name":"Horne-Badovinac","first_name":"Sally"},{"first_name":"Yutaka","last_name":"Matsubayashi","full_name":"Matsubayashi, Yutaka"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"11","external_id":{"pmid":["40946811"],"isi":["001583892100002"]},"citation":{"chicago":"Ishikawa, Yoshihiro, Melissa A Toups, Marwan N Elkrewi, Allison L. Zajac, Sally Horne-Badovinac, and Yutaka Matsubayashi. “Evidence for the Major Role of PH4⍺EFB in the Prolyl 4-Hydroxylation of Drosophila Collagen IV.” <i>Matrix Biology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1016/j.matbio.2025.09.002\">https://doi.org/10.1016/j.matbio.2025.09.002</a>.","ama":"Ishikawa Y, Toups MA, Elkrewi MN, Zajac AL, Horne-Badovinac S, Matsubayashi Y. Evidence for the major role of PH4⍺EFB in the prolyl 4-hydroxylation of Drosophila collagen IV. <i>Matrix Biology</i>. 2025;141(11):101-113. doi:<a href=\"https://doi.org/10.1016/j.matbio.2025.09.002\">10.1016/j.matbio.2025.09.002</a>","ista":"Ishikawa Y, Toups MA, Elkrewi MN, Zajac AL, Horne-Badovinac S, Matsubayashi Y. 2025. Evidence for the major role of PH4⍺EFB in the prolyl 4-hydroxylation of Drosophila collagen IV. Matrix Biology. 141(11), 101–113.","short":"Y. Ishikawa, M.A. Toups, M.N. Elkrewi, A.L. Zajac, S. Horne-Badovinac, Y. Matsubayashi, Matrix Biology 141 (2025) 101–113.","apa":"Ishikawa, Y., Toups, M. A., Elkrewi, M. N., Zajac, A. L., Horne-Badovinac, S., &#38; Matsubayashi, Y. (2025). Evidence for the major role of PH4⍺EFB in the prolyl 4-hydroxylation of Drosophila collagen IV. <i>Matrix Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1016/j.matbio.2025.09.002\">https://doi.org/10.1016/j.matbio.2025.09.002</a>","ieee":"Y. Ishikawa, M. A. Toups, M. N. Elkrewi, A. L. Zajac, S. Horne-Badovinac, and Y. Matsubayashi, “Evidence for the major role of PH4⍺EFB in the prolyl 4-hydroxylation of Drosophila collagen IV,” <i>Matrix Biology</i>, vol. 141, no. 11. Springer Nature, pp. 101–113, 2025.","mla":"Ishikawa, Yoshihiro, et al. “Evidence for the Major Role of PH4⍺EFB in the Prolyl 4-Hydroxylation of Drosophila Collagen IV.” <i>Matrix Biology</i>, vol. 141, no. 11, Springer Nature, 2025, pp. 101–13, doi:<a href=\"https://doi.org/10.1016/j.matbio.2025.09.002\">10.1016/j.matbio.2025.09.002</a>."},"publication_identifier":{"eissn":["1569-1802"],"issn":["0945-053X"]},"PlanS_conform":"1","title":"Evidence for the major role of PH4⍺EFB in the prolyl 4-hydroxylation of Drosophila collagen IV","date_updated":"2026-01-05T13:09:08Z","publisher":"Springer Nature","year":"2025","publication":"Matrix Biology"},{"article_processing_charge":"Yes","quality_controlled":"1","article_type":"original","file_date_updated":"2025-12-15T09:25:51Z","abstract":[{"lang":"eng","text":"Rapid prophase chromosome movements ensure faithful alignment of the parental homologous chromosomes and successful synapsis formation during meiosis. These movements are driven by cytoplasmic forces transmitted to the nuclear periphery, where chromosome ends are attached through transmembrane proteins. During many developmental stages a specific genome architecture with chromatin nuclear periphery contacts mediates specific gene expression. Whether chromatin is removed from the nuclear periphery as a consequence of chromosome motions or by a specific mechanism is not fully understood. Here, we identify a mechanism to remove chromatin from the nuclear periphery through vaccinia related kinase (VRK-1)–dependent phosphorylation of Barrier to Autointegration Factor 1 (BAF-1) in Caenorhabditis elegans early prophase of meiosis. Interfering with chromatin removal delays chromosome pairing, impairs synapsis, produces oocytes with abnormal chromosomes and elevated apoptosis. Long read sequencing reveals deletions and duplications in offspring lacking VRK-1 underscoring the importance of the BAF-1–VRK-1 module in preserving genome stability in gametes during rapid chromosome movements."}],"language":[{"iso":"eng"}],"oa_version":"Published Version","type":"journal_article","status":"public","intvolume":"        16","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":16,"article_number":"10446","date_published":"2025-11-25T00:00:00Z","DOAJ_listed":"1","acknowledgement":"We are grateful to Monique Zetka, Nicola Silva, and Yumi Kim, Needhi Bhalla, George Krohne and Rueyling Lin for providing reagents; Scott Kennedy for sharing the multiplexed FISH library; and members of the Max Perutz Labs’ BioOptics facility (Irmgard Fischer, Josef Gotzmann, Thomas Peterbauer, Clara Bodner, and Nick Wedige) for training and support in image acquisition. We also thank the members of the NGS facility at the Vienna Biocenter. This work was funded by the Austrian Science Fund (FWF) SFB projects F 8805-B (VJ), https://doi.org/10.55776/F88, F 8809-B (ITB), and F8810-B (BV). We are also grateful to members of the V. Jantsch laboratory for helpful discussions. Some strains were provided by the Caenorhabditis Genetics Center, which is funded by the National Institutes of Health Office of Research Infrastructure Programs (P40OD010440).","has_accepted_license":"1","scopus_import":"1","department":[{"_id":"BeVi"}],"project":[{"grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"OA_place":"publisher","pmid":1,"_id":"20796","day":"25","OA_type":"gold","oa":1,"ddc":["570"],"date_created":"2025-12-11T10:45:06Z","publication_status":"published","file":[{"access_level":"open_access","date_created":"2025-12-15T09:25:51Z","file_size":8096309,"relation":"main_file","content_type":"application/pdf","creator":"dernst","checksum":"a952f7ea050242b79008540de49a0e61","date_updated":"2025-12-15T09:25:51Z","success":1,"file_name":"2025_NatureComm_Paouneskou.pdf","file_id":"20823"}],"external_id":{"pmid":["41290579"]},"citation":{"apa":"Paouneskou, D., Baudrimont, A., Kelemen, R. K., Elkrewi, M. N., Graf, A., Moukbel Ali Aldawla, S., … Jantsch, V. (2025). BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-65420-9\">https://doi.org/10.1038/s41467-025-65420-9</a>","short":"D. Paouneskou, A. Baudrimont, R.K. Kelemen, M.N. Elkrewi, A. Graf, S. Moukbel Ali Aldawla, C. Kölbl, I. Tiemann-Boege, B. Vicoso, V. Jantsch, Nature Communications 16 (2025).","ieee":"D. Paouneskou <i>et al.</i>, “BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","mla":"Paouneskou, Dimitra, et al. “BAF-1–VRK-1 Mediated Release of Meiotic Chromosomes from the Nuclear Periphery Is Important for Genome Integrity.” <i>Nature Communications</i>, vol. 16, 10446, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-65420-9\">10.1038/s41467-025-65420-9</a>.","chicago":"Paouneskou, Dimitra, Antoine Baudrimont, Réka K Kelemen, Marwan N Elkrewi, Angela Graf, Shehab Moukbel Ali Aldawla, Claudia Kölbl, Irene Tiemann-Boege, Beatriz Vicoso, and Verena Jantsch. “BAF-1–VRK-1 Mediated Release of Meiotic Chromosomes from the Nuclear Periphery Is Important for Genome Integrity.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-65420-9\">https://doi.org/10.1038/s41467-025-65420-9</a>.","ama":"Paouneskou D, Baudrimont A, Kelemen RK, et al. BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-65420-9\">10.1038/s41467-025-65420-9</a>","ista":"Paouneskou D, Baudrimont A, Kelemen RK, Elkrewi MN, Graf A, Moukbel Ali Aldawla S, Kölbl C, Tiemann-Boege I, Vicoso B, Jantsch V. 2025. BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity. Nature Communications. 16, 10446."},"doi":"10.1038/s41467-025-65420-9","author":[{"first_name":"Dimitra","last_name":"Paouneskou","full_name":"Paouneskou, Dimitra"},{"full_name":"Baudrimont, Antoine","last_name":"Baudrimont","first_name":"Antoine"},{"full_name":"Kelemen, Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","last_name":"Kelemen","orcid":"0000-0002-8489-9281","first_name":"Réka K"},{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","first_name":"Marwan N"},{"last_name":"Graf","full_name":"Graf, Angela","first_name":"Angela"},{"first_name":"Shehab","full_name":"Moukbel Ali Aldawla, Shehab","last_name":"Moukbel Ali Aldawla"},{"first_name":"Claudia","last_name":"Kölbl","full_name":"Kölbl, Claudia"},{"last_name":"Tiemann-Boege","full_name":"Tiemann-Boege, Irene","first_name":"Irene"},{"last_name":"Vicoso","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306"},{"first_name":"Verena","last_name":"Jantsch","full_name":"Jantsch, Verena"}],"month":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-12-15T09:28:37Z","publisher":"Springer Nature","year":"2025","publication":"Nature Communications","publication_identifier":{"eissn":["2041-1723"]},"title":"BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity","PlanS_conform":"1"},{"date_updated":"2026-04-16T12:20:41Z","publisher":"Institute of Science and Technology Austria","corr_author":"1","year":"2025","OA_embargo":"12","publication_identifier":{"eissn":["2663-337X"],"isbn":["9783990780534"]},"title":"Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp","acknowledged_ssus":[{"_id":"ScienComp"}],"citation":{"short":"M.N. Elkrewi, Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp, Institute of Science and Technology Austria, 2025.","apa":"Elkrewi, M. N. (2025). <i>Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19386\">https://doi.org/10.15479/AT-ISTA-19386</a>","ieee":"M. N. Elkrewi, “Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp,” Institute of Science and Technology Austria, 2025.","mla":"Elkrewi, Marwan N. <i>Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19386\">10.15479/AT-ISTA-19386</a>.","chicago":"Elkrewi, Marwan N. “Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19386\">https://doi.org/10.15479/AT-ISTA-19386</a>.","ama":"Elkrewi MN. Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19386\">10.15479/AT-ISTA-19386</a>","ista":"Elkrewi MN. 2025. Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp. Institute of Science and Technology Austria."},"author":[{"first_name":"Marwan N","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi"}],"doi":"10.15479/AT-ISTA-19386","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"03","publication_status":"published","file":[{"date_updated":"2026-03-26T23:30:03Z","file_id":"19462","file_name":"Thesis_Marwan_Elkrewi.docx","creator":"melkrewi","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"5549a8216c07e4c39281648912d72246","date_created":"2025-03-26T07:06:56Z","access_level":"closed","file_size":25019680,"embargo_to":"open_access","relation":"source_file"},{"date_updated":"2026-03-26T23:30:03Z","file_id":"19463","file_name":"Thesis_Marwan_Elkrewi.pdf","access_level":"open_access","embargo":"2026-03-26","date_created":"2025-03-26T07:06:22Z","relation":"main_file","file_size":17294844,"content_type":"application/pdf","checksum":"aed2ba9965aa89b3414deae1ae9f4321","creator":"melkrewi"}],"_id":"19386","day":"14","oa":1,"ddc":["570","576"],"date_created":"2025-03-11T12:54:31Z","OA_place":"publisher","project":[{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810"}],"supervisor":[{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"date_published":"2025-03-14T00:00:00Z","acknowledgement":"My PhD work was funded by the Austrian science fund (FWF), as part of the SFB Meiosis consortium (https://sfbmeiosis.org/, grant ID FWF SFB F88-10).","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"type":"dissertation","status":"public","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"status":"public","id":"12248","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"10167"},{"status":"public","id":"10767","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"15009"},{"status":"public","id":"14613","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"17890","status":"public"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","degree_awarded":"PhD","file_date_updated":"2026-03-26T23:30:03Z","abstract":[{"text":"Crustaceans are a large group of arthropods with a great diversity of species and\r\ndifferent types of sex determination systems and reproductive modes (Subramoniam, 2017).\r\nThis makes them a great model for exploring the evolution of sex chromosomes and sexual\r\ndimorphism and investigating the evolutionary mechanisms driving and maintaining the\r\ndiversity of reproductive systems. Within this taxon, Brine shrimp of the genus Artemia, a\r\nbranchiopod crustacean, are well suited for such explorations, as they have both highly\r\ndimorphic traits and closely related sexual and asexual species. Although brine shrimp are\r\nknown to have ZW sex chromosomes (Bowen, 1963; Parraguez et al., 2009), the sex\r\nchromosomes are still not well characterized at the genomic level, the sex-determination gene\r\nis unknown, and it is still unclear whether the same sex chromosomes as shared by the\r\ndifferent species.\r\nThe first part of this thesis was to characterize the Z and W chromosomes in Artemia\r\nusing an array of methods, from generating multiple chromosome and contig level genome\r\nassemblies to identifying W-linked scaffolds and transcripts in multiple species using k-mer\r\nbased approaches.\r\nThe second part tackles the conservation of the cell type specific regulatory pathways\r\nin the female reproductive system between Artemia and Drosophila, and the expression of the\r\nZ-specific region throughout meiosis using single-nucleus RNA-seq data. Our results show\r\nthat germline cells lack dosage compensation, with a subset of cells showing evidence of\r\nextreme repression of the Z chromosome.\r\nWith multiple sexual species and several asexual lineages of parthenogenetic females\r\nthat produce rare males at low frequencies, Brine shrimp present the perfect opportunity to\r\nexplore the transition to asexuality and shed light on the prerequisites and repercussions of\r\nthe form of modified meiosis maintaining the asexual lineages. The last chapter is an\r\ninvestigation of the molecular pathways involved in asexual reproduction in Artemia using\r\nnewly generated single nucleus RNAseq and WGS data and previously published data. ","lang":"eng"}],"page":"170","language":[{"iso":"eng"}],"oa_version":"Published Version"},{"month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.15479/AT:ISTA:14705","author":[{"full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","first_name":"Marwan N","orcid":"0000-0002-5328-7231"}],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"citation":{"ieee":"M. N. Elkrewi, “Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.’” Institute of Science and Technology Austria, 2024.","mla":"Elkrewi, Marwan N. <i>Data from “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.”</i> Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14705\">10.15479/AT:ISTA:14705</a>.","apa":"Elkrewi, M. N. (2024). Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14705\">https://doi.org/10.15479/AT:ISTA:14705</a>","short":"M.N. Elkrewi, (2024).","ista":"Elkrewi MN. 2024. Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14705\">10.15479/AT:ISTA:14705</a>.","chicago":"Elkrewi, Marwan N. “Data from ‘Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.’” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:14705\">https://doi.org/10.15479/AT:ISTA:14705</a>.","ama":"Elkrewi MN. Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14705\">10.15479/AT:ISTA:14705</a>"},"date_published":"2024-01-02T00:00:00Z","has_accepted_license":"1","title":"Data from \"Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation\"","year":"2024","project":[{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction"}],"corr_author":"1","date_updated":"2025-09-04T12:05:42Z","publisher":"Institute of Science and Technology Austria","abstract":[{"lang":"eng","text":"Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, are still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of Artemia franciscana (Kellogg 1906), from the Great Salt Lake, USA. The genome is 1GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species."}],"file_date_updated":"2023-12-22T14:14:06Z","oa":1,"date_created":"2023-12-22T13:40:48Z","oa_version":"Published Version","ddc":["576"],"day":"02","_id":"14705","article_processing_charge":"No","contributor":[{"last_name":"Bett","id":"57854184-AAE0-11E9-8D04-98D6E5697425","contributor_type":"researcher","first_name":"Vincent K"},{"contributor_type":"project_member","first_name":"Ariana","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","contributor_type":"supervisor","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"},{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","first_name":"Marwan N","orcid":"0000-0002-5328-7231","contributor_type":"researcher"}],"related_material":{"record":[{"status":"public","id":"15009","relation":"used_in_publication"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"creator":"melkrewi","content_type":"text/plain","checksum":"bdaf1392867786634ec5466d528c36ca","relation":"main_file","file_size":847,"date_created":"2023-12-22T13:54:21Z","access_level":"open_access","date_updated":"2023-12-22T13:54:21Z","file_name":"readme.txt.txt","file_id":"14707","success":1},{"creator":"melkrewi","checksum":"973e1cbdab923a71709782177980829f","content_type":"application/x-zip-compressed","access_level":"open_access","date_created":"2023-12-22T14:14:06Z","file_size":343632753,"relation":"main_file","file_id":"14708","file_name":"data_artemia_franciscana_genome.zip","success":1,"date_updated":"2023-12-22T14:14:06Z"}],"status":"public","type":"research_data","keyword":["sex chromosome evolution","genome assembly","dosage compensation"]},{"title":"Data for: \"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome\"","acknowledged_ssus":[{"_id":"ScienComp"}],"publisher":"Institute of Science and Technology Austria","date_updated":"2026-04-16T12:20:41Z","corr_author":"1","year":"2024","project":[{"name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"author":[{"orcid":"0000-0002-5328-7231","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306"}],"doi":"10.15479/AT:ISTA:17362","month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"date_published":"2024-08-05T00:00:00Z","citation":{"ieee":"M. N. Elkrewi and B. Vicoso, “Data for: ‘Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.’” Institute of Science and Technology Austria, 2024.","mla":"Elkrewi, Marwan N., and Beatriz Vicoso. <i>Data for: “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.”</i> Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17362\">10.15479/AT:ISTA:17362</a>.","apa":"Elkrewi, M. N., &#38; Vicoso, B. (2024). Data for: “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:17362\">https://doi.org/10.15479/AT:ISTA:17362</a>","short":"M.N. Elkrewi, B. Vicoso, (2024).","ista":"Elkrewi MN, Vicoso B. 2024. Data for: ‘Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:17362\">10.15479/AT:ISTA:17362</a>.","chicago":"Elkrewi, Marwan N, and Beatriz Vicoso. “Data for: ‘Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.’” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:17362\">https://doi.org/10.15479/AT:ISTA:17362</a>.","ama":"Elkrewi MN, Vicoso B. Data for: “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.” 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17362\">10.15479/AT:ISTA:17362</a>"},"has_accepted_license":"1","file":[{"date_created":"2024-08-05T22:24:18Z","access_level":"open_access","relation":"main_file","file_size":2465,"creator":"melkrewi","content_type":"text/plain","checksum":"26b5d41b3103f4284dd97d56e370a5b6","success":1,"file_id":"17394","file_name":"README.txt","date_updated":"2024-08-05T22:24:18Z"},{"file_id":"17395","file_name":"Data_artemia_single_nucleus_atlas.zip","success":1,"date_updated":"2024-08-05T23:28:52Z","content_type":"application/x-zip-compressed","creator":"melkrewi","checksum":"95adab5e36148015da313505e3910707","relation":"main_file","file_size":2526735400,"date_created":"2024-08-05T23:28:52Z","access_level":"open_access"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"17890"}]},"type":"research_data","status":"public","oa":1,"file_date_updated":"2024-08-05T23:28:52Z","abstract":[{"text":"This is the supplementary data for the paper titled \"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome\", where we described the generation and analysis of single-nucleus expression and chromatin-accessibility data from the female reproductive system of Artemia franciscana. We compared our dataset to the published Drosophila single-nucleus data (over 400 million years of divergence) and highlighted the extreme conservation of several of the molecular pathways of oogenesis and meiosis. We found evidence of global transcriptional quiescence and chromatin condensation in late germ cells, highlighting the conserved role of this repressive stage in arthropod oogenesis. Additionally, we explored the expression patterns of the ZW sex chromosomes during oogenesis. Our data shows that the Z-chromosome is consistently downregulated in germline cells. While this is partly driven by a lack of dosage compensation in the germline, a subset of cells show stronger repression of the Z chromosome.","lang":"eng"}],"ddc":["576"],"oa_version":"Published Version","date_created":"2024-08-02T07:27:45Z","_id":"17362","article_processing_charge":"No","day":"05"},{"OA_type":"gold","_id":"17890","day":"30","ddc":["570"],"date_created":"2024-09-08T22:01:11Z","oa":1,"issue":"8","file":[{"creator":"dernst","checksum":"f5d96b9af57126fc1063e951440477d6","content_type":"application/pdf","access_level":"open_access","date_created":"2024-09-11T07:54:12Z","file_size":8962687,"relation":"main_file","file_id":"18056","file_name":"2024_PloSGenetics_Elkrewi.pdf","success":1,"date_updated":"2024-09-11T07:54:12Z"}],"publication_status":"published","citation":{"ieee":"M. N. Elkrewi and B. Vicoso, “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome,” <i>PLoS Genetics</i>, vol. 20, no. 8. Public Library of Science, 2024.","mla":"Elkrewi, Marwan N., and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” <i>PLoS Genetics</i>, vol. 20, no. 8, e1011376, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1011376\">10.1371/journal.pgen.1011376</a>.","apa":"Elkrewi, M. N., &#38; Vicoso, B. (2024). Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1011376\">https://doi.org/10.1371/journal.pgen.1011376</a>","short":"M.N. Elkrewi, B. Vicoso, PLoS Genetics 20 (2024).","ista":"Elkrewi MN, Vicoso B. 2024. Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. PLoS Genetics. 20(8), e1011376.","chicago":"Elkrewi, Marwan N, and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” <i>PLoS Genetics</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pgen.1011376\">https://doi.org/10.1371/journal.pgen.1011376</a>.","ama":"Elkrewi MN, Vicoso B. Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. <i>PLoS Genetics</i>. 2024;20(8). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1011376\">10.1371/journal.pgen.1011376</a>"},"external_id":{"isi":["001304090200001"],"pmid":["39213449"]},"doi":"10.1371/journal.pgen.1011376","author":[{"orcid":"0000-0002-5328-7231","first_name":"Marwan N","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"last_name":"Vicoso","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"08","publication":"PLoS Genetics","publisher":"Public Library of Science","date_updated":"2026-05-29T22:31:21Z","corr_author":"1","year":"2024","publication_identifier":{"eissn":["1553-7404"],"issn":["1553-7390"]},"title":"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome","acknowledged_ssus":[{"_id":"ScienComp"}],"quality_controlled":"1","article_type":"original","article_processing_charge":"Yes","language":[{"iso":"eng"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Our understanding of the molecular pathways that regulate oogenesis and define cellular identity in the Arthropod female reproductive system and the extent of their conservation is currently very limited. This is due to the focus on model systems, including Drosophila and Daphnia, which do not reflect the observed diversity of morphologies, reproductive modes, and sex chromosome systems. We use single-nucleus RNA and ATAC sequencing to produce a comprehensive single nucleus atlas of the adult Artemia franciscana female reproductive system. We map our data to the Fly Cell Atlas single-nucleus dataset of the Drosophila melanogaster ovary, shedding light on the conserved regulatory programs between the two distantly related Arthropod species. We identify the major cell types known to be present in the Artemia ovary, including germ cells, follicle cells, and ovarian muscle cells. Additionally, we use the germ cells to explore gene regulation and expression of the Z chromosome during meiosis, highlighting its unique regulatory dynamics and allowing us to explore the presence of meiotic sex chromosome silencing in this group."}],"file_date_updated":"2024-09-11T07:54:12Z","type":"journal_article","status":"public","volume":20,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"intvolume":"        20","related_material":{"record":[{"relation":"research_data","id":"17362","status":"public"},{"id":"19386","relation":"dissertation_contains","status":"public"}],"link":[{"url":"https://github.com/Melkrewi/Artemia-snRNAseq-Project","relation":"software"}]},"has_accepted_license":"1","article_number":"e1011376","date_published":"2024-08-30T00:00:00Z","DOAJ_listed":"1","acknowledgement":"We thank the Vicoso group for their valuable comments on the earlier draft of the manuscript. We would also like to thank the Vienna BioCenter Next Generation Sequencing (NGS) facility staff, and in particular, Thomas Grentzinger for his support with the handling and sequencing of the samples, the scientific computing unit at ISTA for the computational resources, Brittney Wick for the help with hosting our data on the UCSC Cell Browser, and Lora B. Sweeney for her valuable input at the different stages of the project.\r\nThis research was funded by the Austrian science fund (FWF), as part of the SFB Meiosis consortium https://sfbmeiosis.org/, grant ID FWF SFB F88-10) to BV. ","isi":1,"department":[{"_id":"BeVi"}],"scopus_import":"1","pmid":1,"APC_amount":"3145,39 EUR","OA_place":"publisher","project":[{"name":"FWF Open Access Fund","call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"},{"grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}]},{"publication_status":"published","issue":"1","file":[{"relation":"main_file","file_size":5213306,"access_level":"open_access","date_created":"2024-02-26T09:54:59Z","content_type":"application/pdf","checksum":"106a40f10443b2e7ba66749844ebbdf1","creator":"dernst","success":1,"file_name":"2024_GBE_Bett.pdf","file_id":"15029","date_updated":"2024-02-26T09:54:59Z"}],"_id":"15009","day":"20","OA_type":"gold","oa":1,"ddc":["570"],"date_created":"2024-02-18T23:01:02Z","publisher":"Oxford University Press","date_updated":"2026-05-29T22:31:21Z","year":"2024","corr_author":"1","publication":"Genome Biology and Evolution","publication_identifier":{"eissn":["1759-6653"]},"title":"Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation","citation":{"ista":"Bett VK, Macon A, Vicoso B, Elkrewi MN. 2024. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. 16(1), evae006.","ama":"Bett VK, Macon A, Vicoso B, Elkrewi MN. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. <i>Genome Biology and Evolution</i>. 2024;16(1). doi:<a href=\"https://doi.org/10.1093/gbe/evae006\">10.1093/gbe/evae006</a>","chicago":"Bett, Vincent K, Ariana Macon, Beatriz Vicoso, and Marwan N Elkrewi. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/gbe/evae006\">https://doi.org/10.1093/gbe/evae006</a>.","mla":"Bett, Vincent K., et al. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” <i>Genome Biology and Evolution</i>, vol. 16, no. 1, evae006, Oxford University Press, 2024, doi:<a href=\"https://doi.org/10.1093/gbe/evae006\">10.1093/gbe/evae006</a>.","ieee":"V. K. Bett, A. Macon, B. Vicoso, and M. N. Elkrewi, “Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation,” <i>Genome Biology and Evolution</i>, vol. 16, no. 1. Oxford University Press, 2024.","short":"V.K. Bett, A. Macon, B. Vicoso, M.N. Elkrewi, Genome Biology and Evolution 16 (2024).","apa":"Bett, V. K., Macon, A., Vicoso, B., &#38; Elkrewi, M. N. (2024). Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evae006\">https://doi.org/10.1093/gbe/evae006</a>"},"external_id":{"pmid":["38245839"],"isi":["001153952800001"]},"doi":"10.1093/gbe/evae006","author":[{"first_name":"Vincent K","full_name":"Bett, Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","last_name":"Bett"},{"full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","first_name":"Ariana"},{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","first_name":"Marwan N"}],"month":"01","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"record":[{"status":"public","relation":"research_data","id":"14705"},{"id":"20444","relation":"dissertation_contains","status":"private"},{"relation":"dissertation_contains","id":"20449","status":"public"},{"id":"19386","relation":"dissertation_contains","status":"public"}]},"intvolume":"        16","volume":16,"article_processing_charge":"Yes","quality_controlled":"1","article_type":"original","abstract":[{"text":"Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, is still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of A. franciscana (Kellogg 1906), from the Great Salt Lake, United States. The genome is 1 GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species.","lang":"eng"}],"file_date_updated":"2024-02-26T09:54:59Z","language":[{"iso":"eng"}],"oa_version":"Published Version","OA_place":"publisher","pmid":1,"article_number":"evae006","date_published":"2024-01-20T00:00:00Z","DOAJ_listed":"1","has_accepted_license":"1","scopus_import":"1","isi":1,"department":[{"_id":"BeVi"}]},{"oa":1,"file_date_updated":"2023-11-30T14:16:59Z","abstract":[{"lang":"eng","text":"Many insects carry an ancient X chromosome—the Drosophila Muller element F—that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 My. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of scorpionflies (genus Panorpa), an insect belonging to a long overlooked sister-order to Diptera: Mecoptera. Combining our genome assembly with genomic short-read data, we obtain genome coverage and identify X-linked super-scaffolds. We further perform a gene homology analysis between the Panorpa X and a closely related Diptera species, and we assess the conservation of the Panorpa X-linked gene content with that of more distantly related insect species. We explored the structure of the Panorpa X by determining its repeat content, GC content, and nucleotide diversity. Finally, we used RNAseq data to detect the presence of dosage compensation in somatic tissues, as well as to explore gene expression tissue-specificity, and sex-bias in gene expression. We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the 2 homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects."}],"ddc":["576"],"oa_version":"Published Version","date_created":"2023-11-27T16:39:19Z","article_processing_charge":"No","_id":"14614","day":"01","contributor":[{"contributor_type":"researcher","first_name":"Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"record":[{"id":"14613","relation":"used_in_publication","status":"public"}]},"file":[{"checksum":"cd0f13322b5156819ecaebd2bc8e7d12","creator":"clasne","content_type":"application/zip","relation":"main_file","file_size":404968272,"access_level":"open_access","date_created":"2023-11-28T13:15:26Z","date_updated":"2023-11-28T13:15:26Z","file_name":"panorpaX.zip","file_id":"14625","success":1},{"success":1,"file_id":"14634","file_name":"panorpa_readme.txt","date_updated":"2023-11-30T14:16:59Z","access_level":"open_access","date_created":"2023-11-30T14:16:59Z","relation":"main_file","file_size":2625,"checksum":"9ff600416577687a737cb3c96dfcb26c","creator":"clasne","content_type":"text/plain"}],"keyword":["Panorpa","scorpionfly","genome","transcriptome"],"type":"research_data","status":"public","author":[{"first_name":"Clementine","orcid":"0000-0002-1197-8616","full_name":"Lasne, Clementine","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","last_name":"Lasne"},{"first_name":"Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"}],"doi":"10.15479/AT:ISTA:14614","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","department":[{"_id":"BeVi"}],"date_published":"2023-12-01T00:00:00Z","citation":{"short":"C. Lasne, M.N. Elkrewi, (2023).","apa":"Lasne, C., &#38; Elkrewi, M. N. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14614\">https://doi.org/10.15479/AT:ISTA:14614</a>","mla":"Lasne, Clementine, and Marwan N. Elkrewi. <i>The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14614\">10.15479/AT:ISTA:14614</a>.","ieee":"C. Lasne and M. N. Elkrewi, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome.” Institute of Science and Technology Austria, 2023.","ama":"Lasne C, Elkrewi MN. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14614\">10.15479/AT:ISTA:14614</a>","chicago":"Lasne, Clementine, and Marwan N Elkrewi. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:14614\">https://doi.org/10.15479/AT:ISTA:14614</a>.","ista":"Lasne C, Elkrewi MN. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14614\">10.15479/AT:ISTA:14614</a>."},"has_accepted_license":"1","title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","publisher":"Institute of Science and Technology Austria","date_updated":"2025-09-09T13:33:22Z","year":"2023","corr_author":"1"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":40,"intvolume":"        40","related_material":{"record":[{"status":"public","id":"14614","relation":"research_data"},{"status":"public","id":"19386","relation":"dissertation_contains"}],"link":[{"description":"News on ISTA webpage","relation":"press_release","url":"https://ista.ac.at/en/news/on-the-hunt/"}]},"status":"public","type":"journal_article","abstract":[{"lang":"eng","text":"Many insects carry an ancient X chromosome - the Drosophila Muller element F - that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 MY. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the two homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects."}],"file_date_updated":"2024-01-02T11:39:38Z","oa_version":"Published Version","language":[{"iso":"eng"}],"article_processing_charge":"Yes","article_type":"original","quality_controlled":"1","project":[{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction"},{"_id":"ebb230e0-77a9-11ec-83b8-87a37e0241d3","name":"Mechanisms and Evolution of Reproductive Plasticity","grant_number":"ESP39 49461"}],"pmid":1,"scopus_import":"1","isi":1,"department":[{"_id":"BeVi"}],"acknowledgement":"We thank the Vicoso lab for their assistance with specimen collection, and Tim Connallon for valuable comments and suggestions on earlier versions of the manuscript. Computational resources and support were provided by the Scientific Computing unit at the ISTA. This research was supported by grants from the Austrian Science Foundation to C.L.\r\n(FWF ESP 39), and to B.V. (FWF SFB F88-10).","article_number":"msad245","date_published":"2023-12-01T00:00:00Z","has_accepted_license":"1","publication_status":"published","file":[{"date_updated":"2024-01-02T11:39:38Z","file_name":"2023_MolecularBioEvo_Lasne.pdf","file_id":"14727","success":1,"creator":"dernst","content_type":"application/pdf","checksum":"47c1c72fb499f26ea52d216b242208c8","file_size":8623505,"relation":"main_file","date_created":"2024-01-02T11:39:38Z","access_level":"open_access"}],"issue":"12","keyword":["Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"oa":1,"date_created":"2023-11-27T16:14:37Z","ddc":["570"],"day":"01","_id":"14613","acknowledged_ssus":[{"_id":"ScienComp"}],"title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"corr_author":"1","year":"2023","date_updated":"2026-05-29T22:31:21Z","publisher":"Oxford University Press","publication":"Molecular Biology and Evolution","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"12","doi":"10.1093/molbev/msad245","author":[{"orcid":"0000-0002-1197-8616","first_name":"Clementine","last_name":"Lasne","full_name":"Lasne, Clementine","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237"},{"orcid":"0000-0002-5328-7231","first_name":"Marwan N","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"first_name":"Melissa A","orcid":"0000-0002-9752-7380","last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A"},{"last_name":"Layana Franco","full_name":"Layana Franco, Lorena Alexandra","id":"02814589-eb8f-11eb-b029-a70074f3f18f","orcid":"0000-0002-1253-6297","first_name":"Lorena Alexandra"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana","last_name":"Macon","first_name":"Ariana"},{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"citation":{"apa":"Lasne, C., Elkrewi, M. N., Toups, M. A., Layana Franco, L. A., Macon, A., &#38; Vicoso, B. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msad245\">https://doi.org/10.1093/molbev/msad245</a>","short":"C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso, Molecular Biology and Evolution 40 (2023).","mla":"Lasne, Clementine, et al. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” <i>Molecular Biology and Evolution</i>, vol. 40, no. 12, msad245, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/molbev/msad245\">10.1093/molbev/msad245</a>.","ieee":"C. Lasne, M. N. Elkrewi, M. A. Toups, L. A. Layana Franco, A. Macon, and B. Vicoso, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome,” <i>Molecular Biology and Evolution</i>, vol. 40, no. 12. Oxford University Press, 2023.","ama":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. <i>Molecular Biology and Evolution</i>. 2023;40(12). doi:<a href=\"https://doi.org/10.1093/molbev/msad245\">10.1093/molbev/msad245</a>","chicago":"Lasne, Clementine, Marwan N Elkrewi, Melissa A Toups, Lorena Alexandra Layana Franco, Ariana Macon, and Beatriz Vicoso. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/molbev/msad245\">https://doi.org/10.1093/molbev/msad245</a>.","ista":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 40(12), msad245."},"external_id":{"pmid":["37988296"],"isi":["001122489000003"]}},{"publisher":"Institute of Science and Technology Austria","date_updated":"2025-04-15T08:34:17Z","corr_author":"1","year":"2022","title":"Data from Elkrewi, Khauratovich, Toups et al. 2022, \"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp\"","date_published":"2022-08-05T00:00:00Z","citation":{"mla":"Elkrewi, Marwan N. <i>Data from Elkrewi, Khauratovich, Toups et Al. 2022, “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.”</i> Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>.","ieee":"M. N. Elkrewi, “Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2022.","apa":"Elkrewi, M. N. (2022). Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>","short":"M.N. Elkrewi, (2022).","ista":"Elkrewi MN. 2022. Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>.","ama":"Elkrewi MN. Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>","chicago":"Elkrewi, Marwan N. “Data from Elkrewi, Khauratovich, Toups et Al. 2022, ‘ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>."},"has_accepted_license":"1","author":[{"first_name":"Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"}],"doi":"10.15479/AT:ISTA:11653","month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"type":"research_data","status":"public","related_material":{"record":[{"id":"12248","relation":"used_in_publication","status":"public"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"description":"The folder contains the following datasets (fasta files, and text files):\nSup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan\nmale draft assembly\nSup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana\nSup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and\nA. parthenogenetica females and rare male.\nSup. Dataset 4: Artemia sinica Male:female FST per 1Kb window\nSup. Dataset 5: FASTA file with candidate W scaffolds\nSup. Dataset 6: Candidate W-derived transcripts and alignments\nSup. Dataset 7: Gene expression with genomic location\nSup. Dataset 8: VCF for asexual female and rare male\nSup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis)\nSup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using\nA. sp. Kazakhstan as the reference), and inferred ancestry\nSup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their\nlocations in the Artemia sinica male genome.\n","creator":"melkrewi","content_type":"application/x-zip-compressed","checksum":"5f1d7c6d7ab5375ed2564521432bed0c","date_created":"2022-07-26T12:37:52Z","access_level":"open_access","embargo":"2022-08-07","relation":"main_file","file_size":2209382998,"date_updated":"2022-08-08T22:30:04Z","file_id":"11655","file_name":"Data.zip","title":"Supplementary Datasets"}],"article_processing_charge":"No","_id":"11653","day":"05","contributor":[{"first_name":"Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"last_name":"Khauratovich","first_name":"Uladzislava"},{"first_name":"Melissa A","last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Vincent K","last_name":"Bett","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","first_name":"Ariana"},{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075"},{"last_name":"Sax","first_name":"Luca"},{"first_name":"Ann K","last_name":"Huylmans","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hontoria ","first_name":"Francisco"},{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"}],"oa":1,"abstract":[{"text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.","lang":"eng"}],"file_date_updated":"2022-08-08T22:30:04Z","ddc":["570"],"oa_version":"Published Version","date_created":"2022-07-26T11:01:47Z"},{"acknowledged_ssus":[{"_id":"ScienComp"}],"title":"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp","publication_identifier":{"issn":["1943-2631"]},"publication":"Genetics","corr_author":"1","year":"2022","date_updated":"2026-05-29T22:31:20Z","publisher":"Oxford University Press","month":"10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"orcid":"0000-0002-5328-7231","first_name":"Marwan N","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"last_name":"Khauratovich","full_name":"Khauratovich, Uladzislava","id":"5eba06f4-97d8-11ed-9f8f-d826ebdd9434","first_name":"Uladzislava"},{"full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","orcid":"0000-0002-9752-7380","first_name":"Melissa A"},{"full_name":"Bett, Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","last_name":"Bett","first_name":"Vincent K"},{"id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac","first_name":"Andrea"},{"full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","first_name":"Ariana"},{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","first_name":"Christelle"},{"id":"701c5602-97d8-11ed-96b5-b52773c70189","full_name":"Sax, Luca","last_name":"Sax","first_name":"Luca"},{"full_name":"Huylmans, Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans","orcid":"0000-0001-8871-4961","first_name":"Ann K"},{"first_name":"Francisco","full_name":"Hontoria, Francisco","last_name":"Hontoria"},{"last_name":"Vicoso","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"doi":"10.1093/genetics/iyac123","external_id":{"isi":["000850270300001"],"pmid":["35977389"]},"citation":{"ama":"Elkrewi MN, Khauratovich U, Toups MA, et al. ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. <i>Genetics</i>. 2022;222(2). doi:<a href=\"https://doi.org/10.1093/genetics/iyac123\">10.1093/genetics/iyac123</a>","chicago":"Elkrewi, Marwan N, Uladzislava Khauratovich, Melissa A Toups, Vincent K Bett, Andrea Mrnjavac, Ariana Macon, Christelle Fraisse, et al. “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” <i>Genetics</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/genetics/iyac123\">https://doi.org/10.1093/genetics/iyac123</a>.","ista":"Elkrewi MN, Khauratovich U, Toups MA, Bett VK, Mrnjavac A, Macon A, Fraisse C, Sax L, Huylmans AK, Hontoria F, Vicoso B. 2022. ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. Genetics. 222(2), iyac123.","apa":"Elkrewi, M. N., Khauratovich, U., Toups, M. A., Bett, V. K., Mrnjavac, A., Macon, A., … Vicoso, B. (2022). ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyac123\">https://doi.org/10.1093/genetics/iyac123</a>","short":"M.N. Elkrewi, U. Khauratovich, M.A. Toups, V.K. Bett, A. Mrnjavac, A. Macon, C. Fraisse, L. Sax, A.K. Huylmans, F. Hontoria, B. Vicoso, Genetics 222 (2022).","mla":"Elkrewi, Marwan N., et al. “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” <i>Genetics</i>, vol. 222, no. 2, iyac123, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/genetics/iyac123\">10.1093/genetics/iyac123</a>.","ieee":"M. N. Elkrewi <i>et al.</i>, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp,” <i>Genetics</i>, vol. 222, no. 2. Oxford University Press, 2022."},"file":[{"date_updated":"2023-01-30T08:59:58Z","success":1,"file_id":"12440","file_name":"2022_Genetics_Elkrewi.pdf","access_level":"open_access","date_created":"2023-01-30T08:59:58Z","relation":"main_file","file_size":1347136,"content_type":"application/pdf","creator":"dernst","checksum":"f79ff5383e882ea3f95f3da47a78029d"}],"issue":"2","publication_status":"published","keyword":["Genetics"],"date_created":"2023-01-16T09:56:10Z","ddc":["570"],"oa":1,"ec_funded":1,"day":"01","_id":"12248","pmid":1,"project":[{"call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"},{"name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"isi":1,"department":[{"_id":"BeVi"}],"scopus_import":"1","has_accepted_license":"1","acknowledgement":"This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 715257) and by the Austrian Science Foundation (FWF SFB F88-10).\r\nWe thank the Vicoso group for comments on the manuscript and the ISTA Scientific computing team and the Vienna Biocenter Sequencing facility for technical support.","article_number":"iyac123","date_published":"2022-10-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":222,"related_material":{"record":[{"relation":"research_data","id":"11653","status":"public"},{"relation":"dissertation_contains","id":"19386","status":"public"}]},"intvolume":"       222","type":"journal_article","status":"public","oa_version":"Published Version","language":[{"iso":"eng"}],"abstract":[{"text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species Artemia sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species Artemia sp. Kazakhstan and several asexual lineages of Artemia parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.","lang":"eng"}],"file_date_updated":"2023-01-30T08:59:58Z","article_type":"original","quality_controlled":"1","article_processing_charge":"No"},{"ec_funded":1,"_id":"10767","day":"09","ddc":["570"],"date_created":"2022-02-20T23:01:31Z","oa":1,"issue":"1968","file":[{"date_updated":"2022-02-21T08:17:38Z","success":1,"file_id":"10779","file_name":"2022_ProceedingsRoyalSocB_Kelemen.pdf","access_level":"open_access","date_created":"2022-02-21T08:17:38Z","relation":"main_file","file_size":2366976,"creator":"dernst","checksum":"27042a3706ae52a919fed1ac114bf7bb","content_type":"application/pdf"}],"publication_status":"published","external_id":{"isi":["000752812800012"],"pmid":["35135349"]},"citation":{"chicago":"Kelemen, Réka K, Marwan N Elkrewi, Anna K. Lindholm, and Beatriz Vicoso. “Novel Patterns of Expression and Recruitment of New Genes on the T-Haplotype, a Mouse Selfish Chromosome.” <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society, 2022. <a href=\"https://doi.org/10.1098/rspb.2021.1985\">https://doi.org/10.1098/rspb.2021.1985</a>.","ama":"Kelemen RK, Elkrewi MN, Lindholm AK, Vicoso B. Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. <i>Proceedings of the Royal Society B: Biological Sciences</i>. 2022;289(1968):20211985. doi:<a href=\"https://doi.org/10.1098/rspb.2021.1985\">10.1098/rspb.2021.1985</a>","ista":"Kelemen RK, Elkrewi MN, Lindholm AK, Vicoso B. 2022. Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. Proceedings of the Royal Society B: Biological Sciences. 289(1968), 20211985.","apa":"Kelemen, R. K., Elkrewi, M. N., Lindholm, A. K., &#38; Vicoso, B. (2022). Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2021.1985\">https://doi.org/10.1098/rspb.2021.1985</a>","short":"R.K. Kelemen, M.N. Elkrewi, A.K. Lindholm, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 289 (2022) 20211985.","ieee":"R. K. Kelemen, M. N. Elkrewi, A. K. Lindholm, and B. Vicoso, “Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome,” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 289, no. 1968. The Royal Society, p. 20211985, 2022.","mla":"Kelemen, Réka K., et al. “Novel Patterns of Expression and Recruitment of New Genes on the T-Haplotype, a Mouse Selfish Chromosome.” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 289, no. 1968, The Royal Society, 2022, p. 20211985, doi:<a href=\"https://doi.org/10.1098/rspb.2021.1985\">10.1098/rspb.2021.1985</a>."},"author":[{"first_name":"Réka K","orcid":"0000-0002-8489-9281","last_name":"Kelemen","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","full_name":"Kelemen, Réka K"},{"last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","first_name":"Marwan N"},{"full_name":"Lindholm, Anna K.","last_name":"Lindholm","first_name":"Anna K."},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306"}],"doi":"10.1098/rspb.2021.1985","month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Proceedings of the Royal Society B: Biological Sciences","date_updated":"2026-05-29T22:31:20Z","publisher":"The Royal Society","corr_author":"1","year":"2022","publication_identifier":{"eissn":["1471-2954"]},"title":"Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome","quality_controlled":"1","article_type":"original","article_processing_charge":"No","page":"20211985","language":[{"iso":"eng"}],"oa_version":"Published Version","file_date_updated":"2022-02-21T08:17:38Z","abstract":[{"lang":"eng","text":"The t-haplotype of mice is a classical model for autosomal transmission distortion. A largely non-recombining variant of the proximal region of chromosome 17, it is transmitted to more than 90% of the progeny of heterozygous males through the disabling of sperm carrying a standard chromosome. While extensive genetic and functional work has shed light on individual genes involved in drive, much less is known about the evolution and function of the rest of its hundreds of genes. Here, we characterize the sequence and expression of dozens of t-specific transcripts and of their chromosome 17 homologues. Many genes showed reduced expression of the t-allele, but an equal number of genes showed increased expression of their t-copy, consistent with increased activity or a newly evolved function. Genes on the t-haplotype had a significantly higher non-synonymous substitution rate than their homologues on the standard chromosome, with several genes harbouring dN/dS ratios above 1. Finally, the t-haplotype has acquired at least two genes from other chromosomes, which show high and tissue-specific expression. These results provide a first overview of the gene content of this selfish element, and support a more dynamic evolutionary scenario than expected of a large genomic region with almost no recombination."}],"type":"journal_article","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"intvolume":"       289","volume":289,"related_material":{"record":[{"status":"public","id":"17119","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"19386"}]},"has_accepted_license":"1","date_published":"2022-02-09T00:00:00Z","acknowledgement":"This project has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 715257) and from the Swiss National Science Foundation (grant no. 310030_189145).\r\nWe thank Jari Garbely of the Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland, for conducting the PCR verification. Barbara\r\nKonig, Gabi Stichel and A.K.L. collected mouse tissue samples, from the field study led by R.K.K. ","isi":1,"department":[{"_id":"BeVi"}],"scopus_import":"1","pmid":1,"project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}]},{"project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"pmid":1,"scopus_import":"1","isi":1,"department":[{"_id":"BeVi"}],"date_published":"2021-06-19T00:00:00Z","acknowledgement":"The authors thank IT support at IST Austria for providing an optimal environment for bioinformatic analyses. This work was supported by an Austrian Science Foundation FWF grant (Project P28842) to B.V.","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19386"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"intvolume":"       138","volume":138,"type":"journal_article","status":"public","abstract":[{"text":"Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group.","lang":"eng"}],"file_date_updated":"2022-05-06T09:47:18Z","language":[{"iso":"eng"}],"page":"5345-58","oa_version":"Published Version","article_processing_charge":"No","quality_controlled":"1","article_type":"original","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"title":"Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination","publisher":"Oxford University Press ","date_updated":"2026-05-29T22:31:20Z","corr_author":"1","year":"2021","publication":"Molecular Biology and Evolution","doi":"10.1093/molbev/msab178","author":[{"last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","orcid":"0000-0002-5328-7231"},{"first_name":"Mikhail A.","orcid":"0000-0002-8876-6494","last_name":"Moldovan","id":"c8bb7f32-3315-11ec-b58b-e5950e6c14a0","full_name":"Moldovan, Mikhail A."},{"orcid":"0000-0002-8101-2518","first_name":"Marion A L","last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","full_name":"Picard, Marion A L"},{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","external_id":{"pmid":["34146097"],"isi":["000741368600009"]},"citation":{"ista":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. 2021. Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. 138(12), 5345–58.","ama":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. 2021;138(12):5345-5358. doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>","chicago":"Elkrewi, Marwan N, Mikhail A. Moldovan, Marion A L Picard, and Beatriz Vicoso. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>. Oxford University Press , 2021. <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>.","mla":"Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>, vol. 138, no. 12, Oxford University Press , 2021, pp. 5345–58, doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>.","ieee":"M. N. Elkrewi, M. A. Moldovan, M. A. L. Picard, and B. Vicoso, “Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination,” <i>Molecular Biology and Evolution</i>, vol. 138, no. 12. Oxford University Press , pp. 5345–58, 2021.","short":"M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution 138 (2021) 5345–58.","apa":"Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., &#38; Vicoso, B. (2021). Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. Oxford University Press . <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>"},"publication_status":"published","issue":"12","file":[{"file_name":"2021_MolecularBiolEvolution_Elkrewi.pdf","file_id":"11352","success":1,"date_updated":"2022-05-06T09:47:18Z","checksum":"1b096702fb356d9c0eb88e1b3fcff5f8","content_type":"application/pdf","creator":"dernst","file_size":1008594,"relation":"main_file","access_level":"open_access","date_created":"2022-05-06T09:47:18Z"}],"keyword":["sex chromosomes","evolutionary strata","W-linked gene","sex determining gene","schistosome parasites"],"oa":1,"ddc":["610"],"date_created":"2021-10-21T07:49:12Z","_id":"10167","day":"19"}]