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Kuhl H, Euclide PT, Klopp C, Cabau C, Zahm M, Lopez-Roques C, Iampietro C, Kuchly C, Donnadieu C, Feron R, Parrinello H, Poncet C, Jaffrelo L, Confolent C, Wen M, Herpin A, Jouanno E, Bestin A, Haffray P, Morvezen R, de Almeida TR, Lecocq T, Schaerlinger B, Chardard D, Żarski D, Larson WA, Postlethwait JH, Timirkhanov S, Kloas W, Wuertz S, Stöck M, Guiguen Y. Multi-genome comparisons reveal gain-and-loss evolution of anti-Mullerian hormone receptor type 2 as a candidate master sex-determining gene in Percidae. BMC Biol 2024; 22:141. [PMID: 38926709 PMCID: PMC11209984 DOI: 10.1186/s12915-024-01935-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii, and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. RESULTS We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex-determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplicates (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19-27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been likely lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome 18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variations (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex-determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in the testis than in the ovary. CONCLUSIONS Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.
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Affiliation(s)
- Heiner Kuhl
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587, Berlin, Germany.
| | - Peter T Euclide
- Department of Forestry and Natural Resources | Illinois-Indiana Sea Grant, Purdue University, West Lafayette, USA
| | - Christophe Klopp
- Sigenae, Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Cédric Cabau
- Sigenae, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Margot Zahm
- Sigenae, Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | | | | | - Claire Kuchly
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | | | - Romain Feron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Hugues Parrinello
- Montpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, 34094, Montpellier Cedex 05, France
| | - Charles Poncet
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Lydia Jaffrelo
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Carole Confolent
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ming Wen
- INRAE, LPGP, 35000, Rennes, France
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | | | | | - Anastasia Bestin
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Pierrick Haffray
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes Cedex, France
| | - Romain Morvezen
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes Cedex, France
| | | | | | | | | | - Daniel Żarski
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, ul. Tuwima 10, 10-748, Olsztyn, Poland
| | - Wesley A Larson
- National Oceanographic and Atmospheric Administration, National Marine Fisheries Service, Alaska Fisheries Science Center, 17109 Point Lena Loop Road, Auke Bay LaboratoriesJuneau, AK, 99801, USA
| | | | | | - Werner Kloas
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587, Berlin, Germany
| | - Sven Wuertz
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587, Berlin, Germany
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587, Berlin, Germany
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Kitano J, Ansai S, Takehana Y, Yamamoto Y. Diversity and Convergence of Sex-Determination Mechanisms in Teleost Fish. Annu Rev Anim Biosci 2024; 12:233-259. [PMID: 37863090 DOI: 10.1146/annurev-animal-021122-113935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
Sexual reproduction is prevalent across diverse taxa. However, sex-determination mechanisms are so diverse that even closely related species often differ in sex-determination systems. Teleost fish is a taxonomic group with frequent turnovers of sex-determining mechanisms and thus provides us with great opportunities to investigate the molecular and evolutionary mechanisms underlying the turnover of sex-determining systems. Here, we compile recent studies on the diversity of sex-determination mechanisms in fish. We demonstrate that genes in the TGF-β signaling pathway are frequently used for master sex-determining (MSD) genes. MSD genes arise via two main mechanisms, duplication-and-transposition and allelic mutations, with a few exceptions. We also demonstrate that temperature influences sex determination in many fish species, even those with sex chromosomes, with higher temperatures inducing differentiation into males in most cases. Finally, we review theoretical models for the turnover of sex-determining mechanisms and discuss what questions remain elusive.
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Affiliation(s)
- Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan;
| | - Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan;
| | - Yusuke Takehana
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan;
| | - Yoji Yamamoto
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan;
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Shi R, Li X, Xu X, Chen Z, Zhu Y, Wang N. Genome-wide analysis of BMP/GDF family and DAP-seq of YY1 suggest their roles in Cynoglossus semilaevis sexual size dimorphism. Int J Biol Macromol 2023; 253:127201. [PMID: 37793513 DOI: 10.1016/j.ijbiomac.2023.127201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/28/2023] [Accepted: 09/30/2023] [Indexed: 10/06/2023]
Abstract
Sexual size dimorphism (SSD) characterized by different body size between females and males have been reported in various animals. Gonadectomy experiments have implied important regulatory roles of the gonad in SSD. Among multiple factors from the gonad, TGF-β superfamily (especially BMP/GDF family) attracted our interest due to its pleiotropy in growth and reproduction regulations. Thus, whether BMP/GDF family members serve as crucial regulators for SSD was studied in a typically female-biased SSD flatfish named Chinese tongue sole (Cynoglossus semilaevis). Firstly, a total of 26 BMP/GDF family members were identified. The PPI network analysis showed that they may interact with ACVR2a, ACVR2b, ACVR1, BMPR2, SMAD3, BMPR1a, and other proteins. Subsequently, DAP-seq was employed to reveal the binding sites for yin yang 1 (yy1), a transcription factor involved in gonad function and cell growth partly by regulating TGF-β superfamily. The results revealed that two yy1 homologues yy1a and yy1b in C. semilaevis could regulate Hippo signaling pathway, mTOR signaling pathway, and AMPK signaling pathway. Moreover, BMP/GDF family genes including bmp2, bmp4, bmp5, gdf6a, and gdf6b were important components of Hippo pathway. In future, the crosstalk among yy1a, yy1b, and TGF-β family would provide more insight into sexual size dimorphism in C. semilaevis.
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Affiliation(s)
- Rui Shi
- Function Laboratory for Marine Science and Food Production Process, Laoshan laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xihong Li
- Function Laboratory for Marine Science and Food Production Process, Laoshan laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xiwen Xu
- Function Laboratory for Marine Science and Food Production Process, Laoshan laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Zhangfan Chen
- Function Laboratory for Marine Science and Food Production Process, Laoshan laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Ying Zhu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China.
| | - Na Wang
- Function Laboratory for Marine Science and Food Production Process, Laoshan laboratory, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China.
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4
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Kuhl H, Euclide PT, Klopp C, Cabau C, Zahm M, Roques C, Iampietro C, Kuchly C, Donnadieu C, Feron R, Parrinello H, Poncet C, Jaffrelo L, Confolent C, Wen M, Herpin A, Jouanno E, Bestin A, Haffray P, Morvezen R, de Almeida TR, Lecocq T, Schaerlinger B, Chardard D, Żarski D, Larson W, Postlethwait JH, Timirkhanov S, Kloas W, Wuertz S, Stöck M, Guiguen Y. Multi-genome comparisons reveal gain-and-loss evolution of the anti-Mullerian hormone receptor type 2 gene, an old master sex determining gene, in Percidae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566804. [PMID: 38014084 PMCID: PMC10680665 DOI: 10.1101/2023.11.13.566804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplications (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19-27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome-18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variants (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in testis than ovary. Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.
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Affiliation(s)
- Heiner Kuhl
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries – IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587 Berlin, Germany
| | - Peter T Euclide
- Department of Forestry and Natural Resources | Illinois-Indiana Sea Grant, Purdue University, West Lafayette, Indiana, USA
| | - Christophe Klopp
- Sigenae, Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Cedric Cabau
- Sigenae, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Margot Zahm
- Sigenae, Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Céline Roques
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | | | - Claire Kuchly
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | | | - Romain Feron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Hugues Parrinello
- Montpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, 34094, Montpellier Cedex 05, France
| | - Charles Poncet
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Lydia Jaffrelo
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Carole Confolent
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ming Wen
- INRAE, LPGP, 35000, Rennes, France
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | | | | | - Anastasia Bestin
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes cedex, France
| | - Pierrick Haffray
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes cedex, France
| | - Romain Morvezen
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes cedex, France
| | | | - Thomas Lecocq
- University of Lorraine, INRAE, UR AFPA, Nancy, France
| | | | | | - Daniel Żarski
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, ul. Tuwima 10, 10-748, Olsztyn, Poland
| | - Wes Larson
- National Oceanographic and Atmospheric Administration, National Marine Fisheries Service, Alaska Fisheries Science Center, Auke Bay Laboratories, 17109 Point Lena Loop Road, Juneau, AK, 99801, USA
| | | | | | - Werner Kloas
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries – IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587 Berlin, Germany
| | - Sven Wuertz
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries – IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587 Berlin, Germany
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries – IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587 Berlin, Germany
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Master-Key Regulators of Sex Determination in Fish and Other Vertebrates-A Review. Int J Mol Sci 2023; 24:ijms24032468. [PMID: 36768795 PMCID: PMC9917144 DOI: 10.3390/ijms24032468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/12/2023] [Accepted: 01/25/2023] [Indexed: 02/01/2023] Open
Abstract
In vertebrates, mainly single genes with an allele ratio of 1:1 trigger sex-determination (SD), leading to initial equal sex-ratios. Such genes are designated master-key regulators (MKRs) and are frequently associated with DNA structural variations, such as copy-number variation and null-alleles. Most MKR knowledge comes from fish, especially cichlids, which serve as a genetic model for SD. We list 14 MKRs, of which dmrt1 has been identified in taxonomically distant species such as birds and fish. The identification of MKRs with known involvement in SD, such as amh and fshr, indicates that a common network drives SD. We illustrate a network that affects estrogen/androgen equilibrium, suggesting that structural variation may exert over-expression of the gene and thus form an MKR. However, the reason why certain factors constitute MKRs, whereas others do not is unclear. The limited number of conserved MKRs suggests that their heterologous sequences could be used as targets in future searches for MKRs of additional species. Sex-specific mortality, sex reversal, the role of temperature in SD, and multigenic SD are examined, claiming that these phenomena are often consequences of artificial hybridization. We discuss the essentiality of taxonomic authentication of species to validate purebred origin before MKR searches.
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6
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Jeffries DL, Mee JA, Peichel CL. Identification of a candidate sex determination gene in Culaea inconstans suggests convergent recruitment of an Amh duplicate in two lineages of stickleback. J Evol Biol 2022; 35:1683-1695. [PMID: 35816592 PMCID: PMC10083969 DOI: 10.1111/jeb.14034] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/07/2022] [Accepted: 05/19/2022] [Indexed: 11/29/2022]
Abstract
Sex chromosomes vary greatly in their age and levels of differentiation across the tree of life. This variation is largely due to the rates of sex chromosome turnover in different lineages; however, we still lack an explanation for why sex chromosomes are so conserved in some lineages (e.g. mammals, birds) but so labile in others (e.g. teleosts, amphibians). To identify general mechanisms driving transitions in sex determination systems or forces which favour their conservation, we first require empirical data on sex chromosome systems from multiple lineages. Stickleback fishes are a valuable model lineage for the study of sex chromosome evolution due to variation in sex chromosome systems between closely-related species. Here, we identify the sex chromosome and a strong candidate for the master sex determination gene in the brook stickleback, Culaea inconstans. Using whole-genome sequencing of wild-caught samples and a lab cross, we identify AmhY, a male specific duplication of the gene Amh, as the candidate master sex determination gene. AmhY resides on Chromosome 20 in C. inconstans and is likely a recent duplication, as both AmhY and the sex-linked region of Chromosome 20 show little sequence divergence. Importantly, this duplicate AmhY represents the second independent duplication and recruitment of Amh as the sex determination gene in stickleback and the eighth example known across teleosts. We discuss this convergence in the context of sex chromosome turnovers and the role that the Amh/AmhrII pathway, which is crucial for sex determination, may play in the evolution of sex chromosomes in teleosts.
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Affiliation(s)
- Daniel L Jeffries
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Jonathan A Mee
- Department of Biology, Mount Royal University, Calgary, Alberta, Canada
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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7
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Liu X, Dai S, Wu J, Wei X, Zhou X, Chen M, Tan D, Pu D, Li M, Wang D. Roles of anti-Müllerian hormone and its duplicates in sex determination and germ cell proliferation of Nile tilapia. Genetics 2021; 220:6486528. [PMID: 35100374 PMCID: PMC9208641 DOI: 10.1093/genetics/iyab237] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/17/2021] [Indexed: 12/30/2022] Open
Abstract
Duplicates of amh are crucial for fish sex determination and differentiation. In Nile tilapia, unlike in other teleosts, amh is located on X chromosome. The Y chromosome amh (amhΔ-y) is mutated with 5 bp insertion and 233 bp deletion in the coding sequence, and tandem duplicate of amh on Y chromosome (amhy) has been identified as the sex determiner. However, the expression of amh, amhΔ-y, and amhy, their roles in germ cell proliferation and the molecular mechanism of how amhy determines sex is still unclear. In this study, expression and functions of each duplicate were analyzed. Sex reversal occurred only when amhy was mutated as revealed by single, double, and triple mutation of the 3 duplicates in XY fish. Homozygous mutation of amhy in YY fish also resulted in sex reversal. Earlier and higher expression of amhy/Amhy was observed in XY gonads compared with amh/Amh during sex determination. Amhy could inhibit the transcription of cyp19a1a through Amhr2/Smads signaling. Loss of cyp19a1a rescued the sex reversal phenotype in XY fish with amhy mutation. Interestingly, mutation of both amh and amhy in XY fish or homozygous mutation of amhy in YY fish resulted in infertile females with significantly increased germ cell proliferation. Taken together, these results indicated that up-regulation of amhy during the critical period of sex determination makes it the sex-determining gene, and it functions through repressing cyp19a1a expression via Amhr2/Smads signaling pathway. Amh retained its function in controlling germ cell proliferation as reported in other teleosts, while amhΔ-y was nonfunctionalized.
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Affiliation(s)
- Xingyong Liu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Shengfei Dai
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jiahong Wu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xueyan Wei
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xin Zhou
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Mimi Chen
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Dejie Tan
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Deyong Pu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Minghui Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China,Corresponding author: Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China. ; Corresponding author: Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China,Corresponding author: Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China. ; Corresponding author: Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
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Holborn MK, Einfeldt AL, Kess T, Duffy SJ, Messmer AM, Langille BL, Gauthier J, Bentzen P, Knutsen TM, Kent M, Boyce D, Bradbury IR. Reference genome of Lumpfish Cyclopterus lumpus Linnaeus provides evidence of male heterogametic sex determination through the AMH pathway. Mol Ecol Resour 2021; 22:1427-1439. [PMID: 34859595 DOI: 10.1111/1755-0998.13565] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 11/15/2021] [Accepted: 11/23/2021] [Indexed: 11/30/2022]
Abstract
Teleosts exhibit extensive diversity of sex determination (SD) systems and mechanisms, providing the opportunity to study the evolution of sex determination and sex chromosomes. Here we sequenced the genome of the Common Lumpfish (Cyclopterus lumpus Linnaeus), a species of increasing importance to aquaculture, and identified the SD region and master SD locus using a 70K SNP array and tissue-specific expression data. The chromosome-level assembly identified 25 diploid chromosomes with a total size of 572.89 Mb, a scaffold N50 of 23.86 Mb, and genome annotation predicted 21,480 protein-coding genes. Genome wide association analysis located a highly sex-associated region on chromosome 13, suggesting that anti-Müllerian hormone (AMH) is the putative SD factor. Linkage disequilibrium and heterozygosity across chromosome 13 support a proto-XX/XY system, with an absence of widespread chromosome divergence between sexes. We identified three copies of AMH in the Lumpfish primary and alternate haplotype assemblies localized in the SD region. Comparison to sequences from other teleosts suggested a monophyletic relationship and conservation within the Cottioidei. One AMH copy showed similarity to AMH/AMHY in a related species and was also the only copy with expression in testis tissue, suggesting this copy may be the functional copy of AMH in Lumpfish. The two other copies arranged in tandem inverted duplication were highly similar, suggesting a recent duplication event. This study provides a resource for the study of early sex chromosome evolution and novel genomic resources that benefits Lumpfish conservation management and aquaculture.
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Affiliation(s)
- Melissa K Holborn
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, NL, A1C 5X1, Canada
| | - Anthony L Einfeldt
- Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Tony Kess
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, NL, A1C 5X1, Canada
| | - Steve J Duffy
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, NL, A1C 5X1, Canada
| | - Amber M Messmer
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, NL, A1C 5X1, Canada
| | - Barbara L Langille
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, NL, A1C 5X1, Canada
| | - Johanne Gauthier
- Maurice Lamontagne Institute, Fisheries and Oceans Canada, Mont-Joli, QC, G5H 3Z4, Canada
| | - Paul Bentzen
- Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | | | - Matthew Kent
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Danny Boyce
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Ian R Bradbury
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, NL, A1C 5X1, Canada
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9
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Ferchaud AL, Mérot C, Normandeau E, Ragoussis J, Babin C, Djambazian H, Bérubé P, Audet C, Treble M, Walkusz W, Bernatchez L. Chromosome-level assembly reveals a putative Y-autosomal fusion in the sex determination system of the Greenland Halibut (Reinhardtius hippoglossoides). G3-GENES GENOMES GENETICS 2021; 12:6428537. [PMID: 34791178 DOI: 10.1093/g3journal/jkab376] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 10/21/2021] [Indexed: 11/13/2022]
Abstract
Despite the commercial importance of Greenland Halibut (Reinhardtius hippoglossoides), important gaps still persist in our knowledge of this species, including its reproductive biology and sex determination mechanism. Here, we combined single-molecule sequencing of long reads (Pacific Sciences) with chromatin conformation capture sequencing (Hi-C) data to assemble the first chromosome-level reference genome for this species. The high-quality assembly encompassed more than 598 Megabases (Mb) assigned to 1 594 scaffolds (scaffold N50 = 25 Mb) with 96% of its total length distributed among 24 chromosomes. Investigation of the syntenic relationship with other economically important flatfish species revealed a high conservation of synteny blocks among members of this phylogenetic clade. Sex determination analysis revealed that, similar to other teleost fishes, flatfishes also exhibit a high level of plasticity and turnover in sex-determination mechanisms. A low-coverage whole-genome sequence analysis of 198 individuals revealed that Greenland Halibut possesses a male heterogametic XY system and several putative candidate genes implied in the sex determination of this species. Our study also suggests for the first time in flatfishes that a putative Y-autosomal fusion could be associated with a reduction of recombination typical of the early steps of sex chromosome evolution.
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Affiliation(s)
- Anne-Laure Ferchaud
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
| | - Claire Mérot
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
| | - Jiannis Ragoussis
- McGill Genome Centre and Department for Human Genetics, McGill University, Montreal, Quebec, H3A 0G1, Canada
| | - Charles Babin
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
| | - Haig Djambazian
- McGill Genome Centre and Department for Human Genetics, McGill University, Montreal, Quebec, H3A 0G1, Canada
| | - Pierre Bérubé
- McGill Genome Centre and Department for Human Genetics, McGill University, Montreal, Quebec, H3A 0G1, Canada
| | - Céline Audet
- Institut des sciences de la mer de Rimouski, Université du Québec à Rimouski, 310 allée des Ursulines, Rimouski, QC G5L 3A1, Canada
| | - Margaret Treble
- Fisheries and Oceans Canada, Winnipeg Department, Arctic Aquatic Research Division, Freshwater Institute Winnipeg, Manitoba, R3T2N6, Canada
| | - Wocjciech Walkusz
- Fisheries and Oceans Canada, Winnipeg Department, Arctic Aquatic Research Division, Freshwater Institute Winnipeg, Manitoba, R3T2N6, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
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10
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Pan Q, Kay T, Depincé A, Adolfi M, Schartl M, Guiguen Y, Herpin A. Evolution of master sex determiners: TGF-β signalling pathways at regulatory crossroads. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200091. [PMID: 34247498 DOI: 10.1098/rstb.2020.0091] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
To date, more than 20 different vertebrate master sex-determining genes have been identified on different sex chromosomes of mammals, birds, frogs and fish. Interestingly, six of these genes are transcription factors (Dmrt1- or Sox3- related) and 13 others belong to the TGF-β signalling pathway (Amh, Amhr2, Bmpr1b, Gsdf and Gdf6). This pattern suggests that only a limited group of factors/signalling pathways are prone to become top regulators again and again. Although being clearly a subordinate member of the sex-regulatory network in mammals, the TGF-β signalling pathway made it to the top recurrently and independently. Facing this rolling wave of TGF-β signalling pathways, this review will decipher how the TGF-β signalling pathways cope with the canonical sex gene regulatory network and challenge the current evolutionary concepts accounting for the diversity of sex-determining mechanisms. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.
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Affiliation(s)
- Qiaowei Pan
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Tomas Kay
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | | | - Mateus Adolfi
- University of Würzburg, Developmental Biochemistry, Biocenter, 97074 Würzburg, Germany
| | - Manfred Schartl
- University of Würzburg, Developmental Biochemistry, Biocenter, 97074 Würzburg, Germany.,Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX 78666, USA
| | - Yann Guiguen
- INRAE, UR 1037 Fish Physiology and Genomics, 35000 Rennes, France
| | - Amaury Herpin
- INRAE, UR 1037 Fish Physiology and Genomics, 35000 Rennes, France.,State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081 Hunan, People's Republic of China
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11
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Curzon AY, Dor L, Shirak A, Meiri-Ashkenazi I, Rosenfeld H, Ron M, Seroussi E. A novel c.1759T>G variant in follicle-stimulating hormone-receptor gene is concordant with male determination in the flathead grey mullet (Mugil cephalus). G3-GENES GENOMES GENETICS 2021; 11:6046932. [PMID: 33589926 PMCID: PMC8022982 DOI: 10.1093/g3journal/jkaa044] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 12/08/2020] [Indexed: 12/31/2022]
Abstract
Various master key regulators (MKRs) that control a binary switch of sex determination (SD) have been found in fish; these provide an excellent model for the study of vertebrate genetic SD. The SD region in flathead grey mullet has been previously mapped to a 1 Mbp region harboring 27 genes, of which one is follicle-stimulating hormone receptor (fshr). Although this gene is involved in gonad differentiation and function, it has not been considered as an MKR of SD. We systematically investigated polymorphism in mullet fshr using DNA shotgun sequences, and compared them between males and females. Capable of encoding nonconservative amino acid substitutions, c.1732G>A and c.1759T>G exhibited association with sex on a population level (N = 83; P ≤ 6.7 × 10-19). Hence, 1732 A and 1759 G represent a male-specific haplotype of the gene, designated as "fshry." Additional flanking SNPs showed a weaker degree of association with sex, delimiting the SD critical region to 143 nucleotides on exon 14. Lack of homozygotes for fshry, and the resulting divergence from Hardy-Weinberg equilibrium (N = 170; P ≤ 3.9 × 10-5), were compatible with a male heterogametic model (XY/XX). Capable of replacing a phenylalanine with valine, c.1759T>G alters a conserved position across the sixth transmembrane domain of vertebrate FSHRs. Amino acid substitutions in this position in vertebrates are frequently associated with constant receptor activation and consequently with FSH/FSHR signaling alteration; thus, indicating a potential role of fshr as an MKR of SD.
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Affiliation(s)
- Arie Y Curzon
- Agricultural Research Organization, Institute of Animal Science, Rishon LeTsiyon, 7528809, Israel.,Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Lior Dor
- Agricultural Research Organization, Institute of Animal Science, Rishon LeTsiyon, 7528809, Israel.,Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Andrey Shirak
- Agricultural Research Organization, Institute of Animal Science, Rishon LeTsiyon, 7528809, Israel
| | - Iris Meiri-Ashkenazi
- National Center for Mariculture, Israel Oceanographic and Limnological Research, Eilat 88112, Israel
| | - Hana Rosenfeld
- National Center for Mariculture, Israel Oceanographic and Limnological Research, Eilat 88112, Israel
| | - Micha Ron
- Agricultural Research Organization, Institute of Animal Science, Rishon LeTsiyon, 7528809, Israel
| | - Eyal Seroussi
- Agricultural Research Organization, Institute of Animal Science, Rishon LeTsiyon, 7528809, Israel
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12
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Curzon AY, Shirak A, Benet-Perlberg A, Naor A, Low-Tanne SI, Sharkawi H, Ron M, Seroussi E. Gene Variant of Barrier to Autointegration Factor 2 ( Banf2w) Is Concordant with Female Determination in Cichlids. Int J Mol Sci 2021; 22:7073. [PMID: 34209244 PMCID: PMC8268354 DOI: 10.3390/ijms22137073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/23/2021] [Accepted: 06/27/2021] [Indexed: 11/15/2022] Open
Abstract
Oreochromis fishes exhibit variability of sex-determination (SD) genes whose characterization contributes to understanding of the sex differentiation network, and to effective tilapia farming, which requires all-male culture. However, O. niloticus (On) amh is the only master-key regulator (MKR) of SD that has been mapped (XY/XX SD-system on LG23). In O. aureus (Oa), LG3 controls a WZ/ZZ SD-system that has recently been delimited to 9.2 Mbp, with an embedded interval rich with female-specific variation, harboring two paics genes and banf2. Developing genetic markers within this interval and using a hybrid Oa stock that demonstrates no recombination repression in LG3, we mapped the critical SD region to 235 Kbp on the orthologous On physical map (p < 1.5 × 10-26). DNA-seq assembly and peak-proportion analysis of variation based on Sanger chromatograms allowed the characterization of copy-number variation (CNV) of banf2. Oa males had three exons capable of encoding 90-amino-acid polypeptides, yet in Oa females, we found an extra copy with an 89-amino-acid polypeptide and three non-conservative amino acid substitutions, designated as banf2w. CNV analysis suggested the existence of two to five copies of banf2 in diploidic Cichlidae. Disrupting the Hardy-Weinberg equilibrium (p < 4.2 × 10-3), banf2w was concordant with female determination in Oa and in three cichlids with LG3 WZ/ZZ SD-systems (O. tanganicae, O. hornorum and Pelmatolapia mariae). Furthermore, exclusive RNA-seq expression in Oa females strengthened the candidacy of banf2w as the long-sought LG3 SD MKR. As banf genes mediate nuclear assembly, chromatin organization, gene expression and gonad development, banf2w may play a fundamental role inducing female nucleus formation that is essential for WZ/ZZ SD.
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Affiliation(s)
- Arie Yehuda Curzon
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 7528809, Israel; (A.Y.C.); (A.S.); (M.R.)
- Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Andrey Shirak
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 7528809, Israel; (A.Y.C.); (A.S.); (M.R.)
| | - Ayana Benet-Perlberg
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Alon Naor
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Shai Israel Low-Tanne
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Haled Sharkawi
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Micha Ron
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 7528809, Israel; (A.Y.C.); (A.S.); (M.R.)
| | - Eyal Seroussi
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 7528809, Israel; (A.Y.C.); (A.S.); (M.R.)
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13
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Tao W, Conte MA, Wang D, Kocher TD. Network architecture and sex chromosome turnovers: Do epistatic interactions shape patterns of sex chromosome replacement? Bioessays 2020; 43:e2000161. [PMID: 33283342 DOI: 10.1002/bies.202000161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 11/11/2022]
Abstract
Recent studies have revealed an astonishing diversity of sex chromosomes in many vertebrate lineages, prompting questions about the mechanisms of sex chromosome turnover. While there is considerable population genetic theory about the evolutionary forces promoting sex chromosome replacement, this theory has not yet been integrated with our understanding of the molecular and developmental genetics of sex determination. Here, we review recent data to examine four questions about how the structure of gene networks influences the evolution of sex determination. We argue that patterns of epistasis, arising from the structure of genetic networks, may play an important role in regulating the rates and patterns of sex chromosome replacement.
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Affiliation(s)
- Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Matthew A Conte
- Department of Biology, University of Maryland, College Park, Maryland, USA
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, Maryland, USA
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14
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Longo GC, Lam L, Basnett B, Samhouri J, Hamilton S, Andrews K, Williams G, Goetz G, McClure M, Nichols KM. Strong population differentiation in lingcod ( Ophiodon elongatus) is driven by a small portion of the genome. Evol Appl 2020; 13:2536-2554. [PMID: 33294007 PMCID: PMC7691466 DOI: 10.1111/eva.13037] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 05/19/2020] [Accepted: 05/26/2020] [Indexed: 12/15/2022] Open
Abstract
Delimiting intraspecific genetic variation in harvested species is crucial to the assessment of population status for natural resource management and conservation purposes. Here, we evaluated genetic population structure in lingcod (Ophiodon elongatus), a commercially and recreationally important fishery species along the west coast of North America. We used 16,749 restriction site-associated DNA sequencing (RADseq) markers, in 611 individuals collected from across the bulk of the species range from Southeast Alaska to Baja California, Mexico. In contrast to previous population genetic work on this species, we found strong evidence for two distinct genetic clusters. These groups separated latitudinally with a break near Point Reyes off Northern California, and there was a high frequency of admixed individuals in close proximity to the break. F-statistics corroborate this genetic break between northern and southern sampling sites, although most loci are characterized by low FST values, suggesting high gene flow throughout most of the genome. Outlier analyses identified 182 loci putatively under divergent selection, most of which mapped to a single genomic region. When individuals were grouped by cluster assignment (northern, southern, and admixed), 71 loci were fixed between the northern and southern cluster, all of which were identified in the outlier scans. All individuals identified as admixed exhibited near 50:50 assignment to northern and southern clusters and were heterozygous for most fixed loci. Alignments of RADseq loci to a draft lingcod genome assembly and three other teleost genomes with chromosome-level assemblies suggest that outlier and fixed loci are concentrated on a single chromosome. Similar genomic patterns have been attributed to chromosomal inversions in diverse taxonomic groups. Regardless of the evolutionary mechanism, these results represent novel observations of genetic structure in lingcod and designate clear evolutionary units that could be used to inform fisheries management.
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Affiliation(s)
- Gary C. Longo
- NRC Research Associateship ProgramNorthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
| | - Laurel Lam
- Pacific States Marine Fisheries CommissionUnder contract to Northwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
- Moss Landing Marine LaboratoriesMoss LandingCAUSA
| | | | - Jameal Samhouri
- Conservation Biology DivisionNorthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
| | | | - Kelly Andrews
- Conservation Biology DivisionNorthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
| | - Greg Williams
- Pacific States Marine Fisheries CommissionUnder contract to Northwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
| | - Giles Goetz
- UWJISAOUnder contract to Northwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
| | - Michelle McClure
- Fisheries Resource Analysis and Monitoring DivisionNorthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
- Pacific Marine Environmental LaboratoryNational Oceanic and Atmospheric AdministrationSeattleWAUSA
| | - Krista M. Nichols
- Conservation Biology DivisionNorthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleWAUSA
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15
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Curzon AY, Shirak A, Dor L, Zak T, Perelberg A, Seroussi E, Ron M. A duplication of the Anti-Müllerian hormone gene is associated with genetic sex determination of different Oreochromis niloticus strains. Heredity (Edinb) 2020; 125:317-327. [PMID: 32647338 PMCID: PMC7555829 DOI: 10.1038/s41437-020-0340-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 06/25/2020] [Indexed: 11/08/2022] Open
Abstract
Sex determination (SD) mechanisms are ancient and conserved, yet much diversity is exhibited in primary sex-determining signals that trigger male or female development. In O. niloticus, SD is associated with a male-specific locus on linkage group (LG) 23 which harbors the Y-linked Anti-Müllerian hormone (amh) gene, and a truncated duplication, denoted amhΔy. We have evaluated the possible role of identified indels and SNPs in the amh gene on SD, based on conservation in different O. niloticus strains. A fluorescent assay for the detection of a 5 bp insertion in amhΔy exon VI, efficiently discriminated between XX, XY, and YY genotypes. Concordance rate between amhΔy and sex varied in six Oreochromis strains, from 100% (Ghana) through 90% (Swansea) to 85% (Thai-Chitralada). The association of amhΔy with sex was found to be conserved in all tested O. niloticus strains, and thus supports its key role in SD. However, the previously identified missense SNP (C/T) in amh exon II was found only in the Swansea strain, thus excluding its candidacy for the causal variation of SD across all strains. Effects of markers on LGs 1, 3, and 23 (amhΔy) fully explained sex distribution in one Thai-Chitralada family (R2 = 1.0), whereas in another family only the major effect of LG23 (amhΔy) was significant (R2 = 0.37). Thus, amhΔy on LG23 is associated with genetic SD, either as a single causal gene in different O. niloticus strains, or in combination with segregating genes on LGs 1 and 3 in the Thai-Chitralada hybrid strain.
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Affiliation(s)
- A Y Curzon
- Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, 76100, Rehovot, Israel
- Institute of Animal Science, Agricultural Research Organization, 50250, Bet Dagan, Israel
| | - A Shirak
- Institute of Animal Science, Agricultural Research Organization, 50250, Bet Dagan, Israel
| | - L Dor
- Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, 76100, Rehovot, Israel
- Institute of Animal Science, Agricultural Research Organization, 50250, Bet Dagan, Israel
| | - T Zak
- Dor Research Station, Fisheries and Aquaculture Department, Ministry of Agriculture and Rural Development, Bet Dagan, Israel
| | - A Perelberg
- Dor Research Station, Fisheries and Aquaculture Department, Ministry of Agriculture and Rural Development, Bet Dagan, Israel
| | - E Seroussi
- Institute of Animal Science, Agricultural Research Organization, 50250, Bet Dagan, Israel
| | - M Ron
- Institute of Animal Science, Agricultural Research Organization, 50250, Bet Dagan, Israel.
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16
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Wen M, Feron R, Pan Q, Guguin J, Jouanno E, Herpin A, Klopp C, Cabau C, Zahm M, Parrinello H, Journot L, Burgess SM, Omori Y, Postlethwait JH, Schartl M, Guiguen Y. Sex chromosome and sex locus characterization in goldfish, Carassius auratus (Linnaeus, 1758). BMC Genomics 2020; 21:552. [PMID: 32781981 PMCID: PMC7430817 DOI: 10.1186/s12864-020-06959-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 07/29/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Goldfish is an important model for various areas of research, including neural development and behavior and a species of significant importance in aquaculture, especially as an ornamental species. It has a male heterogametic (XX/XY) sex determination system that relies on both genetic and environmental factors, with high temperatures being able to produce female-to-male sex reversal. Little, however, is currently known on the molecular basis of genetic sex determination in this important cyprinid model. Here we used sequencing approaches to better characterize sex determination and sex-chromosomes in an experimental strain of goldfish. RESULTS Our results confirmed that sex determination in goldfish is a mix of environmental and genetic factors and that its sex determination system is male heterogametic (XX/XY). Using reduced representation (RAD-seq) and whole genome (pool-seq) approaches, we characterized sex-linked polymorphisms and developed male specific genetic markers. These male specific markers were used to distinguish sex-reversed XX neomales from XY males and to demonstrate that XX female-to-male sex reversal could even occur at a relatively low rearing temperature (18 °C), for which sex reversal has been previously shown to be close to zero. We also characterized a relatively large non-recombining region (~ 11.7 Mb) on goldfish linkage group 22 (LG22) that contained a high-density of male-biased genetic polymorphisms. This large LG22 region harbors 373 genes, including a single candidate as a potential master sex gene, i.e., the anti-Mullerian hormone gene (amh). However, no sex-linked polymorphisms were detected in the coding DNA sequence of the goldfish amh gene. CONCLUSIONS These results show that our goldfish strain has a relatively large sex locus on LG22, which is likely the Y chromosome of this experimental population. The presence of a few XX males even at low temperature also suggests that other environmental factors in addition to temperature could trigger female-to-male sex reversal. Finally, we also developed sex-linked genetic markers, which will be important tools for future research on sex determination in our experimental goldfish population. However, additional work would be needed to explore whether this sex locus is conserved in other populations of goldfish.
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Affiliation(s)
- Ming Wen
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
- INRAE, LPGP, 35000, Rennes, France
| | - Romain Feron
- INRAE, LPGP, 35000, Rennes, France
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Qiaowei Pan
- INRAE, LPGP, 35000, Rennes, France
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | | | | | | | - Christophe Klopp
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRAE, Castanet Tolosan, France
- SIGENAE, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Cedric Cabau
- SIGENAE, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Margot Zahm
- SIGENAE, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Hugues Parrinello
- Montpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, 34094, Montpellier Cedex 05, France
| | - Laurent Journot
- Montpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, 34094, Montpellier Cedex 05, France
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Yoshihiro Omori
- Laboratory of Functional Genomics, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, Japan
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | | | - Manfred Schartl
- Developmental Biochemistry, Biozentrum, University of Würzburg, Würzburg, Germany
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
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17
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Dor L, Shirak A, Kohn YY, Gur T, Weller JI, Zilberg D, Seroussi E, Ron M. Mapping of the Sex Determining Region on Linkage Group 12 of Guppy ( Poecilia reticulata). G3 (BETHESDA, MD.) 2019; 9:3867-3875. [PMID: 31551287 PMCID: PMC6829149 DOI: 10.1534/g3.119.400656] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 09/19/2019] [Indexed: 11/18/2022]
Abstract
Poecilia reticulata is one of the most popular ornamental fish species with a higher demand for males due to their large colorful fins. The objectives of this study were mapping of the sex-determining (SD) region on linkage group 12 of guppy, and identification of a sex specific marker. We generated eight polymorphic microsatellite markers distributed along the distal 5.4 Mbp sequence of the previously identified SD region on linkage group (LG) 12. The markers were tested for association with sex in 156 individuals of the Red Blonde and Flame strains, and 126 progeny of four full-sibs Red Blonde families. A male-specific allele was found for microsatellite gu1066 at position of 25.3 Mbp on LG12 for both strains, and gu832 at position 24.4 Mbp for the Flame strain. Thus, a region of 0.9 Mbp between these markers, harboring 27 annotated genes, was selected for analysis. Based on association of copy number variation and sex determination we mapped a duplicated region between LGs 9 and 12, of 1.26 Mbp, containing 59 genes on LG12. The common interval between the segment bounded by gu1066 and gu832, and the duplicated region of 0.43 Mbp on LG12 harbors 11 genes of which 6 have multiple copies (54%). Growth arrest and DNA damage inducible gamma-like (GADD45G-like) is a plausible positional and functional candidate gene for its role in male fertility. We characterized the genomic structure of the gene in guppy, and found two isoforms; but no sex-biased differences were evident in genomic sequence and gene expression.
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Affiliation(s)
- Lior Dor
- Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 76100, Israel
- Agricultural Research Organization (ARO), Volcani Center, Institute of Animal Science, HaMaccabim Road, P.O.B 15159, 7528809, Rishon LeTsiyon, Israel
| | - Andrey Shirak
- Agricultural Research Organization (ARO), Volcani Center, Institute of Animal Science, HaMaccabim Road, P.O.B 15159, 7528809, Rishon LeTsiyon, Israel
| | - Yair Yaacov Kohn
- Central and Northern Arava Research and Development D.N. Arava Sapir, 86825 Israel, and
| | - Tal Gur
- Central and Northern Arava Research and Development D.N. Arava Sapir, 86825 Israel, and
| | - Joel Ira Weller
- Agricultural Research Organization (ARO), Volcani Center, Institute of Animal Science, HaMaccabim Road, P.O.B 15159, 7528809, Rishon LeTsiyon, Israel
| | - Dina Zilberg
- The French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Eyal Seroussi
- Agricultural Research Organization (ARO), Volcani Center, Institute of Animal Science, HaMaccabim Road, P.O.B 15159, 7528809, Rishon LeTsiyon, Israel
| | - Micha Ron
- Agricultural Research Organization (ARO), Volcani Center, Institute of Animal Science, HaMaccabim Road, P.O.B 15159, 7528809, Rishon LeTsiyon, Israel,
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Yan YL, Batzel P, Titus T, Sydes J, Desvignes T, BreMiller R, Draper B, Postlethwait JH. A Hormone That Lost Its Receptor: Anti-Müllerian Hormone (AMH) in Zebrafish Gonad Development and Sex Determination. Genetics 2019; 213:529-553. [PMID: 31399485 PMCID: PMC6781894 DOI: 10.1534/genetics.119.302365] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/04/2019] [Indexed: 12/26/2022] Open
Abstract
Fetal mammalian testes secrete Anti-Müllerian hormone (Amh), which inhibits female reproductive tract (Müllerian duct) development. Amh also derives from mature mammalian ovarian follicles, which marks oocyte reserve and characterizes polycystic ovarian syndrome. Zebrafish (Danio rerio) lacks Müllerian ducts and the Amh receptor gene amhr2 but, curiously, retains amh To discover the roles of Amh in the absence of Müllerian ducts and the ancestral receptor gene, we made amh null alleles in zebrafish. Results showed that normal amh prevents female-biased sex ratios. Adult male amh mutants had enormous testes, half of which contained immature oocytes, demonstrating that Amh regulates male germ cell accumulation and inhibits oocyte development or survival. Mutant males formed sperm ducts and some produced a few offspring. Young female mutants laid a few fertile eggs, so they also had functional sex ducts. Older amh mutants accumulated nonvitellogenic follicles in exceedingly large but sterile ovaries, showing that Amh helps control ovarian follicle maturation and proliferation. RNA-sequencing data partitioned juveniles at 21 days postfertilization (dpf) into two groups that each contained mutant and wild-type fish. Group21-1 upregulated ovary genes compared to Group21-2, which were likely developing as males. By 35 dpf, transcriptomes distinguished males from females and, within each sex, mutants from wild types. In adult mutants, ovaries greatly underexpressed granulosa and theca genes, and testes underexpressed Leydig cell genes. These results show that ancestral Amh functions included development of the gonadal soma in ovaries and testes and regulation of gamete proliferation and maturation. A major gap in our understanding is the identity of the gene encoding a zebrafish Amh receptor; we show here that the loss of amhr2 is associated with the breakpoint of a chromosome rearrangement shared among cyprinid fishes.
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Affiliation(s)
- Yi-Lin Yan
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - Tom Titus
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - Ruth BreMiller
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - Bruce Draper
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
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19
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Pan Q, Feron R, Yano A, Guyomard R, Jouanno E, Vigouroux E, Wen M, Busnel JM, Bobe J, Concordet JP, Parrinello H, Journot L, Klopp C, Lluch J, Roques C, Postlethwait J, Schartl M, Herpin A, Guiguen Y. Identification of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation. PLoS Genet 2019; 15:e1008013. [PMID: 31437150 PMCID: PMC6726246 DOI: 10.1371/journal.pgen.1008013] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 09/04/2019] [Accepted: 07/26/2019] [Indexed: 01/17/2023] Open
Abstract
Teleost fishes, thanks to their rapid evolution of sex determination mechanisms, provide remarkable opportunities to study the formation of sex chromosomes and the mechanisms driving the birth of new master sex determining (MSD) genes. However, the evolutionary interplay between the sex chromosomes and the MSD genes they harbor is rather unexplored. We characterized a male-specific duplicate of the anti-Müllerian hormone (amh) as the MSD gene in Northern Pike (Esox lucius), using genomic and expression evidence as well as by loss-of-function and gain-of-function experiments. Using RAD-Sequencing from a family panel, we identified Linkage Group (LG) 24 as the sex chromosome and positioned the sex locus in its sub-telomeric region. Furthermore, we demonstrated that this MSD originated from an ancient duplication of the autosomal amh gene, which was subsequently translocated to LG24. Using sex-specific pooled genome sequencing and a new male genome sequence assembled using Nanopore long reads, we also characterized the differentiation of the X and Y chromosomes, revealing a small male-specific insertion containing the MSD gene and a limited region with reduced recombination. Our study reveals an unexpectedly low level of differentiation between a pair of sex chromosomes harboring an old MSD gene in a wild teleost fish population, and highlights both the pivotal role of genes from the amh pathway in sex determination, as well as the importance of gene duplication as a mechanism driving the turnover of sex chromosomes in this clade. In stark contrast to mammals and birds, a high proportion of teleosts have homomorphic sex chromosomes and display a high diversity of sex determining genes. Yet, population level knowledge of both the sex chromosome and the master sex determining gene is only available for the Japanese medaka, a model species. Here we identified and provided functional proofs of an old duplicate of anti-Müllerian hormone (Amh), a member of the Tgf- β family, as the male master sex determining gene in the Northern pike, Esox lucius. We found that this duplicate, named amhby (Y-chromosome-specific anti-Müllerian hormone paralog b), was translocated to the sub-telomeric region of the new sex chromosome, and now amhby shows strong sequence divergence as well as substantial expression pattern differences from its autosomal paralog, amha. We assembled a male genome sequence using Nanopore long reads and identified a restricted region of differentiation within the sex chromosome pair in a wild population. Our results provide insight on the conserved players in sex determination pathways, the mechanisms of sex chromosome turnover, and the diversity of levels of differentiation between homomorphic sex chromosomes in teleosts.
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Affiliation(s)
- Qiaowei Pan
- INRA, UR1037 LPGP, Campus de Beaulieu, Rennes, France
- Department of Ecology and Evolution, University of Lausanne,1015, Lausanne, Switzerland
| | - Romain Feron
- INRA, UR1037 LPGP, Campus de Beaulieu, Rennes, France
- Department of Ecology and Evolution, University of Lausanne,1015, Lausanne, Switzerland
| | - Ayaka Yano
- INRA, UR1037 LPGP, Campus de Beaulieu, Rennes, France
| | - René Guyomard
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | | | | | - Ming Wen
- INRA, UR1037 LPGP, Campus de Beaulieu, Rennes, France
| | - Jean-Mickaël Busnel
- Fédération d’Ille-et-Vilaine pour la pêche et la protection du milieu aquatique (FDPPMA35), CS 26713, Rennes, France
| | - Julien Bobe
- INRA, UR1037 LPGP, Campus de Beaulieu, Rennes, France
| | - Jean-Paul Concordet
- INSERM U1154, CNRS UMR7196, MNHN, Muséum National d'Histoire Naturelle, France
| | - Hugues Parrinello
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Laurent Journot
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Christophe Klopp
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet Tolosan, France
- SIGENAE, GenPhySE, Université de Toulouse, INRA, ENVT, Castanet Tolosan, France
| | - Jérôme Lluch
- INRA, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Céline Roques
- INRA, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - John Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, United States of America
| | - Manfred Schartl
- University of Wuerzburg, Physiological Chemistry, Biocenter, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University Hospital, Würzburg, Germany
- Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, Texas, United States of America
| | - Amaury Herpin
- INRA, UR1037 LPGP, Campus de Beaulieu, Rennes, France
| | - Yann Guiguen
- INRA, UR1037 LPGP, Campus de Beaulieu, Rennes, France
- * E-mail:
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20
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Characterization of a male specific region containing a candidate sex determining gene in Atlantic cod. Sci Rep 2019; 9:116. [PMID: 30644412 PMCID: PMC6333804 DOI: 10.1038/s41598-018-36748-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/25/2018] [Indexed: 12/26/2022] Open
Abstract
The genetic mechanisms determining sex in teleost fishes are highly variable and the master sex determining gene has only been identified in few species. Here we characterize a male-specific region of 9 kb on linkage group 11 in Atlantic cod (Gadus morhua) harboring a single gene named zkY for zinc knuckle on the Y chromosome. Diagnostic PCR test of phenotypically sexed males and females confirm the sex-specific nature of the Y-sequence. We identified twelve highly similar autosomal gene copies of zkY, of which eight code for proteins containing the zinc knuckle motif. 3D modeling suggests that the amino acid changes observed in six copies might influence the putative RNA-binding specificity. Cod zkY and the autosomal proteins zk1 and zk2 possess an identical zinc knuckle structure, but only the Y-specific gene zkY was expressed at high levels in the developing larvae before the onset of sex differentiation. Collectively these data suggest zkY as a candidate master masculinization gene in Atlantic cod. PCR amplification of Y-sequences in Arctic cod (Arctogadus glacialis) and Greenland cod (Gadus macrocephalus ogac) suggests that the male-specific region emerged in codfishes more than 7.5 million years ago.
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