@phdthesis{20449,
  abstract     = {Males and females of many  species differ in morphology, physiology, and behavior. In taxa
with genetic sex determination, sexual differentiation arises largely from sex-biased gene
expression, which varies across tissues, developmental stages, and lineages. Increasing
evidence highlights chromatin configuration, which can exist in open or closed states, and can
be shaped by sex-determination path ways, as a key regulatory layer of this dimorphism.
Degeneration of the Y or W chromosome further contributes to sex -specific differences by
altering gene copy numbers relative to autosomes in heterogametic sex. To mitigate these
imbalances, many eukaryotes have independently evolved dosage compensation mechanisms,
often mediated through chromatin -level regulation. In this thesis, we investigate the
evolutionary dynamics of sex chromosome differentiation in two species, Artemia franciscana
and Cameraria  ohridella , with a particular focus on the extent of dosage compensation
following gene loss in the heterogametic sex and the potential chromatin-based mechanisms
underlying this process. We further characterize sex -biased gene expression and its regulation
through histone modifications. Our analyses also reveal that the A. franciscana genome is
highly repetitive, with many genes containing intronic transposable elements. We find that
enrichment of histonemo difications associated with constitutive heterochromatin, positively
correlates with variation in gene expression levels. Collectively, these findings underscore role
of chromatin regulation in shaping the evolution of sex chromosomes and sexual
differentiation. },
  author       = {Bett, Vincent K},
  issn         = {2663-337X},
  pages        = {114},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Evolution and regulation of the Z chromosome}},
  doi          = {10.15479/AT-ISTA-20449},
  year         = {2025},
}

@article{19735,
  abstract     = {The males and females of the brine shrimp Artemia franciscana are highly dimorphic, and this dimorphism is associated with substantial sex-biased gene expression in heads and gonads. How these sex-specific patterns of expression are regulated at the molecular level is unknown. A. franciscana also has differentiated ZW sex chromosomes, with complete dosage compensation, but the molecular mechanism through which compensation is achieved is unknown. Here, we conducted CUT&TAG assays targeting 7 post-translational histone modifications (H3K27me3, H3K9me2, H3K9me3, H3K36me3, H3K27ac, H3K4me3, and H4K16ac) in heads and gonads of A. franciscana, allowing us to divide the genome into 12 chromatin states. We further defined functional chromatin signatures for all genes, which were correlated with transcript level abundances. Differences in the occupancy of the profiled epigenetic marks between sexes were associated with differential gene expression between males and females. Finally, we found a significant enrichment of the permissive H4K16ac histone mark in the Z-specific region in both tissues of females but not males, supporting the role of this histone mark in mediating dosage compensation of the Z chromosome.},
  author       = {Bett, Vincent K and Trejo Arellano, Minerva S and Vicoso, Beatriz},
  issn         = {1537-1719},
  journal      = {Molecular Biology and Evolution},
  number       = {5},
  publisher    = {Oxford University Press},
  title        = {{Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana}},
  doi          = {10.1093/molbev/msaf085},
  volume       = {42},
  year         = {2025},
}

@article{15009,
  abstract     = {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.},
  author       = {Bett, Vincent K and Macon, Ariana and Vicoso, Beatriz and Elkrewi, Marwan N},
  issn         = {1759-6653},
  journal      = {Genome Biology and Evolution},
  number       = {1},
  publisher    = {Oxford University Press},
  title        = {{Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation}},
  doi          = {10.1093/gbe/evae006},
  volume       = {16},
  year         = {2024},
}

@article{12248,
  abstract     = {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.},
  author       = {Elkrewi, Marwan N and Khauratovich, Uladzislava and Toups, Melissa A and Bett, Vincent K and Mrnjavac, Andrea and Macon, Ariana and Fraisse, Christelle and Sax, Luca and Huylmans, Ann K and Hontoria, Francisco and Vicoso, Beatriz},
  issn         = {1943-2631},
  journal      = {Genetics},
  keywords     = {Genetics},
  number       = {2},
  publisher    = {Oxford University Press},
  title        = {{ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp}},
  doi          = {10.1093/genetics/iyac123},
  volume       = {222},
  year         = {2022},
}