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Wang J, Tao W, Kocher TD, Wang D. Sex chromosome turnover and biodiversity in fishes. J Genet Genomics 2024:S1673-8527(24)00222-4. [PMID: 39233051 DOI: 10.1016/j.jgg.2024.08.008] [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: 06/12/2024] [Revised: 08/22/2024] [Accepted: 08/26/2024] [Indexed: 09/06/2024]
Abstract
The impact of sex chromosomes and their turnover in speciation remains a subject of ongoing debate in the field of evolutionary biology. Fishes are the largest group of vertebrates, and they exhibit unparalleled sexual plasticity, as well as diverse sex-determining (SD) genes, sex chromosomes, and sex determination mechanisms. This diversity is hypothesized to be associated with the frequent turnover of sex chromosomes in fishes. Although it is evident that amh and amhr2 are repeatedly and independently recruited as SD genes, their relationship with the rapid turnover of sex chromosomes and the biodiversity of fishes remains unknown. We summarize the canonical models of sex chromosome turnover and highlight the vital roles of gene mutation and hybridization with empirical evidence. We revisit Haldane's rule and the large X-effect and propose the hypothesis that sex chromosomes accelerate speciation by multiplying genotypes via hybridization. By integrating recent findings on the turnover of SD genes, sex chromosomes, and sex determination systems in fish species, this review provides insights into the relationship between sex chromosome evolution and biodiversity in fishes.
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Affiliation(s)
- Jingrong Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Wenjing Tao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
| | - Deshou Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
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Behrens KA, Zimmermann H, Blažek R, Reichard M, Koblmüller S, Kocher TD. Turnover of sex chromosomes in the Lake Tanganyika cichlid tribe Tropheini (Teleostei: Cichlidae). Sci Rep 2024; 14:2471. [PMID: 38291228 PMCID: PMC10828463 DOI: 10.1038/s41598-024-53021-3] [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: 07/14/2023] [Accepted: 01/25/2024] [Indexed: 02/01/2024] Open
Abstract
Sex chromosome replacement is frequent in many vertebrate clades, including fish, frogs, and lizards. In order to understand the mechanisms responsible for sex chromosome turnover and the early stages of sex chromosome divergence, it is necessary to study lineages with recently evolved sex chromosomes. Here we examine sex chromosome evolution in a group of African cichlid fishes (tribe Tropheini) which began to diverge from one another less than 4 MYA. We have evidence for a previously unknown sex chromosome system, and preliminary indications of several additional systems not previously reported in this group. We find a high frequency of sex chromosome turnover and estimate a minimum of 14 turnovers in this tribe. We date the origin of the most common sex determining system in this tribe (XY-LG5/19) near the base of one of two major sub-clades of this tribe, about 3.4 MY ago. Finally, we observe variation in the size of one sex-determining region that suggests independent evolution of evolutionary strata in species with a shared sex-determination system. Our results illuminate the rapid rate of sex chromosome turnover in the tribe Tropheini and set the stage for further studies of the dynamics of sex chromosome evolution in this group.
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Affiliation(s)
- Kristen A Behrens
- Department of Biology, University of Maryland, College Park, MD, 20742, USA.
| | - Holger Zimmermann
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 00, Brno, Czech Republic
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Radim Blažek
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 00, Brno, Czech Republic
| | - Martin Reichard
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 00, Brno, Czech Republic
- Department of Ecology and Vertebrate Zoology, University of Łódź, Łódź, Poland
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD, 20742, USA
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Lukšíková K, Pavlica T, Altmanová M, Štundlová J, Pelikánová Š, Simanovsky SA, Krysanov EY, Jankásek M, Hiřman M, Reichard M, Ráb P, Sember A. Conserved satellite DNA motif and lack of interstitial telomeric sites in highly rearranged African Nothobranchius killifish karyotypes. JOURNAL OF FISH BIOLOGY 2023; 103:1501-1514. [PMID: 37661806 DOI: 10.1111/jfb.15550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/27/2023] [Accepted: 08/29/2023] [Indexed: 09/05/2023]
Abstract
Using African annual killifishes of the genus Nothobranchius from temporary savannah pools with rapid karyotype and sex chromosome evolution, we analysed the chromosomal distribution of telomeric (TTAGGG)n repeat and Nfu-SatC satellite DNA (satDNA; isolated from Nothobranchius furzeri) in 15 species across the Nothobranchius killifish phylogeny, and with Fundulosoma thierryi as an out-group. Our fluorescence in situ hybridization experiments revealed that all analysed taxa share the presence of Nfu-SatC repeat but with diverse organization and distribution on chromosomes. Nfu-SatC landscape was similar in conspecific populations of Nothobranchius guentheri and Nothobranchius melanospilus but slightly-to-moderately differed between populations of Nothobranchius pienaari, and between closely related Nothobranchius kuhntae and Nothobranchius orthonotus. Inter-individual variability in Nfu-SatC patterns was found in N. orthonotus and Nothobranchius krysanovi. We revealed mostly no sex-linked patterns of studied repetitive DNA distribution. Only in Nothobranchius brieni, possessing multiple sex chromosomes, Nfu-SatC repeat occupied a substantial portion of the neo-Y chromosome, similarly as formerly found in the XY sex chromosome system of turquoise killifish N. furzeri and its sister species Nothobranchius kadleci-representatives not closely related to N. brieni. All studied species further shared patterns of expected telomeric repeats at the ends of all chromosomes and no additional interstitial telomeric sites. In summary, we revealed (i) the presence of conserved satDNA class in Nothobranchius clades (a rare pattern among ray-finned fishes); (ii) independent trajectories of Nothobranchius sex chromosome differentiation, with recurrent and convergent accumulation of Nfu-SatC on the Y chromosome in some species; and (iii) genus-wide shared tendency to loss of telomeric repeats during interchromosomal rearrangements. Collectively, our findings advance our understanding of genome structure, mechanisms of karyotype reshuffling, and sex chromosome differentiation in Nothobranchius killifishes from the genus-wide perspective.
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Affiliation(s)
- Karolína Lukšíková
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tomáš Pavlica
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Marie Altmanová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jana Štundlová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
| | - Šárka Pelikánová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Sergey A Simanovsky
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Eugene Yu Krysanov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Marek Jankásek
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Matyáš Hiřman
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Reichard
- Institute of Vertebrate Biology, Czech Academy of Sciences, Czech Republic
- Department of Ecology and Vertebrate Zoology, University of Łódź, Łódź, Poland
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petr Ráb
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Alexandr Sember
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
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Smith CH, Mejia-Trujillo R, Breton S, Pinto BJ, Kirkpatrick M, Havird JC. Mitonuclear Sex Determination? Empirical Evidence from Bivalves. Mol Biol Evol 2023; 40:msad240. [PMID: 37935058 PMCID: PMC10653589 DOI: 10.1093/molbev/msad240] [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: 06/28/2023] [Revised: 10/04/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
Genetic elements encoded in nuclear DNA determine the sex of an individual in many animals. In certain bivalve lineages that possess doubly uniparental inheritance (DUI), mitochondrial DNA (mtDNA) has been hypothesized to contribute to sex determination. In these cases, females transmit a female mtDNA to all offspring, while male mtDNA (M mtDNA) is transmitted only from fathers to sons. Because M mtDNA is inherited in the same way as Y chromosomes, it has been hypothesized that mtDNA may be responsible for sex determination. However, the role of mitochondrial and nuclear genes in sex determination has yet to be validated in DUI bivalves. In this study, we used DNA, RNA, and mitochondrial short noncoding RNA (sncRNA) sequencing to explore the role of mitochondrial and nuclear elements in the sexual development pathway of the freshwater mussel Potamilus streckersoni (Bivalvia: Unionida). We found that the M mtDNA sheds a sncRNA partially within a male-specific mitochondrial gene that targets a pathway hypothesized to be involved in female development and mitophagy. RNA-seq confirmed the gene target was significantly upregulated in females, supporting a direct role of mitochondrial sncRNAs in gene silencing. These findings support the hypothesis that M mtDNA inhibits female development. Genome-wide patterns of genetic differentiation and heterozygosity did not support a nuclear sex-determining region, although we cannot reject that nuclear factors are involved with sex determination. Our results provide further evidence that mitochondrial loci contribute to diverse, nonrespiratory functions and additional insights into an unorthodox sex-determining system.
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Affiliation(s)
- Chase H Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Sophie Breton
- Department of Biological Sciences, University of Montreal, Montreal, Canada
| | - Brendan J Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Justin C Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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Sassi FDMC, Deon GA, Sember A, Liehr T, Oyakawa OT, Moreira Filho O, Bertollo LAC, Vicari MR, Cioffi MDB. Turnover of multiple sex chromosomes in Harttia catfish (Siluriformes, Loricariidae): a glimpse from whole chromosome painting. Front Genet 2023; 14:1226222. [PMID: 37576550 PMCID: PMC10421700 DOI: 10.3389/fgene.2023.1226222] [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: 05/20/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023] Open
Abstract
The remarkable fish biodiversity encompasses also great sex chromosome variability. Harttia catfish belong to Neotropical models for karyotype and sex chromosome research. Some species possess one of the three male-heterogametic sex chromosome systems, XY, X1X2Y or XY1Y2, while other members of the genus have yet uncharacterized modes of sex determination. Particularly the XY1Y2 multiple sex chromosome system shows a relatively low incidence among vertebrates, and it has not been yet thoroughly investigated. Previous research suggested two independent X-autosome fusions in Harttia which led to the emergence of XY1Y2 sex chromosome system in three of its species. In this study, we investigated evolutionary trajectories of synteny blocks involved in this XY1Y2 system by probing six Harttia species with whole chromosome painting (WCP) probes derived from the X (HCA-X) and the chromosome 9 (HCA-9) of H. carvalhoi. We found that both painting probes hybridize to two distinct chromosome pairs in Amazonian species, whereas the HCA-9 probe paints three chromosome pairs in H. guianensis, endemic to Guyanese drainages. These findings demonstrate distinct evolutionary fates of mapped synteny blocks and thereby elevated karyotype dynamics in Harttia among the three evolutionary clades.
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Affiliation(s)
| | - Geize Aparecida Deon
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czechia
| | - Thomas Liehr
- Institut für Humangenetik, Universitätsklinikum Jena, Jena, Germany
| | | | - Orlando Moreira Filho
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Luiz Antonio Carlos Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Marcelo Ricardo Vicari
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Marcelo de Bello Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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Smith CH, Mejia-Trujillo R, Breton S, Pinto BJ, Kirkpatrick M, Havird JC. Mitonuclear sex determination? Empirical evidence from bivalves. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.05.547839. [PMID: 37461691 PMCID: PMC10349986 DOI: 10.1101/2023.07.05.547839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
Genetic elements encoded in nuclear DNA determine the sex of an individual in many animals. In bivalves, however, mitochondrial DNA (mtDNA) has been hypothesized to contribute to sex determination in lineages that possess doubly uniparental inheritance (DUI). In these cases, females transmit a female mtDNA (F mtDNA) to all offspring, while male mtDNA (M mtDNA) is transmitted only from fathers to sons. Because M mtDNA is inherited in the same way as Y chromosomes, it has been hypothesized that mtDNA may be responsible for sex determination. However, the role of mitochondrial and nuclear genes in sex determination has yet to be validated in DUI bivalves. In this study, we used DNA, RNA, and mitochondrial short non-coding RNA (sncRNA) sequencing to explore the role of mitochondrial and nuclear elements in the sexual development pathway of the freshwater mussel Potamilus streckersoni (Bivalvia: Unionida). We found that the M mtDNA shed a sncRNA partially within a male-specific mitochondrial gene that targeted pathways hypothesized to be involved in female development and mitophagy. RNA-seq confirmed the gene target was significantly upregulated in females, supporting a direct role of mitochondrial sncRNAs in gene silencing. These findings support the hypothesis that M mtDNA inhibits female development. Genome-wide patterns of genetic differentiation and heterozygosity did not support a nuclear sex determining region, although we cannot reject that nuclear factors are involved with sex determination. Our results provide further evidence that mitochondrial loci contribute to diverse, non-respiratory functions and provide a first glimpse into an unorthodox sex determining system.
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Affiliation(s)
- Chase H. Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Sophie Breton
- Department of Biological Sciences, University of Montreal, Montreal, Canada
| | - Brendan J. Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Justin C. Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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