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Andree KB, Loi B, Vallainc D, Concu D, Duncan N, Carboni S. Investigation of the utility of PCR-RFLP as a rapid alternative to DNA sequencing for interrogation of the genetic sex of Mugil cephalus. Anim Reprod Sci 2024; 270:107614. [PMID: 39366166 DOI: 10.1016/j.anireprosci.2024.107614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Accepted: 09/26/2024] [Indexed: 10/06/2024]
Abstract
Mugil cephalus is a species of considerable interest for aquaculture. As a species that is not sexually dimorphic, when building a brood stock with a balanced sex ratio there is difficulty for identification of sex until the animals are quite mature. When mono-sex populations of this species is desired, as in the case of production of females for "bottarga", considerable resource expenditure could be saved if early sorting of sexes were possible to enable selection of a single sex. A recently described sex-associated loci within the follicle stimulating hormone receptor gene (fshr) was identified using genomic DNA sequencing and shown to contain some non-synonymous mutations wherein the females have a tendency to be homozygous and the males heterozygous. The loci identification method is time-consuming and somewhat expensive. We propose that the method described for the identification of the genetic sex of Mugil cephalus, prior to sexual maturation should be rapid and not require DNA sequencing. In this work, we demonstrate the utilization of one of these fshr mutations within this genetic marker in a PCR-RFLP assay. Using this new method, the loci in question shows 77.8 % partitioning with males and 88.9 % partition with females, as referenced to phenotypic sex characterized by histology, thus confirming the partitioning of the genetic marker as seen previously using DNA sequencing. Future applications of this relatively rapid and inexpensive method could contribute to the production of mono-sex farmed stock and open new opportunities for more efficient broodstock management practices in the species.
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Affiliation(s)
- Karl B Andree
- Institute for Research and Technology in Agroalimentaries, Crta. Poble Nou. Km 5.5, La Ràpita, Tarragona 43540, Spain.
| | - Barbara Loi
- IMC - International Marine Centre, Località Sa Mardini 09170, Torregrande, Oristano, Sardinia, Italy
| | - Dario Vallainc
- IMC - International Marine Centre, Località Sa Mardini 09170, Torregrande, Oristano, Sardinia, Italy
| | - Danilo Concu
- IMC - International Marine Centre, Località Sa Mardini 09170, Torregrande, Oristano, Sardinia, Italy
| | - Neil Duncan
- Institute for Research and Technology in Agroalimentaries, Crta. Poble Nou. Km 5.5, La Ràpita, Tarragona 43540, Spain
| | - Stefano Carboni
- IMC - International Marine Centre, Località Sa Mardini 09170, Torregrande, Oristano, Sardinia, Italy
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2
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Wu J, Liu F, Jiao J, Luo H, Fan S, Liu J, Wang H, Cui N, Zhao N, Qu Q, Kuraku S, Huang Z, Xu L. Comparative genomics illuminates karyotype and sex chromosome evolution of sharks. CELL GENOMICS 2024; 4:100607. [PMID: 38996479 PMCID: PMC11406177 DOI: 10.1016/j.xgen.2024.100607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/01/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024]
Abstract
Chondrichthyes is an important lineage to reconstruct the evolutionary history of vertebrates. Here, we analyzed genome synteny for six chondrichthyan chromosome-level genomes. Our comparative analysis reveals a slow evolutionary rate of chromosomal changes, with infrequent but independent fusions observed in sharks, skates, and chimaeras. The chondrichthyan common ancestor had a proto-vertebrate-like karyotype, including the presence of 18 microchromosome pairs. The X chromosome is a conversed microchromosome shared by all sharks, suggesting a likely common origin of the sex chromosome at least 181 million years ago. We characterized the Y chromosomes of two sharks that are highly differentiated from the X except for a small young evolutionary stratum and a small pseudoautosomal region. We found that shark sex chromosomes lack global dosage compensation but that dosage-sensitive genes are locally compensated. Our study on shark chromosome evolution enhances our understanding of shark sex chromosomes and vertebrate chromosome evolution.
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Affiliation(s)
- Jiahong Wu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Fujiang Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jie Jiao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Haoran Luo
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China; Key Laboratory of Ministry of Education for the Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Shiyu Fan
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jiao Liu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Hongxiang Wang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Ning Cui
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Ning Zhao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China; Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Qingming Qu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shigehiro Kuraku
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Shizuoka, Japan; Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan
| | - Zhen Huang
- Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, Fuzhou 350108, China
| | - Luohao Xu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China.
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3
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Zhu Z, Younas L, Zhou Q. Evolution and regulation of animal sex chromosomes. Nat Rev Genet 2024:10.1038/s41576-024-00757-3. [PMID: 39026082 DOI: 10.1038/s41576-024-00757-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2024] [Indexed: 07/20/2024]
Abstract
Animal sex chromosomes typically carry the upstream sex-determining gene that triggers testis or ovary development and, in some species, are regulated by global dosage compensation in response to functional decay of the Y chromosome. Despite the importance of these pathways, they exhibit striking differences across species, raising fundamental questions regarding the mechanisms underlying their evolutionary turnover. Recent studies of non-model organisms, including insects, reptiles and teleosts, have yielded a broad view of the diversity of sex chromosomes that challenges established theories. Moreover, continued studies in model organisms with recently developed technologies have characterized the dynamics of sex determination and dosage compensation in three-dimensional nuclear space and at single-cell resolution. Here, we synthesize recent insights into sex chromosomes from a variety of species to review their evolutionary dynamics with respect to the canonical model, as well as their diverse mechanisms of regulation.
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Affiliation(s)
- Zexian Zhu
- Evolutionary and Organismal Biology Research Center and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lubna Younas
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Qi Zhou
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China.
- State Key Laboratory of Transvascular Implantation Devices, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
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4
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Bogár K, Stanivuk J, Géczi A, Fazekas GL, Kovács B, Lázár B, Molnár M, Ardó L, Ljubobratović U, Kovács G, Péter D, Várkonyi E, Káldy J. Investigation of Sexes and Fertility Potential of Female Russian Sturgeon ( Acipenser gueldenstaedtii) and Male American Paddlefish ( Polyodon spathula) Hybrids. Life (Basel) 2024; 14:818. [PMID: 39063572 PMCID: PMC11277912 DOI: 10.3390/life14070818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/16/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
In the present study, 10 allotriploid (3nALT) and 10 allopentaploid (5nALP) six-month-old hybrid fish and two 3nALT and four 5nALP 40-month-old hybrid fish, which resulted by crossing female Russian sturgeon Acipenser gueldenstaedtii (Brandt and Ratzeberg, 1833) and male American paddlefish Polyodon spathula (Walbaum, 1792), were investigated. It was revealed that six-month-old 3nALT and 5nALP hybrids initially had "undifferentiated" gonads, while in the 40-month-old hybrids, only testes were observed in one case of 3nALT and one case of 5nALP hybrids. The testis of 3nALT hybrids was partially developed with spermatogonia, while the testis of one 5nALP hybrid was in the second developmental stage with low spermatogonia density. We could not determine gonad differentiation in any of the cases when the hybrid individuals had the W sex chromosome. We concluded that the gonad differentiation of these interfamilial hybrids follows a similar pattern to interspecific hybrids of different ploidy parent species of the family Acipenseridae, which is consistent with the classical Haldane's rule. However, it cannot be excluded that the testis of this/these hybrid(s) may produce fertile sperm after sexual maturity, depending on additional genetic, hormonal and environmental factors, and further research is required for its evaluation.
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Affiliation(s)
- Katalin Bogár
- Research Centre for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-5540 Szarvas, Hungary; (K.B.); (J.S.); (A.G.); (G.L.F.); (L.A.); (U.L.); (G.K.)
- PhD School of Animal Biotechnology and Animal Science, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary;
| | - Jelena Stanivuk
- Research Centre for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-5540 Szarvas, Hungary; (K.B.); (J.S.); (A.G.); (G.L.F.); (L.A.); (U.L.); (G.K.)
- PhD School of Animal Biotechnology and Animal Science, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary;
| | - Aliz Géczi
- Research Centre for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-5540 Szarvas, Hungary; (K.B.); (J.S.); (A.G.); (G.L.F.); (L.A.); (U.L.); (G.K.)
- PhD School of Animal Biotechnology and Animal Science, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary;
| | - Georgina Lea Fazekas
- Research Centre for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-5540 Szarvas, Hungary; (K.B.); (J.S.); (A.G.); (G.L.F.); (L.A.); (U.L.); (G.K.)
- PhD School of Animal Biotechnology and Animal Science, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary;
| | - Balázs Kovács
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary; (B.K.); (D.P.)
| | - Bence Lázár
- Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, H-2100 Gödöllő, Hungary; (B.L.); (E.V.)
- Animal Biotechnology Department, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary
| | - Mariann Molnár
- PhD School of Animal Biotechnology and Animal Science, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary;
- Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, H-2100 Gödöllő, Hungary; (B.L.); (E.V.)
| | - László Ardó
- Research Centre for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-5540 Szarvas, Hungary; (K.B.); (J.S.); (A.G.); (G.L.F.); (L.A.); (U.L.); (G.K.)
| | - Uroš Ljubobratović
- Research Centre for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-5540 Szarvas, Hungary; (K.B.); (J.S.); (A.G.); (G.L.F.); (L.A.); (U.L.); (G.K.)
| | - Gyula Kovács
- Research Centre for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-5540 Szarvas, Hungary; (K.B.); (J.S.); (A.G.); (G.L.F.); (L.A.); (U.L.); (G.K.)
| | - Dániel Péter
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary; (B.K.); (D.P.)
| | - Eszter Várkonyi
- Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, H-2100 Gödöllő, Hungary; (B.L.); (E.V.)
| | - Jenő Káldy
- Research Centre for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, H-5540 Szarvas, Hungary; (K.B.); (J.S.); (A.G.); (G.L.F.); (L.A.); (U.L.); (G.K.)
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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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6
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Setti PG, Deon GA, Zeni Dos Santos R, Goes CAG, Garnero ADV, Gunski RJ, de Oliveira EHC, Porto-Foresti F, de Freitas TRO, Silva FAO, Liehr T, Utsunomia R, Kretschmer R, de Bello Cioffi M. Evolution of bird sex chromosomes: a cytogenomic approach in Palaeognathae species. BMC Ecol Evol 2024; 24:51. [PMID: 38654159 PMCID: PMC11036779 DOI: 10.1186/s12862-024-02230-5] [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: 12/07/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Different patterns of sex chromosome differentiation are seen in Palaeognathae birds, a lineage that includes the ratites (Struthioniformes, Rheiformes, Apterygiformes, Casuariiformes, and the sister group Tinamiformes). While some Tinamiform species have well-differentiated W chromosomes, both Z and W of all the flightless ratites are still morphologically undifferentiated. Here, we conducted a comprehensive analysis of the ZW differentiation in birds using a combination of cytogenetic, genomic, and bioinformatic approaches. The whole set of satDNAs from the emu (Dromaius novaehollandiae) was described and characterized. Furthermore, we examined the in situ locations of these satDNAs alongside several microsatellite repeats and carried out Comparative Genomic Hybridizations in two related species: the greater rhea (Rhea americana) and the tataupa tinamou (Crypturellus tataupa). RESULTS From the 24 satDNA families identified (which represent the greatest diversity of satDNAs ever uncovered in any bird species), only three of them were found to accumulate on the emu's sex chromosomes, with no discernible accumulation observed on the W chromosome. The W chromosomes of both the greater rhea and the emu did not exhibit a significant buildup of either C-positive heterochromatin or repetitive DNAs, indicating their large undifferentiation both at morphological and molecular levels. In contrast, the tataupa tinamou has a highly differentiated W chromosome that accumulates several DNA repeats. CONCLUSION The findings provide new information on the architecture of the avian genome and an inside look at the starting points of sex chromosome differentiation in birds.
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Affiliation(s)
- Príncia Grejo Setti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, 13565-905, São Carlos, SP, Brazil
| | - Geize Aparecida Deon
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, 13565-905, São Carlos, SP, Brazil
| | | | | | - Analía Del Valle Garnero
- Campus São Gabriel, Universidade Federal do Pampa, 97307-020, São Gabriel, Rio Grande do Sul, Brazil
| | - Ricardo José Gunski
- Campus São Gabriel, Universidade Federal do Pampa, 97307-020, São Gabriel, Rio Grande do Sul, Brazil
| | - Edivaldo Herculano Corrêa de Oliveira
- Laboratório de Citogenômica e Mutagênese Ambiental, Seção de Meio Ambiente, Instituto Evandro Chagas, 67030-000, Ananindeua, PA, Brazil
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, 66075-110, Belém, PA, Brazil
| | - Fábio Porto-Foresti
- Faculdade de Ciências, Universidade Estadual Paulista, 17033-360, Bauru, São Paulo, Brazil
| | | | - Fábio Augusto Oliveira Silva
- Laboratório de Citogenômica e Mutagênese Ambiental, Seção de Meio Ambiente, Instituto Evandro Chagas, 67030-000, Ananindeua, PA, Brazil
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, 07747, Jena, Germany.
| | - Ricardo Utsunomia
- Faculdade de Ciências, Universidade Estadual Paulista, 17033-360, Bauru, São Paulo, Brazil
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, 96.010-610, Pelotas, RS, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, 13565-905, São Carlos, SP, Brazil
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7
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Wong C. Oldest known animal sex chromosome evolved in octopuses 380 million years ago. Nature 2024:10.1038/d41586-024-00637-0. [PMID: 38438613 DOI: 10.1038/d41586-024-00637-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
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8
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Shen X, Hu J, Yáñez JM, Bastos Gomes G, Poon ZWJ, Foster D, Alarcon JF, Shao L, Guo X, Shao Y, Huerlimann R, Li C, Goulden E, Anderson K, Fan G, Domingos JA. Exploring the cobia (Rachycentron canadum) genome: unveiling putative male heterogametic regions and identification of sex-specific markers. Gigascience 2024; 13:giae034. [PMID: 38995143 PMCID: PMC11240236 DOI: 10.1093/gigascience/giae034] [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: 10/30/2023] [Revised: 04/19/2024] [Accepted: 05/22/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Cobia (Rachycentron canadum) is the only member of the Rachycentridae family and exhibits considerable sexual dimorphism in growth rate. Sex determination in teleosts has been a long-standing basic biological question, and the molecular mechanisms of sex determination/differentiation in cobia are completely unknown. RESULTS Here, we reported 2 high-quality, chromosome-level annotated male and female cobia genomes with assembly sizes of 586.51 Mb (contig/scaffold N50: 86.0 kb/24.3 Mb) and 583.88 Mb (79.9 kb/22.5 Mb), respectively. Synteny inference among perciform genomes revealed that cobia and the remora Echeneis naucrates were sister groups. Further, whole-genome resequencing of 31 males and 60 females, genome-wide association study, and sequencing depth analysis identified 3 short male-specific regions within a 10.7-kb continuous genomic region on male chromosome 18, which hinted at an undifferentiated sex chromosome system with a putative XX/XY mode of sex determination in cobia. Importantly, the only 2 genes within/between the male-specific regions, epoxide hydrolase 1 (ephx1, renamed cephx1y) and transcription factor 24 (tcf24, renamed ctcf24y), showed testis-specific/biased gene expression, whereas their counterparts cephx1x and ctf24x, located in female chromosome 18, were similarly expressed in both sexes. In addition, male-specific PCR targeting the cephx1y gene revealed that this genomic feature is conserved in cobia populations from Panama, Brazil, Australia, and Japan. CONCLUSION The first comprehensive genomic survey presented here is a valuable resource for future studies on cobia population structure and dynamics, conservation, and evolutionary history. Furthermore, it establishes evidence of putative male heterogametic regions with 2 genes playing a potential role in the sex determination of the species, and it provides further support for the rapid evolution of sex-determining mechanisms in teleost fish.
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Affiliation(s)
- Xueyan Shen
- Tropical Futures Institute, James Cook University Singapore, 387380, Singapore
| | - Jie Hu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, 8820808 Santiago, Chile
| | - Giana Bastos Gomes
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore
| | | | | | | | - Libin Shao
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Xinyu Guo
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Yunchang Shao
- China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong 518120, China
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China
- Geogia Tech Shenzhen Institute (GTSI), Tianjin University, Shen Zhen 518067, China
| | - Roger Huerlimann
- Marine Climate Change Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, 904-0495, Japan
| | - Chengze Li
- Marine Climate Change Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, 904-0495, Japan
| | - Evan Goulden
- Department of Agriculture and Fisheries, Queensland Government, Bribie Island Research Centre, Woorim, QLD 4507, Australia
| | - Kelli Anderson
- Department of Agriculture and Fisheries, Queensland Government, Bribie Island Research Centre, Woorim, QLD 4507, Australia
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong 518120, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Jose A Domingos
- Tropical Futures Institute, James Cook University Singapore, 387380, Singapore
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville QLD 4811, Australia
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9
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Lasalle A, Benech-Correa G, Brunet FG, Vizziano-Cantonnet D. hsd17b1 is a key gene for ovarian differentiation of the Siberian sturgeon. Mol Reprod Dev 2024; 91:e23729. [PMID: 38282315 DOI: 10.1002/mrd.23729] [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: 06/21/2023] [Revised: 11/21/2023] [Accepted: 12/28/2023] [Indexed: 01/30/2024]
Abstract
This is the first work using gonads from undifferentiated, genetically-sexed Siberian sturgeon describing expression changes in genes related to steroid synthesis and female and male sex differentiation. One factor identified as relevant for ovarian differentiation was the gene coding for the enzyme Hsd17b1, which converts estrone into estradiol-17β. hsd17b1 was highly activated in female gonads at 2.5 months of age, around the onset of sex differentiation, preceding activation of two other genes involved in estrogen production (cyp19a1 and foxl2). hsd17b1 was also strongly repressed in males. Two known foxl2 paralogs are found in Siberian sturgeon-foxl2 and foxl2l-but only foxl2 appeared to be associated with ovarian differentiation. With regard to the male pathway, neither 11-oxygenated androgens nor classic male genes (amh, dmrt1, sox9, and dhh) were found to be involved in male sex differentiation, leaving open the question of which genes participate in early male gonad development in this ancient fish. Taken together, these results indicate an estrogen-dependence of female sex differentiation and 11-oxygenated androgen-independence of male sex differentiation.
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Affiliation(s)
- André Lasalle
- Laboratorio de Fisiología de la Reproducción y Ecología de Peces, Instituto de Biología, Facultad de Ciencias, Universidad de la República Oriental del Uruguay, Montevideo, Uruguay
| | - Germán Benech-Correa
- Laboratorio de Fisiología de la Reproducción y Ecología de Peces, Instituto de Biología, Facultad de Ciencias, Universidad de la República Oriental del Uruguay, Montevideo, Uruguay
| | - Frédéric G Brunet
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard, Lyon, France
| | - Denise Vizziano-Cantonnet
- Laboratorio de Fisiología de la Reproducción y Ecología de Peces, Instituto de Biología, Facultad de Ciencias, Universidad de la República Oriental del Uruguay, Montevideo, Uruguay
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10
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Ludwig A, Jahrl J, Congiu L, Gessner J, Friedrich T, Lieckfeldt D, Peng Z, Boner M. Poaching and illegal trade of Danube sturgeons. Curr Biol 2023; 33:R1184-R1185. [PMID: 37989093 DOI: 10.1016/j.cub.2023.09.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/26/2023] [Accepted: 09/26/2023] [Indexed: 11/23/2023]
Abstract
A market study on sturgeon products in the Lower Danube countries (Bulgaria, Romania, Serbia and Ukraine) resulted in a total of 149 samples of caviar and meat, which we subjected to genetic-isotope analyses. The samples comprised 31 samples (21%) of illegal wild-caught origin, 17 samples (11.4%) sold in violation of CITES and EU regulations, and 47 cases (32%) of consumer deception. Although poaching and illegal wildlife trade are often considered a problem in developing countries, these findings bear evidence that a high ratio of poached sturgeon products originates from EU and accession candidate states. Therefore, caviar and sturgeon trade urgently needs improvement to ensure that sturgeon populations will have a future.
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Affiliation(s)
- Arne Ludwig
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke Str. 17, 10315 Berlin, Germany; IUCN Sturgeon Specialist Group.
| | - Jutta Jahrl
- WWF Austria, Ottakringer Straße 114-116, 1160 Vienna, Austria
| | - Leonardo Congiu
- IUCN Sturgeon Specialist Group; Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy
| | - Joern Gessner
- IUCN Sturgeon Specialist Group; Department of Fish Biology, Fisheries and Aquaculture, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587 Berlin, Germany
| | - Thomas Friedrich
- IUCN Sturgeon Specialist Group; Institute for Hydrobiology, University of Natural Resources and Life Sciences, Gregor-Mendelstr. 33, 1180 Vienna, Austria
| | - Dietmar Lieckfeldt
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke Str. 17, 10315 Berlin, Germany
| | - Zuogang Peng
- IUCN Sturgeon Specialist Group; School of Life Sciences, Southwest University, No. 1 Tiansheng Road, Chongqing 400715, China
| | - Markus Boner
- Agroisolab GmbH, Prof.-Rehm-Str. 6, 52428 Jülich, Germany
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11
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Ruan R, Li Y, Yue H, Ye H, Jin J, Wu J, Du H, Li C. Transcriptome Analyses Reveal Expression Profiles of Morphologically Undifferentiated and Differentiated Gonads of Yangtze Sturgeon Acipenser dabryanus. Genes (Basel) 2023; 14:2058. [PMID: 38003000 PMCID: PMC10671670 DOI: 10.3390/genes14112058] [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: 10/01/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Sturgeon is known as a primitive fish with the ZZ/ZW sex determination system and is highly prized for its valuable caviar. Exploring the molecular mechanisms underlying gonadal differentiation would contribute to broadening our knowledge on the genetic regulation of sex differentiation of fish, enabling improved artificial breeding and management of sturgeons. However, the mechanisms are still poorly understood in sturgeons. This study aimed to profile expression patterns between female and male gonads at morphologically undifferentiated and early differentiated stages and identify vital genes involved in gonadal sex differentiation of sturgeons. The sexes of Yangtze sturgeon (Acipenser dabryanus) juveniles were identified via the sex-specific DNA marker and histological observation. Transcriptome analyses were carried out on female and male gonads at 30, 80 and 180 days post-hatching. The results showed that there was a total of 17 overlapped DEGs in the comparison groups of between female and male gonads at the three developmental stages, in which there were three DEGs related to ovarian steroidogenesis, including hsd17b1, foxl2 and cyp19a1. The three DEGs were highly expressed in the female gonads, of which the expression levels were gradually increased with the number of days after hatching. No well-known testis-related genes were found in the overlapped DEGs. Additionally, the expression levels of hsd17b1 and cyp19a1 mRNA were decreased with the knockdown of foxl2 mRNA via siRNA. The results further suggested that foxl2 should play a crucial role in the ovarian differentiation of sturgeons. In conclusion, this study showed that more genes involved in ovarian development than testis development emerged with sexually dimorphic expression during early gonadal sex differentiation, and it provided a preliminary understanding of the molecular regulation on gonadal differentiation of sturgeons.
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Affiliation(s)
- Rui Ruan
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (R.R.); (Y.L.); (H.Y.); (H.Y.); (J.J.); (J.W.)
| | - Ying Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (R.R.); (Y.L.); (H.Y.); (H.Y.); (J.J.); (J.W.)
| | - Huamei Yue
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (R.R.); (Y.L.); (H.Y.); (H.Y.); (J.J.); (J.W.)
| | - Huan Ye
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (R.R.); (Y.L.); (H.Y.); (H.Y.); (J.J.); (J.W.)
| | - Jiali Jin
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (R.R.); (Y.L.); (H.Y.); (H.Y.); (J.J.); (J.W.)
| | - Jinping Wu
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (R.R.); (Y.L.); (H.Y.); (H.Y.); (J.J.); (J.W.)
| | - Hao Du
- Laboratory of Freshwater Fish Germplasm Resources and Biotechnology, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Chuangju Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (R.R.); (Y.L.); (H.Y.); (H.Y.); (J.J.); (J.W.)
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12
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Smith SH, Hsiung K, Böhne A. Evaluating the role of sexual antagonism in the evolution of sex chromosomes: new data from fish. Curr Opin Genet Dev 2023; 81:102078. [PMID: 37379742 DOI: 10.1016/j.gde.2023.102078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/07/2023] [Accepted: 06/07/2023] [Indexed: 06/30/2023]
Abstract
The recent increase in available molecular and genomic data for diverse taxa helps to shed new light on long-standing theories. Research into sex chromosome evolution has particularly benefited from a growing number of studies of fish, motivated by their highly diverse mechanisms of sex determination. Sexual antagonism is regularly cited as an influential force in sex chromosome emergence; however, this so far proves difficult to demonstrate. In this review, we highlight recent developments in the investigation of sexual antagonism in sex chromosome research in fish. We find strong emphasis placed on study-organism specific genomic features and patterns of recombination, rather than evidence for a comprehensive role of sexual antagonism. In this light, we discuss the alternative models of sex chromosome evolution. We conclude that fish represents a key resource for further research, provided attention is given to species-specific effects while simultaneously integrating comparative studies across taxa for a vital and comprehensive understanding of sex chromosome evolution and investigation of proposed models.
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Affiliation(s)
- Sophie Helen Smith
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 127, 53113 Bonn, Germany. https://twitter.com/@shg_smith
| | - Kevin Hsiung
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 127, 53113 Bonn, Germany. https://twitter.com/@KevinKHsiung
| | - Astrid Böhne
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 127, 53113 Bonn, Germany.
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13
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Yazdi HP, Olito C, Kawakami T, Unneberg P, Schou MF, Cloete SWP, Hansson B, Cornwallis CK. The evolutionary maintenance of ancient recombining sex chromosomes in the ostrich. PLoS Genet 2023; 19:e1010801. [PMID: 37390104 DOI: 10.1371/journal.pgen.1010801] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/28/2023] [Indexed: 07/02/2023] Open
Abstract
Sex chromosomes have evolved repeatedly across the tree of life and often exhibit extreme size dimorphism due to genetic degeneration of the sex-limited chromosome (e.g. the W chromosome of some birds and Y chromosome of mammals). However, in some lineages, ancient sex-limited chromosomes have escaped degeneration. Here, we study the evolutionary maintenance of sex chromosomes in the ostrich (Struthio camelus), where the W remains 65% the size of the Z chromosome, despite being more than 100 million years old. Using genome-wide resequencing data, we show that the population scaled recombination rate of the pseudoautosomal region (PAR) is higher than similar sized autosomes and is correlated with pedigree-based recombination rate in the heterogametic females, but not homogametic males. Genetic variation within the sex-linked region (SLR) (π = 0.001) was significantly lower than in the PAR, consistent with recombination cessation. Conversely, genetic variation across the PAR (π = 0.0016) was similar to that of autosomes and dependent on local recombination rates, GC content and to a lesser extent, gene density. In particular, the region close to the SLR was as genetically diverse as autosomes, likely due to high recombination rates around the PAR boundary restricting genetic linkage with the SLR to only ~50Kb. The potential for alleles with antagonistic fitness effects in males and females to drive chromosome degeneration is therefore limited. While some regions of the PAR had divergent male-female allele frequencies, suggestive of sexually antagonistic alleles, coalescent simulations showed this was broadly consistent with neutral genetic processes. Our results indicate that the degeneration of the large and ancient sex chromosomes of the ostrich may have been slowed by high recombination in the female PAR, reducing the scope for the accumulation of sexually antagonistic variation to generate selection for recombination cessation.
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Affiliation(s)
| | - Colin Olito
- Department of Biology, Lund University, Lund, Sweden
| | - Takeshi Kawakami
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Per Unneberg
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mads F Schou
- Department of Biology, Lund University, Lund, Sweden
| | - Schalk W P Cloete
- Directorate Animal Sciences, Western Cape Department of Agriculture, Elsenburg, South Africa
- Department of Animal Sciences, Stellenbosch University, Matieland, South Africa
| | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
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14
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Yue J, Krasovec M, Kazama Y, Zhang X, Xie W, Zhang S, Xu X, Kan B, Ming R, Filatov DA. The origin and evolution of sex chromosomes, revealed by sequencing of the Silene latifolia female genome. Curr Biol 2023:S0960-9822(23)00678-4. [PMID: 37290443 DOI: 10.1016/j.cub.2023.05.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/07/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
White campion (Silene latifolia, Caryophyllaceae) was the first vascular plant where sex chromosomes were discovered. This species is a classic model for studies on plant sex chromosomes due to presence of large, clearly distinguishable X and Y chromosomes that originated de novo about 11 million years ago (mya), but lack of genomic resources for this relatively large genome (∼2.8 Gb) remains a significant hurdle. Here we report S. latifolia female genome assembly integrated with sex-specific genetic maps of this species, focusing on sex chromosomes and their evolution. The analysis reveals a highly heterogeneous recombination landscape with strong reduction in recombination rate in the central parts of all chromosomes. Recombination on the X chromosome in female meiosis primarily occurs at the very ends, and over 85% of the X chromosome length is located in a massive (∼330 Mb) gene-poor, rarely recombining pericentromeric region (Xpr). The results indicate that the non-recombining region on the Y chromosome (NRY) initially evolved in a relatively small (∼15 Mb), actively recombining region at the end of the q-arm, possibly as a result of inversion on the nascent X chromosome. The NRY expanded about 6 mya via linkage between the Xpr and the sex-determining region, which may have been caused by expanding pericentromeric recombination suppression on the X chromosome. These findings shed light on the origin of sex chromosomes in S. latifolia and yield genomic resources to assist ongoing and future investigations into sex chromosome evolution.
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Affiliation(s)
- Jingjing Yue
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Marc Krasovec
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK; Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Yusuke Kazama
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Kenjojima, Matsuoka, Eiheiji-cho, Fukui 910-1195, Japan
| | - Xingtan Zhang
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518100, China
| | - Wangyang Xie
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shencheng Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518100, China
| | - Xiuming Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361100, China
| | - Baolin Kan
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ray Ming
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Dmitry A Filatov
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK.
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15
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Nacif CL, Kratochwil CF, Kautt AF, Nater A, Machado-Schiaffino G, Meyer A, Henning F. Molecular parallelism in the evolution of a master sex-determining role for the anti-Mullerian hormone receptor 2 gene (amhr2) in Midas cichlids. Mol Ecol 2023; 32:1398-1410. [PMID: 35403749 DOI: 10.1111/mec.16466] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/28/2022] [Accepted: 03/25/2022] [Indexed: 12/01/2022]
Abstract
The evolution of sex chromosomes and their differentiation from autosomes is a major event during genome evolution that happened many times in several lineages. The repeated evolution and lability of sex-determination mechanisms in fishes makes this a well-suited system to test for general patterns in evolution. According to current theory, differentiation is triggered by the suppression of recombination following the evolution of a new master sex-determining gene. However, the molecular mechanisms that establish recombination suppression are known from few examples, owing to the intrinsic difficulties of assembling sex-determining regions (SDRs). The development of forward-genetics and long-read sequencing have generated a wealth of data questioning central aspects of the current theory. Here, we demonstrate that sex in Midas cichlids is determined by an XY system, and identify and assemble the SDR by combining forward-genetics, long-read sequencing and optical mapping. We show how long-reads aid in the detection of artefacts in genotype-phenotype mapping that arise from incomplete genome assemblies. The male-specific region is restricted to a 100-kb segment on chromosome 4 that harbours transposable elements and a Y-specific duplicate of the anti-Mullerian receptor 2 gene, which has evolved master sex-determining functions repeatedly. Our data suggest that amhr2Y originated by an interchromosomal translocation from chromosome 20 to 4 pre-dating the split of Midas and Flier cichlids. In the latter, it is pseudogenized and translocated to another chromosome. Duplication of anti-Mullerian genes is a common route to establishing new sex determiners, highlighting the role of molecular parallelism in the evolution of sex determination.
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Affiliation(s)
- Camila L Nacif
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Cidade Universitária, Rio de Janeiro, Brazil
| | | | - Andreas F Kautt
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Alexander Nater
- Department of Biology, University of Konstanz, Konstanz, Germany
| | | | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Frederico Henning
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Cidade Universitária, Rio de Janeiro, Brazil.,Department of Biology, University of Konstanz, Konstanz, Germany
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16
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Wang Y, Cai X, Zhang Y, Hörandl E, Zhang Z, He L. The male-heterogametic sex determination system on chromosome 15 of Salix triandra and Salix arbutifolia reveals ancestral male heterogamety and subsequent turnover events in the genus Salix. Heredity (Edinb) 2023; 130:122-134. [PMID: 36593355 PMCID: PMC9981616 DOI: 10.1038/s41437-022-00586-2] [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: 09/14/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 01/03/2023] Open
Abstract
Dioecious Salix evolved more than 45 million years ago, but have homomorphic sex chromosomes, suggesting that turnover event(s) prevented major differentiation. Sex chromosome turnover events have been inferred in the sister genus Populus. The genus Salix includes two main clades, Salix and Vetrix, with several previously studied Vetrix clade species having female-heterogametic (ZW) or male-heterogametic (XY) sex-determining systems (SDSs) on chromosome 15, while three Salix clade species have XY SDSs on chromosome 7. We here studied two basal taxa of the Vetrix clade, S. arbutifolia and S. triandra using S. purpurea as the reference genome. Analyses of whole genome resequencing data for genome-wide associations (GWAS) with the sexes and genetic differentiation between the sexes (FST values) showed that both species have male heterogamety with a sex-determining locus on chromosome 15, suggesting an early turnover event within the Vetrix clade, perhaps promoted by sexually antagonistic or (and) sex-ratio selection. Changepoint analysis based on FST values identified small sex-linked regions of ~3.33 Mb and ~2.80 Mb in S. arbutifolia and S. triandra, respectively. The SDS of S. arbutifolia was consistent with recent results that used its own genome as reference. Ancestral state reconstruction of SDS suggests that at least two turnover events occurred in Salix.
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Affiliation(s)
- Yi Wang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Xinjie Cai
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yue Zhang
- Shenyang Arboretum, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Göttingen, Germany
| | - Zhixiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.
| | - Li He
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
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17
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Charlesworth D. Why and how do Y chromosome stop recombining? J Evol Biol 2023; 36:632-636. [PMID: 36683363 DOI: 10.1111/jeb.14137] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/21/2022] [Accepted: 11/24/2022] [Indexed: 01/24/2023]
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18
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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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19
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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; 12:260. [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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Affiliation(s)
| | | | | | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
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20
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Rare but Not Gone: A Relict Population of the Black Sea Ship Sturgeon Acipenser nudiventris Persists in the Rioni River, Georgia. DIVERSITY 2022. [DOI: 10.3390/d14121102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Historically, the ship sturgeon (Acipenser nudiventris) occurred in the Aral, Caspian, Azov, and Black Sea basins. However, its numbers decreased dramatically during the 20th century. It is now considered extirpated from the Aral, Azov, and Black Seas, and has almost disappeared in the Caspian Sea. A. nudiventris is listed as Critically Endangered on the IUCN Red List and, in Georgia, the species has been undetected for the last three decades. We collected 22 sightings, including nine genetic samples taken from fin clips of ship sturgeon from the Rioni River in Georgia during 2020–2022. For the genetic samples, the mitochondrial DNA control region was used for species identification. Because cases of sturgeon inter-species hybridization have been reported in the Rioni River, we used species-specific diagnostic markers and ship sturgeon-specific microsatellite markers for detecting hybridization with other sturgeon species. In addition, we used a sex-specific marker for sex identification. Based on the maternal identification, all nine individuals are identified as ship sturgeon, representing one haplotype, and the haplotype is different from all other A. nudiventris haplotypes available in GenBank. Based on genetic analysis, the specimens did not show signs of hybridization with other locally occurring species. We conclude that ship sturgeon still live in the Rioni River, and are a remnant of an older, preexisting Black Sea ship sturgeon population.
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21
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Han W, Liu L, Wang J, Wei H, Li Y, Zhang L, Guo Z, Li Y, Liu T, Zeng Q, Xing Q, Shu Y, Wang T, Yang Y, Zhang M, Li R, Yu J, Pu Z, Lv J, Lian S, Hu J, Hu X, Bao Z, Bao L, Zhang L, Wang S. Ancient homomorphy of molluscan sex chromosomes sustained by reversible sex-biased genes and sex determiner translocation. Nat Ecol Evol 2022; 6:1891-1906. [PMID: 36280781 DOI: 10.1038/s41559-022-01898-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 09/05/2022] [Indexed: 12/15/2022]
Abstract
Contrary to classic theory prediction, sex-chromosome homomorphy is prevalent in the animal kingdom but it is unclear how ancient homomorphic sex chromosomes avoid chromosome-scale degeneration. Molluscs constitute the second largest, Precambrian-originated animal phylum and have ancient, uncharacterized homomorphic sex chromosomes. Here, we profile eight genomes of the bivalve mollusc family of Pectinidae in a phylogenetic context and show 350 million years sex-chromosome homomorphy, which is the oldest known sex-chromosome homomorphy in the animal kingdom, far exceeding the ages of well-known heteromorphic sex chromosomes such as 130-200 million years in mammals, birds and flies. The long-term undifferentiation of molluscan sex chromosomes is potentially sustained by the unexpected intertwined regulation of reversible sex-biased genes, together with the lack of sexual dimorphism and occasional sex chromosome turnover. The pleiotropic constraint of regulation of reversible sex-biased genes is widely present in ancient homomorphic sex chromosomes and might be resolved in heteromorphic sex chromosomes through gene duplication followed by subfunctionalization. The evolutionary dynamics of sex chromosomes suggest a mechanism for 'inheritance' turnover of sex-determining genes that is mediated by translocation of a sex-determining enhancer. On the basis of these findings, we propose an evolutionary model for the long-term preservation of homomorphic sex chromosomes.
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Affiliation(s)
- Wentao Han
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Liangjie Liu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jing Wang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Huilan Wei
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuli Li
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lijing Zhang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhenyi Guo
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yajuan Li
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Tian Liu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qifan Zeng
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Qiang Xing
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ya Shu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Tong Wang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yaxin Yang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Meiwei Zhang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Ruojiao Li
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jiachen Yu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhongqi Pu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jia Lv
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Shanshan Lian
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jingjie Hu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Xiaoli Hu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenmin Bao
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Lisui Bao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China.
| | - Lingling Zhang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Shi Wang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China.
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22
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He L, Hörandl E. Does polyploidy inhibit sex chromosome evolution in angiosperms? FRONTIERS IN PLANT SCIENCE 2022; 13:976765. [PMID: 36212292 PMCID: PMC9541106 DOI: 10.3389/fpls.2022.976765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Dioecy is rare in flowering plants (5-6% of species), but is often controlled genetically by sex-linked regions (SLRs). It has so far been unclear whether, polyploidy affects sex chromosome evolution, as it does in animals, though polyploidy is quite common in angiosperms, including in dioecious species. Plants could be different, as, unlike many animal systems, degenerated sex chromosomes, are uncommon in plants. Here we consider sex determination in plants and plant-specific factors, and propose that constraints created at the origin of polyploids limit successful polyploidization of species with SLRs. We consider the most likely case of a polyploid of a dioecious diploid with an established SLR, and discuss the outcome in autopolyploids and allopolyploids. The most stable system possibly has an SLR on just one chromosome, with a strongly dominant genetic factor in the heterogametic sex (e.g., xxxY male in a tetraploid). If recombination occurs with its homolog, this will prevent Y chromosome degeneration. Polyploidy may also allow for reversibility of multiplied Z or X chromosomes into autosomes. Otherwise, low dosage of Y-linked SLRs compared to their multiple homologous x copies may cause loss of reliable sex-determination at higher ploidy levels. We discuss some questions that can be studied using genome sequencing, chromosome level-assemblies, gene expression studies and analysis of loci under selection.
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Affiliation(s)
- Li He
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants, University of Göttingen, Göttingen, Germany
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23
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Whole-Genome Inter-Sex Variation in Russian Sturgeon ( Acipenser gueldenstaedtii). Int J Mol Sci 2022; 23:ijms23169469. [PMID: 36012734 PMCID: PMC9409348 DOI: 10.3390/ijms23169469] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 08/17/2022] [Accepted: 08/17/2022] [Indexed: 11/17/2022] Open
Abstract
The Russian sturgeon (Acipenser gueldenstaedtii, AG) is an endangered fish species increasingly raised on fish farms for black caviar. Understanding the process of sex determination in AG is, therefore, of scientific and commercial importance. AG lacks sexual dimorphism until sexual maturation and has a predominantly octoploid genome without a definite sex chromosome. A conserved short female-specific genomic sequence was recently described, leading to the development of a genetic sex marker. However, no biological function has been reported for this sequence. Thus, the mechanism of sex determination and the overall inter-sex genomic variation in AG are still unknown. To comprehensively analyze the inter-sex genomic variation and assess the overall inter-species variation between AG and A. ruthenus (AR, sterlet), a related tetraploid sturgeon species, we performed whole-genome sequencing on DNA from 10 fish-farm-raised adult AG (5 males and 5 females). We produced a partially assembled, ~2390 MBp draft genome for AG. We validated in AG the female-specific region previously described in AR. We identified ~2.8 million loci (SNP/indels) varying between the species, but only ~7400 sex-associated loci in AG. We mapped the sex-associated AG loci to the AR genome and identified 15 peaks of sex-associated variation (10 kb segments with 30 or more sex-associated variants), 1 of which matched the previously reported sex-variable region. Finally, we identified 14 known and predicted genes in proximity to these peaks. Our analysis suggests that one or more of these genes may have functional roles in sex determination and/or sexual differentiation in sturgeons. Further functional studies are required to elucidate these roles.
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24
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Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. PLoS Genet 2022; 18:e1010226. [PMID: 35793353 PMCID: PMC9292114 DOI: 10.1371/journal.pgen.1010226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 07/18/2022] [Accepted: 04/29/2022] [Indexed: 11/19/2022] Open
Abstract
Polyploidization may precipitate dramatic changes to the genome, including chromosome rearrangements, gene loss, and changes in gene expression. In dioecious plants, the sex-determining mechanism may also be disrupted by polyploidization, with the potential evolution of hermaphroditism. However, while dioecy appears to have persisted through a ploidy transition in some species, it is unknown whether the newly formed polyploid maintained its sex-determining system uninterrupted, or whether dioecy re-evolved after a period of hermaphroditism. Here, we develop a bioinformatic pipeline using RNA-sequencing data from natural populations to demonstrate that the allopolyploid plant Mercurialis canariensis directly inherited its sex-determining region from one of its diploid progenitor species, M. annua, and likely remained dioecious through the transition. The sex-determining region of M. canariensis is smaller than that of its diploid progenitor, suggesting that the non-recombining region of M. annua expanded subsequent to the polyploid origin of M. canariensis. Homeologous pairs show partial sexual subfunctionalization. We discuss the possibility that gene duplicates created by polyploidization might contribute to resolving sexual antagonism.
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25
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Keating SE, Greenbaum E, Johnson JD, Gamble T. Identification of a cis-sex chromosome transition in banded geckos (Coleonyx, Eublepharidae, Gekkota). J Evol Biol 2022; 35:1675-1682. [PMID: 35665979 DOI: 10.1111/jeb.14022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/13/2022] [Accepted: 04/28/2022] [Indexed: 12/24/2022]
Abstract
Sex-determination systems are highly variable amongst vertebrate groups, and the prevalence of genomic data has greatly expanded our knowledge of how diverse some groups truly are. Gecko lizards are known to possess a variety of sex-determination systems, and each new study increases our knowledge of this diversity. Here, we used RADseq to identify male-specific markers in the banded gecko Coleonyx brevis, indicating this species has a XX/XY sex-determination system. Furthermore, we show that these sex-linked regions are not homologous to the XX/XY sex chromosomes of two related Coleonyx species, C. elegans and C. mitratus, suggesting that a cis-sex chromosome turnover-a change in sex chromosomes without a concomitant change in heterogamety-has occurred within the genus. These findings demonstrate the utility of genome-scale data to uncover novel sex chromosomes and further highlight the diversity of gecko sex chromosomes.
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Affiliation(s)
- Shannon E Keating
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Jerry D Johnson
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA.,Milwaukee Public Museum, Milwaukee, Wisconsin, USA.,Bell Museum of Natural History, University of Minnesota, St. Paul, Minnesota, USA
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26
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Li XY, Mei J, Ge CT, Liu XL, Gui JF. Sex determination mechanisms and sex control approaches in aquaculture animals. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1091-1122. [PMID: 35583710 DOI: 10.1007/s11427-021-2075-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/14/2022] [Indexed: 01/21/2023]
Abstract
Aquaculture is one of the most efficient modes of animal protein production and plays an important role in global food security. Aquaculture animals exhibit extraordinarily diverse sexual phenotypes and underlying mechanisms, providing an ideal system to perform sex determination research, one of the important areas in life science. Moreover, sex is also one of the most valuable traits because sexual dimorphism in growth, size, and other economic characteristics commonly exist in aquaculture animals. Here, we synthesize current knowledge of sex determination mechanisms, sex chromosome evolution, reproduction strategies, and sexual dimorphism, and also review several approaches for sex control in aquaculture animals, including artificial gynogenesis, application of sex-specific or sex chromosome-linked markers, artificial sex reversal, as well as gene editing. We anticipate that better understanding of sex determination mechanisms and innovation of sex control approaches will facilitate sustainable development of aquaculture.
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Affiliation(s)
- Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jie Mei
- College of Fisheries, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chu-Tian Ge
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, China
| | - Xiao-Li Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan, 430072, China.
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27
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Curzon AY, Shirak A, Meerson A, Degani G, Hurvitz A, Ben-Naim N, Domovitz R, Ron M, Seroussi E. Cross-species conservation of a transposase-linked element enables genetic sexing of commercial populations of Russian sturgeon (Acipenser gueldenstaedtii). Anim Genet 2022; 53:441-446. [PMID: 35288964 PMCID: PMC9311079 DOI: 10.1111/age.13188] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/24/2022] [Accepted: 02/28/2022] [Indexed: 12/01/2022]
Abstract
All‐female culture of sturgeon is essential for efficient caviar production. However, Russian sturgeon (Acipenser gueldenstaedtii) does not exhibit external sexual dimorphism, and therefore, commercial farms apply gonadal endoscopy or ultrasound at the earliest age of 4–5 years to separate the sexes, with ~90% accuracy. Recently, a dominant genomic marker (AllWSEX2) has been found with association to femaleness in sturgeons. We developed a duplex PCR (dAllWSEX2) with the adjacent bmp7 gene as an internal control, to validate an effective PCR. Robust amplification of control fragments was observed for all samples of our commercial A. gueldenstaedtii stock (n = 337). The dAllWSEX2 assay was significantly associated with sex (n = 43, p < 1.6 × 10−8), yet four (18%) of the endoscopy‐determined females were genetic males. To examine whether some females display a male genetic profile, we tested 96 egg‐producing females, which were all verified as genetic females, indicating that the observed mismatches may be attributed to wrong sexing by endoscopy. Application of dAllWSEX2 on 100 7‐month‐old fish showed no sex‐dependent differences in body weight, indicating that weighing is not an applicable tool for sorting females at a young age. Sanger sequencing of the bmp7 fragment revealed octaploidy and sex‐independent variation, suggesting that the critical sex‐determining region harboring AllWSEX2 is small. In keeping with a model of a single‐ploidy encoding female determination, AllWSEX2 showed no variation despite being a transposase‐linked repetitive element. Cross‐species conservation of AllWSEX2, and absence of annotated sex‐determination genes in this region suggests that, in sturgeons, the sex‐determining mechanism is different from mechanisms identified in other fish.
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Affiliation(s)
- Arie Y Curzon
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon, Israel.,Robert H. Smith Faculty of Agriculture Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Andrey Shirak
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon, Israel
| | - Ari Meerson
- MIGAL-Galilee Technology Center, Kiryat Shmona, Israel.,School of Science and Technology, Tel-Hai Academic College, Galilee, Israel
| | - Gad Degani
- MIGAL-Galilee Technology Center, Kiryat Shmona, Israel.,School of Science and Technology, Tel-Hai Academic College, Galilee, Israel
| | - Avshalom Hurvitz
- Caviar Galilee Agricultural Cooperative Society Ltd., Kibbutz Dan, Israel
| | - Naama Ben-Naim
- Caviar Galilee Agricultural Cooperative Society Ltd., Kibbutz Dan, Israel
| | - Roee Domovitz
- Caviar Galilee Agricultural Cooperative Society Ltd., Kibbutz Dan, Israel
| | - Micha Ron
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon, Israel
| | - Eyal Seroussi
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon, Israel
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28
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Ramos L, Antunes A. Decoding sex: Elucidating sex determination and how high-quality genome assemblies are untangling the evolutionary dynamics of sex chromosomes. Genomics 2022; 114:110277. [PMID: 35104609 DOI: 10.1016/j.ygeno.2022.110277] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 12/22/2021] [Accepted: 01/26/2022] [Indexed: 11/28/2022]
Abstract
Sexual reproduction is a diverse and widespread process. In gonochoristic species, the differentiation of sexes occurs through diverse mechanisms, influenced by environmental and genetic factors. In most vertebrates, a master-switch gene is responsible for triggering a sex determination network. However, only a few genes have acquired master-switch functions, and this process is associated with the evolution of sex-chromosomes, which have a significant influence in evolution. Additionally, their highly repetitive regions impose challenges for high-quality sequencing, even using high-throughput, state-of-the-art techniques. Here, we review the mechanisms involved in sex determination and their role in the evolution of species, particularly vertebrates, focusing on sex chromosomes and the challenges involved in sequencing these genomic elements. We also address the improvements provided by the growth of sequencing projects, by generating a massive number of near-gapless, telomere-to-telomere, chromosome-level, phased assemblies, increasing the number and quality of sex-chromosome sequences available for further studies.
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Affiliation(s)
- Luana Ramos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal.
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29
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Yano CF, Sember A, Kretschmer R, Bertollo LAC, Ezaz T, Hatanaka T, Liehr T, Ráb P, Al-Rikabi A, Viana PF, Feldberg E, de Oliveira EA, Toma GA, de Bello Cioffi M. Against the mainstream: exceptional evolutionary stability of ZW sex chromosomes across the fish families Triportheidae and Gasteropelecidae (Teleostei: Characiformes). Chromosome Res 2021; 29:391-416. [PMID: 34694531 DOI: 10.1007/s10577-021-09674-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022]
Abstract
Teleost fishes exhibit a breath-taking diversity of sex determination and differentiation mechanisms. They encompass at least nine sex chromosome systems with often low degree of differentiation, high rate of inter- and intra-specific variability, and frequent turnovers. Nevertheless, several mainly female heterogametic systems at an advanced stage of genetic differentiation and high evolutionary stability have been also found across teleosts, especially among Neotropical characiforms. In this study, we aim to characterize the ZZ/ZW sex chromosome system in representatives of the Triportheidae family (Triportheus auritus, Agoniates halecinus, and the basal-most species Lignobrycon myersi) and its sister clade Gasteropelecidae (Carnegiella strigata, Gasteropelecus levis, and Thoracocharax stellatus). We applied both conventional and molecular cytogenetic approaches including chromosomal mapping of 5S and 18S ribosomal DNA clusters, cross-species chromosome painting (Zoo-FISH) with sex chromosome-derived probes and comparative genomic hybridization (CGH). We identified the ZW sex chromosome system for the first time in A. halecinus and G. levis and also in C. strigata formerly reported to lack sex chromosomes. We also brought evidence for possible mechanisms underlying the sex chromosome differentiation, including inversions, repetitive DNA accumulation, and exchange of genetic material. Our Zoo-FISH experiments further strongly indicated that the ZW sex chromosomes of Triportheidae and Gasteropelecidae are homeologous, suggesting their origin before the split of these lineages (approx. 40-70 million years ago). Such extent of sex chromosome stability is almost exceptional in teleosts, and hence, these lineages afford a special opportunity to scrutinize unique evolutionary forces and pressures shaping sex chromosome evolution in fishes and vertebrates in general.
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Affiliation(s)
- Cassia Fernanda Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235, Sao Carlos, SP, 13565-905, Brazil
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Libechov, 277 21, Czech Republic.
| | - Rafael Kretschmer
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235, Sao Carlos, SP, 13565-905, Brazil
| | - Luiz Antônio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235, Sao Carlos, SP, 13565-905, Brazil
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235, Sao Carlos, SP, 13565-905, Brazil
| | - Thomas Liehr
- Jena University Hospital, Institute of Human Genetics, Am Klinikum 1, 07747, Jena, Germany
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Libechov, 277 21, Czech Republic
| | - Ahmed Al-Rikabi
- Jena University Hospital, Institute of Human Genetics, Am Klinikum 1, 07747, Jena, Germany
| | - Patrik Ferreira Viana
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Petropolis, Manaus, AM, Brazil
| | - Eliana Feldberg
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Petropolis, Manaus, AM, Brazil
| | - Ezequiel Aguiar de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235, Sao Carlos, SP, 13565-905, Brazil
| | - Gustavo Akira Toma
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235, Sao Carlos, SP, 13565-905, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235, Sao Carlos, SP, 13565-905, Brazil
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Adding New Pieces to the Puzzle of Karyotype Evolution in Harttia (Siluriformes, Loricariidae): Investigation of Amazonian Species. BIOLOGY 2021; 10:biology10090922. [PMID: 34571799 PMCID: PMC8472603 DOI: 10.3390/biology10090922] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/21/2022]
Abstract
A remarkable morphological diversity and karyotype variability can be observed in the Neotropical armored catfish genus Harttia. These fishes offer a useful model to explore both the evolution of karyotypes and sex chromosomes, since many species possess male-heterogametic sex chromosome systems and a high rate of karyotype repatterning. Based on the karyotype organization, the chromosomal distribution of several repetitive DNA classes, and the rough estimates of genomic divergences at the intraspecific and interspecific levels via Comparative Genomic Hybridization, we identified shared diploid chromosome numbers (2n = 54) but different karyotype compositions in H. dissidens (20m + 26sm + 8a) and Harttia sp. 3 (16m + 18sm + 14st + 6a), and different 2n in H. guianensis (2n = 58; 20m + 26sm + 2st + 10a). All species further displayed similar patterns of chromosomal distribution concerning constitutive heterochromatin, 18S ribosomal DNA (rDNA) sites, and most of the surveyed microsatellite motifs. Furthermore, differences in the distribution of 5S rDNA sites and a subset of microsatellite sequences were identified. Heteromorphic sex chromosomes were lacking in H. dissidens and H. guianensis at the scale of our analysis. However, one single chromosome pair in Harttia sp. 3 males presented a remarkable accumulation of male genome-derived probe after CGH, pointing to a tentative region of early sex chromosome differentiation. Thus, our data support already previously outlined evidence that Harttia is a vital model for the investigation of teleost karyotype and sex chromosome dynamics.
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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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Sember A, Nguyen P, Perez MF, Altmanová M, Ráb P, Cioffi MDB. Multiple sex chromosomes in teleost fishes from a cytogenetic perspective: state of the art and future challenges. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200098. [PMID: 34304595 PMCID: PMC8310710 DOI: 10.1098/rstb.2020.0098] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2020] [Indexed: 12/15/2022] Open
Abstract
Despite decades of cytogenetic and genomic research of dynamic sex chromosome evolution in teleost fishes, multiple sex chromosomes have been largely neglected. In this review, we compiled available data on teleost multiple sex chromosomes, identified major trends in their evolution and suggest further trajectories in their investigation. In a compiled dataset of 440 verified records of fish sex chromosomes, we counted 75 multiple sex chromosome systems with 60 estimated independent origins. We showed that male-heterogametic systems created by Y-autosome fusion predominate and that multiple sex chromosomes are over-represented in the order Perciformes. We documented a striking difference in patterns of differentiation of sex chromosomes between male and female heterogamety and hypothesize that faster W sex chromosome differentiation may constrain sex chromosome turnover in female-heterogametic systems. We also found no significant association between the mechanism of multiple sex chromosome formation and percentage of uni-armed chromosomes in teleost karyotypes. Last but not least, we hypothesized that interaction between fish populations, which differ in their sex chromosomes, can drive the evolution of multiple sex chromosomes in fishes. This underlines the importance of broader inter-population sampling in studies of fish sex chromosomes. 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)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Petr Nguyen
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Manolo F. Perez
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235 cep, 13565-905, São Carlos, Brazil
| | - Marie Altmanová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague, Czech Republic
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235 cep, 13565-905, São Carlos, Brazil
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Kratochvíl L, Gamble T, Rovatsos M. Sex chromosome evolution among amniotes: is the origin of sex chromosomes non-random? Philos Trans R Soc Lond B Biol Sci 2021; 376:20200108. [PMID: 34304592 PMCID: PMC8310715 DOI: 10.1098/rstb.2020.0108] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2021] [Indexed: 12/29/2022] Open
Abstract
Sex chromosomes are a great example of a convergent evolution at the genomic level, having evolved dozens of times just within amniotes. An intriguing question is whether this repeated evolution was random, or whether some ancestral syntenic blocks have significantly higher chance to be co-opted for the role of sex chromosomes owing to their gene content related to gonad development. Here, we summarize current knowledge on the evolutionary history of sex determination and sex chromosomes in amniotes and evaluate the hypothesis of non-random emergence of sex chromosomes. The current data on the origin of sex chromosomes in amniotes suggest that their evolution is indeed non-random. However, this non-random pattern is not very strong, and many syntenic blocks representing putatively independently evolved sex chromosomes are unique. Still, repeatedly co-opted chromosomes are an excellent model system, as independent co-option of the same genomic region for the role of sex chromosome offers a great opportunity for testing evolutionary scenarios on the sex chromosome evolution under the explicit control for the genomic background and gene identity. Future studies should use these systems more to explore the convergent/divergent evolution of sex chromosomes. 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
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
- Bell Museum of Natural History, University of Minnesota, Saint Paul, MN, USA
- Milwaukee Public Museum, Milwaukee, WI, USA
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, 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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Stöck M, Kratochvíl L, Kuhl H, Rovatsos M, Evans BJ, Suh A, Valenzuela N, Veyrunes F, Zhou Q, Gamble T, Capel B, Schartl M, Guiguen Y. A brief review of vertebrate sex evolution with a pledge for integrative research: towards ' sexomics'. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200426. [PMID: 34247497 PMCID: PMC8293304 DOI: 10.1098/rstb.2020.0426] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2021] [Indexed: 02/07/2023] Open
Abstract
Triggers and biological processes controlling male or female gonadal differentiation vary in vertebrates, with sex determination (SD) governed by environmental factors or simple to complex genetic mechanisms that evolved repeatedly and independently in various groups. Here, we review sex evolution across major clades of vertebrates with information on SD, sexual development and reproductive modes. We offer an up-to-date review of divergence times, species diversity, genomic resources, genome size, occurrence and nature of polyploids, SD systems, sex chromosomes, SD genes, dosage compensation and sex-biased gene expression. Advances in sequencing technologies now enable us to study the evolution of SD at broader evolutionary scales, and we now hope to pursue a sexomics integrative research initiative across vertebrates. The vertebrate sexome comprises interdisciplinary and integrated information on sexual differentiation, development and reproduction at all biological levels, from genomes, transcriptomes and proteomes, to the organs involved in sexual and sex-specific processes, including gonads, secondary sex organs and those with transcriptional sex-bias. The sexome also includes ontogenetic and behavioural aspects of sexual differentiation, including malfunction and impairment of SD, sexual differentiation and fertility. Starting from data generated by high-throughput approaches, we encourage others to contribute expertise to building understanding of the sexomes of many key vertebrate species. 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)
- 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
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czech Republic
| | - Heiner Kuhl
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries—IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
| | - Michail Rovatsos
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Ben J. Evans
- Department of Biology, McMaster University, Life Sciences Building Room 328, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK
- Department of Organismal Biology—Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Frédéric Veyrunes
- Institut des Sciences de l'Evolution de Montpellier, ISEM UMR 5554 (CNRS/Université de Montpellier/IRD/EPHE), Montpellier, France
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
- Department of Neuroscience and Developmental Biology, University of Vienna, A-1090 Vienna, Austria
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
| | - Blanche Capel
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Würzburg, 97074 Würzburg, Germany
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
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