[{"publication":"Genome Biology and Evolution","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","scopus_import":"1","article_processing_charge":"Yes","publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BeVi"}],"pmid":1,"article_number":"evae006","title":"Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation","author":[{"last_name":"Bett","first_name":"Vincent K","full_name":"Bett, Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"last_name":"Macon","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso"},{"orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","first_name":"Marwan N","last_name":"Elkrewi"}],"day":"20","file":[{"file_size":5213306,"content_type":"application/pdf","relation":"main_file","creator":"dernst","file_name":"2024_GBE_Bett.pdf","success":1,"date_created":"2024-02-26T09:54:59Z","access_level":"open_access","file_id":"15029","date_updated":"2024-02-26T09:54:59Z","checksum":"106a40f10443b2e7ba66749844ebbdf1"}],"issue":"1","language":[{"iso":"eng"}],"doi":"10.1093/gbe/evae006","quality_controlled":"1","publication_identifier":{"eissn":["1759-6653"]},"_id":"15009","year":"2024","volume":16,"file_date_updated":"2024-02-26T09:54:59Z","date_created":"2024-02-18T23:01:02Z","oa_version":"Published Version","month":"01","type":"journal_article","date_updated":"2025-07-24T11:06:42Z","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"}],"intvolume":"        16","related_material":{"record":[{"status":"public","id":"14705","relation":"research_data"}]},"citation":{"short":"V.K. Bett, A. Macon, B. Vicoso, M.N. Elkrewi, Genome Biology and Evolution 16 (2024).","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.","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>.","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.","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>.","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>","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>"},"status":"public","external_id":{"pmid":["38245839"]},"ddc":["570"],"date_published":"2024-01-20T00:00:00Z","oa":1,"publication_status":"published","has_accepted_license":"1"},{"_id":"14613","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).","year":"2023","volume":40,"file_date_updated":"2024-01-02T11:39:38Z","date_created":"2023-11-27T16:14:37Z","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."}],"date_updated":"2024-02-21T12:18:35Z","month":"12","type":"journal_article","oa_version":"Published Version","intvolume":"        40","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/on-the-hunt/","description":"News on ISTA webpage"}],"record":[{"relation":"research_data","status":"public","id":"14614"}]},"citation":{"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>","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>","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>.","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.","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>.","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.","short":"C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso, Molecular Biology and Evolution 40 (2023)."},"status":"public","external_id":{"pmid":["37988296"]},"date_published":"2023-12-01T00:00:00Z","ddc":["570"],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa":1,"publication_status":"published","has_accepted_license":"1","publication":"Molecular Biology and Evolution","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"department":[{"_id":"BeVi"}],"title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","article_number":"msad245","author":[{"full_name":"Lasne, Clementine","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","orcid":"0000-0002-1197-8616","first_name":"Clementine","last_name":"Lasne"},{"last_name":"Elkrewi","first_name":"Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N"},{"last_name":"Toups","first_name":"Melissa A","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lorena Alexandra","last_name":"Layana Franco","orcid":"0000-0002-1253-6297","id":"02814589-eb8f-11eb-b029-a70074f3f18f","full_name":"Layana Franco, Lorena Alexandra"},{"full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","first_name":"Ariana"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso"}],"day":"01","file":[{"relation":"main_file","content_type":"application/pdf","file_size":8623505,"creator":"dernst","success":1,"file_name":"2023_MolecularBioEvo_Lasne.pdf","date_created":"2024-01-02T11:39:38Z","access_level":"open_access","date_updated":"2024-01-02T11:39:38Z","file_id":"14727","checksum":"47c1c72fb499f26ea52d216b242208c8"}],"keyword":["Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"language":[{"iso":"eng"}],"issue":"12","project":[{"grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"},{"grant_number":"ESP39 49461","name":"Mechanisms and Evolution of Reproductive Plasticity","_id":"ebb230e0-77a9-11ec-83b8-87a37e0241d3"}],"doi":"10.1093/molbev/msad245","quality_controlled":"1","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]}},{"department":[{"_id":"BeVi"},{"_id":"NiBa"},{"_id":"GradSch"}],"publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","scopus_import":"1","ec_funded":1,"article_processing_charge":"Yes","publication":"G3: Genes, Genomes, Genetics","day":"01","file":[{"checksum":"c62e29fc7c5efbf8356f4c60cab4a2d1","date_updated":"2023-11-07T09:00:19Z","file_id":"14498","access_level":"open_access","date_created":"2023-11-07T09:00:19Z","success":1,"file_name":"2023_G3_Puixeu.pdf","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":845642}],"author":[{"last_name":"Puixeu Sala","first_name":"Gemma","full_name":"Puixeu Sala, Gemma","orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ariana","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana"},{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"title":"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","name":"Sexual conflict: resolution, constraints and biomedical implications","grant_number":"25817"}],"issue":"8","language":[{"iso":"eng"}],"keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"isi":1,"publication_identifier":{"issn":["2160-1836"]},"quality_controlled":"1","doi":"10.1093/g3journal/jkad121","year":"2023","acknowledgement":"We thank members of the Vicoso Group for comments on the manuscript, the Scientific Computing Unit at ISTA for technical support, and 2 anonymous reviewers for useful feedback. GP is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (DOC 25817) and received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant (agreement no. 665385).","_id":"14077","month":"08","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed\r\nso far used whole-body data and only single crosses, which may have limited their scope to detect patterns that are robust across tissues\r\nand biological replicates. Here, we use allele-specific gene expression of parental and reciprocal hybrid crosses between 6 Drosophila\r\nmelanogaster inbred lines to quantify cis- and trans-regulatory variation in heads and gonads of both sexes separately across 3 replicate\r\ncrosses. Our results suggest that female and male heads, as well as ovaries, have a similar regulatory architecture. On the other hand,\r\ntestes display more and substantially different cis-regulatory effects, suggesting that sex differences in the regulatory architecture that\r\nhave been previously observed may largely derive from testis-specific effects. We also examine the difference in cis-regulatory variation\r\nof genes across different levels of sex bias in gonads and heads. Consistent with the idea that intersex correlations constrain expression\r\nand can lead to sexual antagonism, we find more cis variation in unbiased and moderately biased genes in heads. In ovaries, reduced cis\r\nvariation is observed for male-biased genes, suggesting that cis variants acting on these genes in males do not lead to changes in ovary\r\nexpression. Finally, we examine the dominance patterns of gene expression and find that sex- and tissue-specific patterns of inheritance\r\nas well as trans-regulatory variation are highly variable across biological crosses, although these were performed in highly controlled\r\nexperimental conditions. This highlights the importance of using various genetic backgrounds to infer generalizable patterns.","lang":"eng"}],"date_updated":"2023-12-13T12:15:37Z","date_created":"2023-08-18T06:52:14Z","file_date_updated":"2023-11-07T09:00:19Z","volume":13,"external_id":{"isi":["001002997200001"]},"status":"public","citation":{"short":"G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023).","chicago":"Puixeu Sala, Gemma, Ariana Macon, and Beatriz Vicoso. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” <i>G3: Genes, Genomes, Genetics</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/g3journal/jkad121\">https://doi.org/10.1093/g3journal/jkad121</a>.","ieee":"G. Puixeu Sala, A. Macon, and B. Vicoso, “Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster,” <i>G3: Genes, Genomes, Genetics</i>, vol. 13, no. 8. Oxford University Press, 2023.","apa":"Puixeu Sala, G., Macon, A., &#38; Vicoso, B. (2023). Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. <i>G3: Genes, Genomes, Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/g3journal/jkad121\">https://doi.org/10.1093/g3journal/jkad121</a>","ista":"Puixeu Sala G, Macon A, Vicoso B. 2023. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. 13(8).","mla":"Puixeu Sala, Gemma, et al. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” <i>G3: Genes, Genomes, Genetics</i>, vol. 13, no. 8, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/g3journal/jkad121\">10.1093/g3journal/jkad121</a>.","ama":"Puixeu Sala G, Macon A, Vicoso B. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. <i>G3: Genes, Genomes, Genetics</i>. 2023;13(8). doi:<a href=\"https://doi.org/10.1093/g3journal/jkad121\">10.1093/g3journal/jkad121</a>"},"related_material":{"record":[{"status":"public","id":"12933","relation":"research_data"},{"relation":"dissertation_contains","id":"14058","status":"public"}]},"intvolume":"        13","has_accepted_license":"1","oa":1,"publication_status":"published","acknowledged_ssus":[{"_id":"ScienComp"}],"ddc":["570"],"date_published":"2023-08-01T00:00:00Z"},{"issue":"2","language":[{"iso":"eng"}],"keyword":["Genetics"],"isi":1,"project":[{"call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257"},{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810"}],"quality_controlled":"1","doi":"10.1093/genetics/iyac123","publication_identifier":{"issn":["1943-2631"]},"article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"scopus_import":"1","article_processing_charge":"No","ec_funded":1,"publication":"Genetics","department":[{"_id":"BeVi"}],"pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Oxford University Press","article_number":"iyac123","title":"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp","file":[{"creator":"dernst","file_size":1347136,"relation":"main_file","content_type":"application/pdf","file_name":"2022_Genetics_Elkrewi.pdf","success":1,"access_level":"open_access","date_created":"2023-01-30T08:59:58Z","checksum":"f79ff5383e882ea3f95f3da47a78029d","file_id":"12440","date_updated":"2023-01-30T08:59:58Z"}],"day":"01","author":[{"first_name":"Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N"},{"id":"5eba06f4-97d8-11ed-9f8f-d826ebdd9434","full_name":"Khauratovich, Uladzislava","last_name":"Khauratovich","first_name":"Uladzislava"},{"full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","first_name":"Melissa A","last_name":"Toups"},{"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","first_name":"Andrea","last_name":"Mrnjavac"},{"last_name":"Macon","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana"},{"first_name":"Christelle","last_name":"Fraisse","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"},{"first_name":"Luca","last_name":"Sax","id":"701c5602-97d8-11ed-96b5-b52773c70189","full_name":"Sax, Luca"},{"last_name":"Huylmans","first_name":"Ann K","orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","full_name":"Huylmans, Ann K"},{"full_name":"Hontoria, Francisco","first_name":"Francisco","last_name":"Hontoria"},{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"citation":{"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).","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>.","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.","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>","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.","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>.","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>"},"related_material":{"record":[{"id":"11653","status":"public","relation":"research_data"}]},"intvolume":"       222","external_id":{"isi":["000850270300001"],"pmid":["35977389"]},"status":"public","acknowledged_ssus":[{"_id":"ScienComp"}],"date_published":"2022-10-01T00:00:00Z","ddc":["570"],"has_accepted_license":"1","oa":1,"publication_status":"published","_id":"12248","year":"2022","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.","file_date_updated":"2023-01-30T08:59:58Z","date_created":"2023-01-16T09:56:10Z","volume":222,"type":"journal_article","oa_version":"Published Version","month":"10","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"}],"date_updated":"2024-03-25T23:30:26Z"},{"project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715257"}],"issue":"1959","language":[{"iso":"eng"}],"keyword":["asexual reproduction","parthenogenesis","sex-biased genes","sexual conflict","automixis","crustaceans"],"isi":1,"publication_identifier":{"issn":["0962-8452"],"eissn":["1471-2954"]},"quality_controlled":"1","doi":"10.1098/rspb.2021.1720","department":[{"_id":"BeVi"}],"pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"The Royal Society","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","ec_funded":1,"publication":"Proceedings of the Royal Society B: Biological Sciences","file":[{"date_created":"2021-10-22T11:48:02Z","access_level":"open_access","file_id":"10172","date_updated":"2021-10-22T11:48:02Z","checksum":"76e7f253b7040bca2ad76f82bd7c45c0","file_size":995806,"content_type":"application/pdf","relation":"main_file","creator":"cchlebak","file_name":"2021_ProRoSocBBioSci_Huylmans.pdf","success":1}],"day":"22","author":[{"first_name":"Ann K","last_name":"Huylmans","full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ariana","last_name":"Macon","full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hontoria, Francisco","first_name":"Francisco","last_name":"Hontoria"},{"first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"article_number":"20211720","title":"Transitions to asexuality and evolution of gene expression in Artemia brine shrimp","external_id":{"pmid":["34547909"],"isi":["000697643700001"]},"status":"public","citation":{"apa":"Huylmans, A. K., Macon, A., Hontoria, F., &#38; Vicoso, B. (2021). Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2021.1720\">https://doi.org/10.1098/rspb.2021.1720</a>","ista":"Huylmans AK, Macon A, Hontoria F, Vicoso B. 2021. Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal Society B: Biological Sciences. 288(1959), 20211720.","mla":"Huylmans, Ann K., et al. “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 288, no. 1959, 20211720, The Royal Society, 2021, doi:<a href=\"https://doi.org/10.1098/rspb.2021.1720\">10.1098/rspb.2021.1720</a>.","ama":"Huylmans AK, Macon A, Hontoria F, Vicoso B. Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. <i>Proceedings of the Royal Society B: Biological Sciences</i>. 2021;288(1959). doi:<a href=\"https://doi.org/10.1098/rspb.2021.1720\">10.1098/rspb.2021.1720</a>","short":"A.K. Huylmans, A. Macon, F. Hontoria, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 288 (2021).","chicago":"Huylmans, Ann K, Ariana Macon, Francisco Hontoria, and Beatriz Vicoso. “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society, 2021. <a href=\"https://doi.org/10.1098/rspb.2021.1720\">https://doi.org/10.1098/rspb.2021.1720</a>.","ieee":"A. K. Huylmans, A. Macon, F. Hontoria, and B. Vicoso, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp,” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 288, no. 1959. The Royal Society, 2021."},"intvolume":"       288","related_material":{"record":[{"relation":"research_data","id":"9949","status":"public"}],"link":[{"relation":"supplementary_material","url":"https://doi.org/10.6084/m9.figshare.c.5615488.v1"}]},"has_accepted_license":"1","oa":1,"publication_status":"published","acknowledged_ssus":[{"_id":"ScienComp"}],"ddc":["595"],"date_published":"2021-09-22T00:00:00Z","year":"2021","acknowledgement":"We thank the Vicoso laboratory, Thomas Lenormand and Tanja Schwander for helpful discussions, the group of Gonzalo Gajardo, especially Cristian Gallardo-Escárate and Margarita Parraguez Donoso, for sequencing data and advice, and the IST Scientific Computing Group for their support. This work was supported by the European Research Council under the European Union's Horizon 2020 research and innovation program (grant agreement no. 715257).","_id":"10166","type":"journal_article","oa_version":"Published Version","month":"09","date_updated":"2024-02-21T12:40:29Z","abstract":[{"lang":"eng","text":"While sexual reproduction is widespread among many taxa, asexual lineages have repeatedly evolved from sexual ancestors. Despite extensive research on the evolution of sex, it is still unclear whether this switch represents a major transition requiring major molecular reorganization, and how convergent the changes involved are. In this study, we investigated the phylogenetic relationship and patterns of gene expression of sexual and asexual lineages of Eurasian Artemia brine shrimp, to assess how gene expression patterns are affected by the transition to asexuality. We find only a few genes that are consistently associated with the evolution of asexuality, suggesting that this shift may not require an extensive overhauling of the meiotic machinery. While genes with sex-biased expression have high rates of expression divergence within Eurasian Artemia, neither female- nor male-biased genes appear to show unusual evolutionary patterns after sexuality is lost, contrary to theoretical expectations."}],"date_created":"2021-10-21T07:46:06Z","file_date_updated":"2021-10-22T11:48:02Z","volume":288},{"year":"2019","_id":"6418","date_updated":"2024-02-21T12:45:41Z","abstract":[{"text":"Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general.","lang":"eng"}],"month":"04","type":"journal_article","oa_version":"Published Version","page":"1033-1044","date_created":"2019-05-13T07:58:38Z","file_date_updated":"2020-07-14T12:47:29Z","volume":11,"status":"public","external_id":{"isi":["000476569800003"]},"citation":{"chicago":"Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger, and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/gbe/evz053\">https://doi.org/10.1093/gbe/evz053</a>.","ieee":"A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso, “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome,” <i>Genome biology and evolution</i>, vol. 11, no. 4. Oxford University Press, pp. 1033–1044, 2019.","short":"A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome Biology and Evolution 11 (2019) 1033–1044.","ama":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. <i>Genome biology and evolution</i>. 2019;11(4):1033-1044. doi:<a href=\"https://doi.org/10.1093/gbe/evz053\">10.1093/gbe/evz053</a>","apa":"Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., &#38; Vicoso, B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evz053\">https://doi.org/10.1093/gbe/evz053</a>","ista":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. 2019. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 11(4), 1033–1044.","mla":"Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” <i>Genome Biology and Evolution</i>, vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:<a href=\"https://doi.org/10.1093/gbe/evz053\">10.1093/gbe/evz053</a>."},"intvolume":"        11","related_material":{"record":[{"relation":"popular_science","status":"public","id":"6060"}]},"has_accepted_license":"1","oa":1,"publication_status":"published","acknowledged_ssus":[{"_id":"ScienComp"}],"date_published":"2019-04-01T00:00:00Z","ddc":["570"],"department":[{"_id":"BeVi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Oxford University Press","ec_funded":1,"scopus_import":"1","article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication":"Genome biology and evolution","day":"01","file":[{"file_name":"2019_GBE_Huylmans.pdf","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":1256303,"checksum":"7d0ede297b6741f3dc89cd59017c7642","date_updated":"2020-07-14T12:47:29Z","file_id":"6446","access_level":"open_access","date_created":"2019-05-14T08:29:38Z"}],"author":[{"first_name":"Ann K","last_name":"Huylmans","full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Melissa A","last_name":"Toups","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ariana","last_name":"Macon","full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"William J","last_name":"Gammerdinger","full_name":"Gammerdinger, William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9638-1220"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"}],"title":"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome","project":[{"grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"language":[{"iso":"eng"}],"issue":"4","isi":1,"publication_identifier":{"eissn":["1759-6653"]},"quality_controlled":"1","doi":"10.1093/gbe/evz053"},{"publication_identifier":{"issn":["07374038"]},"pubrep_id":"848","doi":"10.1093/molbev/msx190","quality_controlled":"1","project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22"}],"isi":1,"issue":"10","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","full_name":"Huylmans, Ann K","first_name":"Ann K","last_name":"Huylmans"},{"last_name":"Macon","first_name":"Ariana","full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"file":[{"file_size":462863,"content_type":"application/pdf","relation":"main_file","creator":"system","file_name":"IST-2017-848-v1+1_2017_Vicoso_GlobalDosage.pdf","date_created":"2018-12-12T10:10:23Z","access_level":"open_access","file_id":"4810","date_updated":"2020-07-14T12:48:15Z","checksum":"009fd68043211d645ceb9d1de28274f2"}],"day":"06","title":"Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome","publist_id":"6472","publisher":"Oxford University Press","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"BeVi"}],"publication":"Molecular Biology and Evolution","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","oa":1,"publication_status":"published","has_accepted_license":"1","ddc":["570","576"],"date_published":"2017-07-06T00:00:00Z","status":"public","external_id":{"isi":["000411814800016"]},"intvolume":"        34","citation":{"ama":"Huylmans AK, Macon A, Vicoso B. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. <i>Molecular Biology and Evolution</i>. 2017;34(10):2637-2649. doi:<a href=\"https://doi.org/10.1093/molbev/msx190\">10.1093/molbev/msx190</a>","mla":"Huylmans, Ann K., et al. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” <i>Molecular Biology and Evolution</i>, vol. 34, no. 10, Oxford University Press, 2017, pp. 2637–49, doi:<a href=\"https://doi.org/10.1093/molbev/msx190\">10.1093/molbev/msx190</a>.","ista":"Huylmans AK, Macon A, Vicoso B. 2017. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. 34(10), 2637–2649.","apa":"Huylmans, A. K., Macon, A., &#38; Vicoso, B. (2017). Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msx190\">https://doi.org/10.1093/molbev/msx190</a>","ieee":"A. K. Huylmans, A. Macon, and B. Vicoso, “Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome,” <i>Molecular Biology and Evolution</i>, vol. 34, no. 10. Oxford University Press, pp. 2637–2649, 2017.","chicago":"Huylmans, Ann K, Ariana Macon, and Beatriz Vicoso. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/molbev/msx190\">https://doi.org/10.1093/molbev/msx190</a>.","short":"A.K. Huylmans, A. Macon, B. Vicoso, Molecular Biology and Evolution 34 (2017) 2637–2649."},"page":"2637 - 2649","oa_version":"Published Version","type":"journal_article","month":"07","abstract":[{"text":"While chromosome-wide dosage compensation of the X chromosome has been found in many species, studies in ZW clades have indicated that compensation of the Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show complete compensation of the Z chromosome, while others lack full equalization, but what drives these inconsistencies is unclear. Here, we compare patterns of male and female gene expression on the Z chromosome of two closely related butterfly species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths species, Plodia interpunctella and Bombyx mori, which were previously found to differ in the extent to which they equalize Z-linked gene expression between the sexes. We find that, while some species and tissues seem to have incomplete dosage compensation, this is in fact due to the accumulation of male-biased genes and the depletion of female-biased genes on the Z chromosome. Once this is accounted for, the Z chromosome is fully compensated in all four species, through the up-regulation of Z expression in females and in some cases additional down-regulation in males. We further find that both sex-biased genes and Z-linked genes have increased rates of expression divergence in this clade, and that this can lead to fast shifts in patterns of gene expression even between closely related species. Taken together, these results show that the uneven distribution of sex-biased genes on sex chromosomes can confound conclusions about dosage compensation and that Z chromosome-wide dosage compensation is not only possible but ubiquitous among Lepidoptera.","lang":"eng"}],"date_updated":"2023-09-26T15:36:34Z","volume":34,"date_created":"2018-12-11T11:49:20Z","file_date_updated":"2020-07-14T12:48:15Z","year":"2017","_id":"945"}]