1
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Scott MF, Immler S. One-factor sex determination evolves without linkage between feminizing and masculinizing mutations. Proc Biol Sci 2024; 291:20240693. [PMID: 38981518 PMCID: PMC11335001 DOI: 10.1098/rspb.2024.0693] [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: 03/22/2024] [Revised: 06/11/2024] [Accepted: 06/21/2024] [Indexed: 07/11/2024] Open
Abstract
The evolution of separate sexes from cosexuality requires at least two mutations: a feminizing allele to cause female development and a masculinizing allele to cause male development. Classically, the double mutant is assumed to be sterile, which leads to two-factor sex determination where male and female sex chromosomes differ at two loci. However, several species appear to have one-factor sex determination where sexual development depends on variation at a single locus. We show that one-factor sex determination evolves when the double mutant develops as a male or a female. The feminizing allele fixes when the double mutant is male, and the masculinizing allele fixes when the double mutant is female. The other locus then gives XY or ZW sex determination based on dominance: for example, a dominant masculinizer becomes a Y chromosome. Although the resulting sex determination system differs, the conditions required for feminizers and masculinizers to spread are the same as in classical models, with the important difference that the two alleles do not need to be linked. Thus, we reveal alternative pathways for the evolution of sex determination and discuss how they can be distinguished using new data on the genetics of sex determination.
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Affiliation(s)
- Michael F. Scott
- School of Biological Sciences, University of East Anglia, Norwich Research Park, NorwichNR4 7TJ, UK
| | - Simone Immler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, NorwichNR4 7TJ, UK
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2
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Kuhl H, Tan WH, Klopp C, Kleiner W, Koyun B, Ciorpac M, Feron R, Knytl M, Kloas W, Schartl M, Winkler C, Stöck M. A candidate sex determination locus in amphibians which evolved by structural variation between X- and Y-chromosomes. Nat Commun 2024; 15:4781. [PMID: 38839766 PMCID: PMC11153619 DOI: 10.1038/s41467-024-49025-2] [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: 10/20/2023] [Accepted: 05/17/2024] [Indexed: 06/07/2024] Open
Abstract
Most vertebrates develop distinct females and males, where sex is determined by repeatedly evolved environmental or genetic triggers. Undifferentiated sex chromosomes and large genomes have caused major knowledge gaps in amphibians. Only a single master sex-determining gene, the dmrt1-paralogue (dm-w) of female-heterogametic clawed frogs (Xenopus; ZW♀/ZZ♂), is known across >8740 species of amphibians. In this study, by combining chromosome-scale female and male genomes of a non-model amphibian, the European green toad, Bufo(tes) viridis, with ddRAD- and whole genome pool-sequencing, we reveal a candidate master locus, governing a male-heterogametic system (XX♀/XY♂). Targeted sequencing across multiple taxa uncovered structural X/Y-variation in the 5'-regulatory region of the gene bod1l, where a Y-specific non-coding RNA (ncRNA-Y), only expressed in males, suggests that this locus initiates sex-specific differentiation. Developmental transcriptomes and RNA in-situ hybridization show timely and spatially relevant sex-specific ncRNA-Y and bod1l-gene expression in primordial gonads. This coincided with differential H3K4me-methylation in pre-granulosa/pre-Sertoli cells, pointing to a specific mechanism of amphibian sex determination.
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Affiliation(s)
- Heiner Kuhl
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Müggelseedamm 301 & 310, 12587, Berlin, Germany
| | - Wen Hui Tan
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Block S1A, Level 6, Singapore, 117543, Singapore
| | - Christophe Klopp
- SIGENAE, Plate-forme Bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRAe, 31326, Castanet-Tolosan, France
| | - Wibke Kleiner
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Müggelseedamm 301 & 310, 12587, Berlin, Germany
| | - Baturalp Koyun
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Müggelseedamm 301 & 310, 12587, Berlin, Germany
- Department of Molecular Biology and Genetics, Genetics, Faculty of Science, Bilkent University, SB Building, Ankara, 06800, Turkey
| | - Mitica Ciorpac
- Danube Delta National Institute for Research and Development, Tulcea, 820112, Romania
- Advanced Research and Development Center for Experimental Medicine-CEMEX, "Grigore T. Popa", University of Medicine and Pharmacy, Mihail Kogălniceanu Street 9-13, Iasi, 700259, Romania
| | - Romain Feron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Martin Knytl
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 12843, Czech Republic
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Ontario, ON, Canada
| | - Werner Kloas
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Müggelseedamm 301 & 310, 12587, Berlin, Germany
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Am Hubland, 97074, Wuerzburg, Germany
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, 78666, USA
| | - Christoph Winkler
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Block S1A, Level 6, Singapore, 117543, Singapore.
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Müggelseedamm 301 & 310, 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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4
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Li M, Sun L, Zhou L, Wang D. Tilapia, a good model for studying reproductive endocrinology. Gen Comp Endocrinol 2024; 345:114395. [PMID: 37879418 DOI: 10.1016/j.ygcen.2023.114395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/07/2023] [Accepted: 10/21/2023] [Indexed: 10/27/2023]
Abstract
The Nile tilapia (Oreochromis niloticus), with a system of XX/XY sex determination, is a worldwide farmed fish with a shorter sexual maturation time than that of most cultured fish. Tilapia show a spawning cycle of approximately 14 days and can be artificially propagated in the laboratory all year round to obtain genetically all female (XX) and all male (XY) fry. Its genome sequence has been opened, and a perfect gene editing platform has been established. With a moderate body size, it is convenient for taking enough blood to measure hormone level. In recent years, using tilapia as animal model, we have confirmed that estrogen is crucial for female development because 1) mutation of star2, cyp17a1 or cyp19a1a (encoding aromatase, the key enzyme for estrogen synthesis) results in sex reversal (SR) due to estrogen deficiency in XX tilapia, while mutation of star1, cyp11a1, cyp17a2, cyp19a1b or cyp11c1 affects fertility due to abnormal androgen, cortisol and DHP levels in XY tilapia; 2) when the estrogen receptors (esr2a/esr2b) are mutated, the sex is reversed from female to male, while when the androgen receptors are mutated, the sex cannot be reversed; 3) the differentiated ovary can be transdifferentiated into functional testis by inhibition of estrogen synthesis, and the differentiated testis can be transdifferentiated into ovary by simultaneous addition of exogenous estrogen and androgen synthase inhibitor; 4) loss of male pathway genes amhy, dmrt1, gsdf causes SR with upregulation of cyp19a1a in XY tilapia. Disruption of estrogen synthesis rescues the male to female SR of amhy and gsdf but not dmrt1 mutants; 5) mutation of female pathway genes foxl2 and sf-1 causes SR with downregulation of cyp19a1a in XX tilapia; 6) the germ cell SR of foxl3 mutants fails to be rescued by estrogen treatment, indicating that estrogen determines female germ cell fate through foxl3. This review also summarized the effects of deficiency of other steroid hormones, such as androgen, DHP and cortisol, on fish reproduction. Overall, these studies demonstrate that tilapia is an excellent animal model for studying reproductive endocrinology of fish.
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Affiliation(s)
- 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, China
| | - Lina Sun
- 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
| | - Linyan 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, 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, China.
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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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6
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Zheng S, Tao W, Tao H, Yang H, Wu L, Shao F, Wang Z, Jin L, Peng Z, Wang D, Zhang Y. Characterization of the male-specific region containing the candidate sex-determining gene in Amur catfish (Silurus asotus) using third-generation- and pool-sequencing data. Int J Biol Macromol 2023; 248:125908. [PMID: 37482150 DOI: 10.1016/j.ijbiomac.2023.125908] [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: 04/18/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
Amur catfish (Silurus asotus) is an ecologically and economically important fish species in Asia. Here, we assembled the female and male Amur catfish genomes, with genome sizes of 757.15 and 755.44 Mb, respectively, at the chromosome level using nanopore and Hi-C technologies. Consistent with the known diploid chromosome count, both genomes contained 29 chromosome-size scaffolds covering 98.80 and 98.73 % of the complete haplotypic assembly with scaffold N50 of 28.87 and 27.29 Mb, respectively. The female (n = 40) and male (n = 40) pools were re-sequenced. Comparative analysis of sequencing and re-sequencing data from both sexes confirmed the presence of an XX/XY sex determination system in Amur catfish and revealed Chr5 as the sex chromosome containing an approximately 400 kb Y-specific region (MSY). Gene annotation revealed a male-specific duplicate of amhr2, namely amhr2y, in MSY, which is male-specific in different wild populations and expressed only in the testes. Amur catfish shared partially syntenic MSY and amhr2y genes with the southern catfish (S. meridionalis, Chr24), which were located on different chromosomes. High sequence divergence between amhr2y and amhr2 and high sequence similarity with amhr2y were observed in both species. These results indicate the common origin of the sex-determining (SD) gene and transition of amhr2y in the two Silurus species. Accumulation of repetitive elements in the MSY of both species may be the main driver of the transition of amhr2y. Overall, our study provides valuable catfish genomic resources. Moreover, determination of amhr2y as the candidate SD gene in Amur catfish provides another example of amhr2 as the SD gene in fish.
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Affiliation(s)
- Shuqing Zheng
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, 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
| | - Wenjing Tao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, 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
| | - Hongyan Tao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, 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
| | - Haowen Yang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, 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
| | - Limin Wu
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, College of Fisheries, Henan Normal University, Xinxiang 453007, China
| | - Feng Shao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, 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
| | - Zhijian Wang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, 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
| | - Li Jin
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, 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
| | - Zuogang Peng
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, 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
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, 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.
| | - Yaoguang Zhang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, 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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7
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Yamaguchi K, Uno Y, Kadota M, Nishimura O, Nozu R, Murakumo K, Matsumoto R, Sato K, Kuraku S. Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization. Genome Res 2023; 33:1527-1540. [PMID: 37591668 PMCID: PMC10620051 DOI: 10.1101/gr.276840.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 07/31/2023] [Indexed: 08/19/2023]
Abstract
Genomic studies of vertebrate chromosome evolution have long been hindered by the scarcity of chromosome-scale DNA sequences of some key taxa. One of those limiting taxa has been the elasmobranchs (sharks and rays), which harbor species often with numerous chromosomes and enlarged genomes. Here, we report the chromosome-scale genome assembly for the zebra shark Stegostoma tigrinum, an endangered species that has a relatively small genome among sharks (3.71 Gb), as well as for the whale shark Rhincodon typus Our analysis using a male-female comparison identified an X Chromosome, the first genomically characterized shark sex chromosome. The X Chromosome harbors the Hox C cluster whose intact linkage has not been shown for an elasmobranch fish. The sequenced shark genomes show a gradualism of chromosome length with remarkable length-dependent characteristics-shorter chromosomes tend to have higher GC content, gene density, synonymous substitution rate, and simple tandem repeat content as well as smaller gene length and lower interspersed repeat content. We challenge the traditional binary classification of karyotypes as with and without so-called microchromosomes. Even without microchromosomes, the length-dependent characteristics persist widely in nonmammalian vertebrates. Our investigation of elasmobranch karyotypes underpins their unique characteristics and provides clues for understanding how vertebrate karyotypes accommodate intragenomic heterogeneity to realize a complex readout. It also paves the way to dissecting more genomes with variable sizes to be sequenced at high quality.
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Affiliation(s)
- Kazuaki Yamaguchi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), 650-0047, Kobe, Japan
| | - Yoshinobu Uno
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), 650-0047, Kobe, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), 650-0047, Kobe, Japan
| | - Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), 650-0047, Kobe, Japan
| | - Ryo Nozu
- Okinawa Churashima Research Center, Okinawa Churashima Foundation, 905-0206, Okinawa, Japan
| | | | | | - Keiichi Sato
- Okinawa Churashima Research Center, Okinawa Churashima Foundation, 905-0206, Okinawa, Japan
- Okinawa Churaumi Aquarium, 905-0206, Okinawa, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), 650-0047, Kobe, Japan;
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, 411-8540, Mishima, Japan
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), 411-8540, Mishima, Japan
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8
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Rondeau EB, Christensen KA, Johnson HA, Sakhrani D, Biagi CA, Wetklo M, Despins CA, Leggatt RA, Minkley DR, Withler RE, Beacham TD, Koop BF, Devlin RH. Insights from a chum salmon (Oncorhynchus keta) genome assembly regarding whole-genome duplication and nucleotide variation influencing gene function. G3 (BETHESDA, MD.) 2023; 13:jkad127. [PMID: 37293843 PMCID: PMC10411575 DOI: 10.1093/g3journal/jkad127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/30/2023] [Accepted: 06/04/2023] [Indexed: 06/10/2023]
Abstract
Chum salmon are ecologically important to Pacific Ocean ecosystems and commercially important to fisheries. To improve the genetic resources available for this species, we sequenced and assembled the genome of a male chum salmon using Oxford Nanopore read technology and the Flye genome assembly software (contig N50: ∼2 Mbp, complete BUSCOs: ∼98.1%). We also resequenced the genomes of 59 chum salmon from hatchery sources to better characterize the genome assembly and the diversity of nucleotide variants impacting phenotype variation. With genomic sequences from a doubled haploid individual, we were able to identify regions of the genome assembly that have been collapsed due to high sequence similarity between homeologous (duplicated) chromosomes. The homeologous chromosomes are relics of an ancient salmonid-specific genome duplication. These regions were enriched with genes whose functions are related to the immune system and responses to toxins. From analyzing nucleotide variant annotations of the resequenced genomes, we were also able to identify genes that have increased levels of variants thought to moderately impact gene function. Genes related to the immune system and the detection of chemical stimuli (olfaction) had increased levels of these variants based on a gene ontology enrichment analysis. The tandem organization of many of the enriched genes raises the question of why they have this organization.
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Affiliation(s)
- Eric B Rondeau
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Kris A Christensen
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
| | - Hollie A Johnson
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
| | - Dionne Sakhrani
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
| | - Carlo A Biagi
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
| | - Mike Wetklo
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Cody A Despins
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
| | - Rosalind A Leggatt
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
| | - David R Minkley
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
| | - Ruth E Withler
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Terry D Beacham
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
| | - Robert H Devlin
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
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9
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Moghadam HK, Fannemel B, Thorland I, Lozano C, Hillestad B. Identification and Genomic Localization of Autosomal sdY Locus in a Population of Atlantic Salmon (Salmo salar). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023:10.1007/s10126-023-10217-4. [PMID: 37233880 DOI: 10.1007/s10126-023-10217-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/14/2023] [Indexed: 05/27/2023]
Abstract
The determination of sex in salmonid fishes is controlled by genetic mechanisms, with males being the heterogametic sex. The master sex-determining gene, the sexually dimorphic gene on the Y chromosome (sdY), is a conserved gene across various salmonid species. Nevertheless, variations in the genomic location of sdY have been observed both within and between species. Furthermore, different studies have reported discordances in the association between the sdY and the phenotypic gender. While some males seem to lack this locus, there have been reports of females carrying sdY. Although the exact reasons behind this discordance remain under investigation, some recent studies have proposed the existence of an autosomal, non-functional copy of sdY as a potential cause. In this study, we confirmed the presence of this autosomal sdY in the SalmoBreed strain of Atlantic salmon using a genotyping platform through a novel approach that allows for high-throughput screening of a large number of individuals. We further characterized the segregation profile of this locus across families and found the ratio of genetically assigned female-to-male progeny to be in accordance with the expected profile of a single autosomal sdY locus. Additionally, our mapping efforts localized this locus to chromosome 3 and suggested a putative copy on chromosome 6.
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10
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Li S, Li W, Jiang S, Jing Y, Xiao L, Yu Y, Liu Y, Li Y, Wang D, Li J, Peng C, Chen J, Lu D, Wu B, Guang X, Ma J, You X, Yang Y, Liu S, Fang X, Gao Q, Shi Q, Lin H, Schartl M, Yue Z, Zhang Y. Mechanisms of sex differentiation and sex reversal in hermaphrodite fish as revealed by the Epinephelus coioides genome. Mol Ecol Resour 2023; 23:920-932. [PMID: 36631404 DOI: 10.1111/1755-0998.13753] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 12/13/2022] [Accepted: 12/28/2022] [Indexed: 01/13/2023]
Abstract
Most grouper species are functional protogynous hermaphrodites, but the genetic basis and the molecular mechanisms underlying the regulation of this unique reproductive strategy remain enigmatic. In this study, we report a high-quality chromosome-level genome assembly of the representative orange-spotted grouper (Epinephelus coioides). No duplication or deletion of sex differentiation-related genes was found in the genome, suggesting that sex development in this grouper may be related to changes in regulatory sequences or environmental factors. Transcriptomic analyses showed that aromatase and retinoic acid are probably critical to promoting ovarian fate determination, and follicle-stimulating hormone triggers the female-to-male sex change. Socially controlled sex-change studies revealed that, in sex-changing fish, the brain's response to the social environment may be mediated by activation of the phototransduction cascade and the melatonin synthesis pathway. In summary, our genomic and experimental results provide novel insights into the molecular mechanisms of sex differentiation and sex change in the protogynous groupers.
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Affiliation(s)
- Shuisheng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | | | - Shoujia Jiang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, Shenzhen, China
| | - Yi Jing
- BGI-Shenzhen, Shenzhen, China.,BGI-Sanya, BGI-Shenzhen, Sanya, China
| | - Ling Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | | | - Yun Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yanhong Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Dengdong Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jiang Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Cheng Peng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jiaxing Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Danqi Lu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Bin Wu
- BGI-Shenzhen, Shenzhen, China
| | | | - Junping Ma
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, Shenzhen, China
| | - Yuqing Yang
- Marine Fisheries Development Center of Guangdong Province, Huizhou, China
| | - Su Liu
- Marine Fisheries Development Center of Guangdong Province, Huizhou, China
| | | | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, Shenzhen, China
| | - Haoran Lin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Manfred Schartl
- Developmental Biochemistry, University of Würzburg, Biozentrum, Am Hubland, Würzburg, and Comprehensive Cancer Center, University Clinic Würzburg, Würzburg, Germany.,Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Zhen Yue
- BGI-Shenzhen, Shenzhen, China.,BGI-Sanya, BGI-Shenzhen, Sanya, China
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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11
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Pensabene E, Yurchenko A, Kratochvíl L, Rovatsos M. Madagascar Leaf-Tail Geckos ( Uroplatus spp.) Share Independently Evolved Differentiated ZZ/ZW Sex Chromosomes. Cells 2023; 12:cells12020260. [PMID: 36672195 PMCID: PMC9856856 DOI: 10.3390/cells12020260] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/10/2023] Open
Abstract
Geckos are an excellent group to study the evolution of sex determination, as they possess a remarkable variability ranging from a complete absence of sex chromosomes to highly differentiated sex chromosomes. We explored sex determination in the Madagascar leaf-tail geckos of the genus Uroplatus. The cytogenetic analyses revealed highly heterochromatic W chromosomes in all three examined species (Uroplatus henkeli, U. alluaudi, U. sikorae). The comparative gene coverage analysis between sexes in U. henkeli uncovered an extensive Z-specific region, with a gene content shared with the chicken chromosomes 8, 20, 26 and 28. The genomic region homologous to chicken chromosome 28 has been independently co-opted for the role of sex chromosomes in several vertebrate lineages, including monitors, beaded lizards and monotremes, perhaps because it contains the amh gene, whose homologs were repeatedly recruited as a sex-determining locus. We demonstrate that all tested species of leaf-tail geckos share homologous sex chromosomes despite the differences in shape and size of their W chromosomes, which are not homologous to the sex chromosomes of other closely related genera. The rather old (at least 40 million years), highly differentiated sex chromosomes of Uroplatus geckos can serve as a great system to study the convergence of sex chromosomes evolved from the same genomic region.
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12
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Pregler KC, Obedzinski M, Gilbert‐Horvath EA, White B, Carlson SM, Garza JC. Assisted gene flow from outcrossing shows the potential for genetic rescue in an endangered salmon population. Conserv Lett 2022. [DOI: 10.1111/conl.12934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Kasey C. Pregler
- Department of Environmental Science, Policy, and Management University of California, Berkeley Berkeley California USA
| | - Mariska Obedzinski
- Department of Environmental Science, Policy, and Management University of California, Berkeley Berkeley California USA
- California Sea Grant Windsor California USA
| | - Elizabeth A. Gilbert‐Horvath
- Southwest Fisheries Science Center National Marine Fisheries Service and University of California, Santa Cruz Santa Cruz California USA
| | - Benjamin White
- U.S. Army Corps of Engineers, Don Clausen/Warm Springs Hatchery Geyserville California USA
| | - Stephanie M. Carlson
- Department of Environmental Science, Policy, and Management University of California, Berkeley Berkeley California USA
| | - John Carlos Garza
- Southwest Fisheries Science Center National Marine Fisheries Service and University of California, Santa Cruz Santa Cruz California USA
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13
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Katsumi T, Shams F, Yanagi H, Ohnishi T, Toda M, Lin SM, Mawaribuchi S, Shimizu N, Ezaz T, Miura I. Highly rapid and diverse sex chromosome evolution in the Odorrana frog species complex. Dev Growth Differ 2022; 64:279-289. [PMID: 35881001 DOI: 10.1111/dgd.12800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/29/2022] [Accepted: 06/10/2022] [Indexed: 11/26/2022]
Abstract
Sex chromosomes in poikilothermal vertebrates are characterized by rapid and diverse evolution at the species or population level. Our previous study revealed that the Taiwanese frog Odorrana swinhoana (2n = 26) has a unique system of multiple sex chromosomes created by three sequential translocations among chromosomes 1, 3, and 7. To reveal the evolutionary history of sex chromosomes in the Odorrana species complex, we first identified the original, homomorphic sex chromosomes, prior to the occurrence of translocations, in the ancestral-type population of O. swinhoana. Then, we extended the investigation to a closely related Japanese species, Odorrana utsunomiyaorum, which is distributed on two small islands. We used a high-throughput nuclear genomic approach to analyze single-nucleotide polymorphisms and identify the sex-linked markers. Those isolated from the O. swinhoana ancestral-type population were found to be aligned to chromosome 1 and showed male heterogamety. In contrast, almost all the sex-linked markers isolated from O. utsunomiyaorum were heterozygous in females and homozygous in males and were aligned to chromosome 9. Morphologically, we confirmed chromosome 9 to be heteromorphic in females, showing a ZZ-ZW sex determination system, in which the W chromosomes were heterochromatinized in a stripe pattern along the chromosome axis. These results indicated that after divergence of the two species, the ancestral homomorphic sex chromosome 1 underwent highly rapid and diverse evolution, i.e., sequential translocations with two autosomes in O. swinhoana, and turnover to chromosome 9 in O. utsunomiyaorum, with a transition from XY to ZW heterogamety and change to heteromorphy.
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Affiliation(s)
- Taito Katsumi
- School of Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Foyez Shams
- Institute for Applied Ecology, University of Canberra, Australia
| | - Hiroaki Yanagi
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | | | - Mamoru Toda
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Si-Min Lin
- School of Life Sciences, National Taiwan Normal University, Taipei, Taiwan
| | - Shuuji Mawaribuchi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Norio Shimizu
- Hiroshima University Museum, Higashi-Hiroshima, Japan
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Australia
| | - Ikuo Miura
- Institute for Applied Ecology, University of Canberra, Australia.,Amphibian Research Center, Hiroshima University, Higashi-Hiroshima, Japan
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14
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Repeated translocation of a supergene underlying rapid sex chromosome turnover in Takifugu pufferfish. Proc Natl Acad Sci U S A 2022; 119:e2121469119. [PMID: 35658077 DOI: 10.1073/pnas.2121469119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceAlthough turnover of sex chromosomes is very common in many vertebrate lineages, the transition process is still elusive. We studied the sex-determining region (SDR) of 12 congeneric fish species of Takifugu fish that compose an important model for the study of genomics and sex determination. We found that while nine species retained their ancestral SDR, three species had acquired derived SDRs. Although the derived SDRs resided in three different chromosomes, they harbored a shared supergene flanked by two putative transposable elements. The results highlight the underestimated role of a mobile supergene in turnover of sex chromosomes in vertebrates.
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15
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Wen M, Pan Q, Jouanno E, Montfort J, Zahm M, Cabau C, Klopp C, Iampietro C, Roques C, Bouchez O, Castinel A, Donnadieu C, Parrinello H, Poncet C, Belmonte E, Gautier V, Avarre J, Dugue R, Gustiano R, Hà TTT, Campet M, Sriphairoj K, Ribolli J, de Almeida FL, Desvignes T, Postlethwait JH, Floi Bucao C, Robinson‐Rechavi M, Bobe J, Herpin A, Guiguen Y. An ancient truncated duplication of the anti‐Mullerian hormone receptor type 2 gene is a potential conserved master sex determinant in the Pangasiidae catfish family. Mol Ecol Resour 2022; 22:2411-2428. [PMID: 35429227 PMCID: PMC9555307 DOI: 10.1111/1755-0998.13620] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/29/2022] [Accepted: 04/11/2022] [Indexed: 11/30/2022]
Abstract
The evolution of sex determination (SD) in teleosts is amazingly dynamic, as reflected by the variety of different master sex-determining genes identified. Pangasiids are economically important catfishes in South Asian countries, but little is known about their SD system. Here, we generated novel genomic resources for 12 Pangasiids and characterized their SD system. Based on a Pangasianodon hypophthalmus chromosome-scale genome assembly, we identified an anti-Müllerian hormone receptor type Ⅱ gene (amhr2) duplication, which was further characterized as being sex-linked in males and expressed only in testes. These results point to a Y chromosome male-specific duplication (amhr2by) of the autosomal amhr2a. Sequence annotation revealed that the P. hypophthalmus Amhr2by is truncated in its N-terminal domain, lacking the cysteine-rich extracellular part of the receptor that is crucial for ligand binding, suggesting a potential route for its neofunctionalization. Reference-guided assembly of 11 additional Pangasiids, along with sex-linkage studies, revealed that this truncated amhr2by duplication is a male-specific conserved gene in Pangasiids. Reconstructions of the amhr2 phylogeny suggested that amhr2by arose from an ancient duplication/insertion event at the root of the Siluroidei radiation that is dated to ~100 million years ago. Together these results bring multiple lines of evidence supporting that amhr2by is an ancient and conserved master sex-determining gene in Pangasiids, a finding that highlights the recurrent use of the transforming growth factor β pathway, which is often used for the recruitment of teleost master SD genes, and provides another empirical case towards firther understanding of dynamics of SD systems.
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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
| | - Qiaowei Pan
- INRAE LPGP 35000 Rennes France
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
| | | | | | - Margot Zahm
- Plate‐forme bio‐informatique Genotoul Mathématiques et Informatique Appliquées de Toulouse INRAE Castanet Tolosan France
| | - Cédric Cabau
- SIGENAE, GenPhySE Université de Toulouse INRAE ENVT Castanet Tolosan France
| | - 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
| | | | - Céline Roques
- INRAE, US 1426, GeT‐PlaGe Genotoul, Castanet‐Tolosan France
| | | | | | | | - Hugues Parrinello
- Montpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle 141 rue de la Cardonille 34094 Montpellier Cedex France
| | - Charles Poncet
- GDEC Gentyane INRAE Université Clermont Auvergne Clermont‐Ferrand France
| | - Elodie Belmonte
- GDEC Gentyane INRAE Université Clermont Auvergne Clermont‐Ferrand France
| | - Véronique Gautier
- GDEC Gentyane INRAE Université Clermont Auvergne Clermont‐Ferrand France
| | | | - Remi Dugue
- ISEM Univ Montpellier CNRS IRD Montpellier France
| | - Rudhy Gustiano
- Research Institute of Freshwater Fisheries (CRIFI‐RIFF) Instalasi Penelitian Perikanan Air Tawar Jalan Ragunan‐Pasar Minggu P.O. Box 7220/jkspm Jakarta 12540 Indonesia
| | - Trần Thị Thúy Hà
- Research Institute for Aquaculture No.1. Dinh Bang Tu Son, Bac Ninh Viet Nam
| | | | - Kednapat Sriphairoj
- Faculty of Natural Resources and Agro‐Industry Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus Sakon Nakhon Thailand
| | - Josiane Ribolli
- Laboratório de Biologia e Cultivo de Peixes de Água Doce Universidade Federal de Santa Catarina Florianópolis SC Brasil
| | | | - Thomas Desvignes
- Institute of Neuroscience University of Oregon Eugene OR 97403 USA
| | | | - Christabel Floi Bucao
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- SIB Swiss Institute of Bioinformatics 1015 Lausanne Switzerland
| | - Marc Robinson‐Rechavi
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- SIB Swiss Institute of Bioinformatics 1015 Lausanne Switzerland
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16
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Bertho S, Herpin A, Jouanno E, Yano A, Bobe J, Parrinello H, Journot L, Guyomard R, Muller T, Swanson P, McKinney G, Williamson K, Meek M, Schartl M, Guiguen Y. A nonfunctional copy of the salmonid sex-determining gene ( sdY) is responsible for the “apparent” XY females in Chinook salmon, Oncorhynchus tshawytscha. G3 GENES|GENOMES|GENETICS 2022; 12:6493265. [PMID: 35100376 PMCID: PMC8824802 DOI: 10.1093/g3journal/jkab451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/03/2021] [Indexed: 11/14/2022]
Abstract
Abstract
Many salmonids have a male heterogametic (XX/XY) sex determination system, and they are supposed to have a conserved master sex-determining gene (sdY) that interacts at the protein level with Foxl2 leading to the blockage of the synergistic induction of Foxl2 and Nr5a1 of the cyp19a1a promoter. However, this hypothesis of a conserved master sex-determining role of sdY in salmonids is challenged by a few exceptions, one of them being the presence of naturally occurring “apparent” XY Chinook salmon, Oncorhynchus tshawytscha, females. Here, we show that some XY Chinook salmon females have a sdY gene (sdY-N183), with 1 missense mutation leading to a substitution of a conserved isoleucine to an asparagine (I183N). In contrast, Chinook salmon males have both a nonmutated sdY-I183 gene and the missense mutation sdY-N183 gene. The 3-dimensional model of SdY-I183N predicts that the I183N hydrophobic to hydrophilic amino acid change leads to a modification in the SdY β-sandwich structure. Using in vitro cell transfection assays, we found that SdY-I183N, like the wild-type SdY, is preferentially localized in the cytoplasm. However, compared to wild-type SdY, SdY-I183N is more prone to degradation, its nuclear translocation by Foxl2 is reduced, and SdY-I183N is unable to significantly repress the synergistic Foxl2/Nr5a1 induction of the cyp19a1a promoter. Altogether, our results suggest that the sdY-N183 gene of XY Chinook females is nonfunctional and that SdY-I183N is no longer able to promote testicular differentiation by impairing the synthesis of estrogens in the early differentiating gonads of wild Chinook salmon XY females.
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Affiliation(s)
- Sylvain Bertho
- INRAE, LPGP, Rennes 35000, France
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg 97074, Germany
| | | | | | | | | | - Hugues Parrinello
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, Montpellier 34094, France
| | - Laurent Journot
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, Montpellier 34094, France
| | - René Guyomard
- GABI, INRAE, AgroParisTech, Université Paris-Saclay, Paris 75005, France
| | - Thomas Muller
- Julius-von-Sachs-Institute, Department of Molecular Plant Physiology and Biophysics, University of Wuerzburg, Wuerzburg 97082, Germany
| | - Penny Swanson
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98112, USA
| | - Garrett McKinney
- Molecular Genetics Laboratory, Washington Department of Fish & Wildlife, Olympia, WA 98501, USA
| | | | - Mariah Meek
- Dept. of Integrative Biology, AgBio Research, and Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
- Department of Developmental Biochemistry, Biocenter, University of Wüerzburg, Wuerzburg 97074, Germany
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17
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Kratochvíl L, Stöck M, Rovatsos M, Bullejos M, Herpin A, Jeffries DL, Peichel CL, Perrin N, Valenzuela N, Pokorná MJ. Expanding the classical paradigm: what we have learnt from vertebrates about sex chromosome evolution. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200097. [PMID: 34304593 PMCID: PMC8310716 DOI: 10.1098/rstb.2020.0097] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2021] [Indexed: 12/15/2022] Open
Abstract
Until recently, the field of sex chromosome evolution has been dominated by the canonical unidirectional scenario, first developed by Muller in 1918. This model postulates that sex chromosomes emerge from autosomes by acquiring a sex-determining locus. Recombination reduction then expands outwards from this locus, to maintain its linkage with sexually antagonistic/advantageous alleles, resulting in Y or W degeneration and potentially culminating in their disappearance. Based mostly on empirical vertebrate research, we challenge and expand each conceptual step of this canonical model and present observations by numerous experts in two parts of a theme issue of Phil. Trans. R. Soc. B. We suggest that greater theoretical and empirical insights into the events at the origins of sex-determining genes (rewiring of the gonadal differentiation networks), and a better understanding of the evolutionary forces responsible for recombination suppression are required. Among others, crucial questions are: Why do sex chromosome differentiation rates and the evolution of gene dose regulatory mechanisms between male versus female heterogametic systems not follow earlier theory? Why do several lineages not have sex chromosomes? And: What are the consequences of the presence of (differentiated) sex chromosomes for individual fitness, evolvability, hybridization and diversification? We conclude that the classical scenario appears too reductionistic. Instead of being unidirectional, we show that sex chromosome evolution is more complex than previously anticipated and principally forms networks, interconnected to potentially endless outcomes with restarts, deletions and additions of new genomic material. 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 II)'.
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Affiliation(s)
- Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Mónica Bullejos
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Las Lagunillas Campus S/N, 23071 Jaén, Spain
| | - Amaury Herpin
- INRAE, LPGP, 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
| | - Daniel L. Jeffries
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Catherine L. Peichel
- Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Martina Johnson Pokorná
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
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Abstract
This preface introduces the two parts of a theme issue on vertebrate sex chromosome evolution (title below). We invited and edited 22 articles concerning the following main topics (Part 1): sex determination without sex chromosomes and/or governed by epigenetics; origin of sex-determining genes; reasons for differentiation of sex chromosomes and differences in their rates of differentiation as well as (Part 2): co-option of the same linkage groups into sex chromosomes; is differentiation of sex chromosomes a unidirectional pathway?; consequences of differentiated sex chromosomes; differences in differentiation of sex chromosomes under male versus female heterogamety; evolution of sex chromosomes under hybridization and polyploidy. 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)
- Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries—IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
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19
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Adolfi MC, Herpin A, Schartl M. The replaceable master of sex determination: bottom-up hypothesis revisited. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200090. [PMID: 34247496 DOI: 10.1098/rstb.2020.0090] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Different group of vertebrates and invertebrates demonstrate an amazing diversity of gene regulations not only at the top but also at the bottom of the sex determination genetic network. As early as 1995, based on emerging findings in Drosophila melanogaster and Caenorhabditis elegans, Wilkins suggested that the evolution of the sex determination pathway evolved from the bottom to the top of the hierarchy. Based on our current knowledge, this review revisits the 'bottom-up' hypothesis and applies its logic to vertebrates. The basic operation of the determination network is through the dynamics of the opposing male and female pathways together with a persistent need to maintain the sexual identity of the cells of the gonad up to the reproductive stage in adults. The sex-determining trigger circumstantially acts from outside the genetic network, but the regulatory network is not built around it as a main node, thus maintaining the genetic structure of the network. New sex-promoting genes arise either through allelic diversification or gene duplication and act specially at the sex-determination period, without integration into the complete network. Due to this peripheral position the new regulator is not an indispensable component of the sex-determining network and can be easily replaced. 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)
- Mateus Contar Adolfi
- Developmental Biochemistry, Biocenter, University of Wuerzburg, 97074 Wuerzburg, Germany
| | - Amaury Herpin
- INRA, 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
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Wuerzburg, 97074 Wuerzburg, Germany.,Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX 78666, USA
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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: 56] [Impact Index Per Article: 18.7] [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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