1
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Aykanat T, Jacobsen JA, Hindar K. Ontogenetic variation in the marine foraging of Atlantic salmon functionally links genomic diversity with a major life history polymorphism. Mol Ecol 2024; 33:e17465. [PMID: 38994907 DOI: 10.1111/mec.17465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 06/26/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024]
Abstract
The ecological role of heritable phenotypic variation in free-living populations remains largely unknown. Knowledge of the genetic basis of functional ecological processes can link genomic and phenotypic diversity, providing insight into polymorphism evolution and how populations respond to environmental changes. By quantifying the marine diet of Atlantic salmon, we assessed how foraging behaviour changes along the ontogeny, and in relation to genetic variation in two loci with major effects on age at maturity (six6 and vgll3). We used a two-component, zero-inflated negative binomial model to simultaneously quantify foraging frequency and foraging outcome, separately for fish and crustaceans diets. We found that older salmon forage for both prey types more actively (as evidenced by increased foraging frequency), but with a decreased efficiency (as evidenced by fewer prey in the diet), suggesting an age-dependent shift in foraging dynamics. The vgll3 locus was linked to age-dependent changes in foraging behaviour: Younger salmon with vgll3LL (the genotype associated with late maturation) tended to forage crustaceans more often than those with vgll3EE (the genotype associated with early maturation), whereas the pattern was reversed in older salmon. Vgll3 LL genotype was also linked to a marginal increase in fish acquisition, especially in younger salmon, while six6 was not a factor explaining the diet variation. Our results suggest a functional role for marine feeding behaviour linking genomic diversity at vgll3 with age at maturity among salmon, with potential age-dependent trade-offs maintaining the genetic variation. A shared genetic basis between dietary ecology and age at maturity likely subjects Atlantic salmon populations to evolution induced by bottom-up changes in marine productivity.
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Affiliation(s)
- Tutku Aykanat
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | - Kjetil Hindar
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
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2
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Hayashi S, Abe T, Igawa T, Katsura Y, Kazama Y, Nozawa M. Sex chromosome cycle as a mechanism of stable sex determination. J Biochem 2024; 176:81-95. [PMID: 38982631 PMCID: PMC11289310 DOI: 10.1093/jb/mvae045] [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: 04/26/2024] [Accepted: 06/27/2024] [Indexed: 07/11/2024] Open
Abstract
Recent advances in DNA sequencing technology have enabled the precise decoding of genomes in non-model organisms, providing a basis for unraveling the patterns and mechanisms of sex chromosome evolution. Studies of different species have yielded conflicting results regarding the traditional theory that sex chromosomes evolve from autosomes via the accumulation of deleterious mutations and degeneration of the Y (or W) chromosome. The concept of the 'sex chromosome cycle,' emerging from this context, posits that at any stage of the cycle (i.e., differentiation, degeneration, or loss), sex chromosome turnover can occur while maintaining stable sex determination. Thus, understanding the mechanisms that drive both the persistence and turnover of sex chromosomes at each stage of the cycle is crucial. In this review, we integrate recent findings on the mechanisms underlying maintenance and turnover, with a special focus on several organisms having unique sex chromosomes. Our review suggests that the diversity of sex chromosomes in the maintenance of stable sex determination is underappreciated and emphasizes the need for more research on the sex chromosome cycle.
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Affiliation(s)
- Shun Hayashi
- Amphibian Research Center, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Takuya Abe
- Division of Biochemistry, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aobaku, Sendai, Miyagi 981-8558, Japan
| | - Takeshi Igawa
- Amphibian Research Center, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Yukako Katsura
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, 41-2 Kanrin, Inuyama, Aichi 484-8506, Japan
| | - Yusuke Kazama
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Kenjojima, Matsuoka, Eiheiji, Fukui 910-1195, Japan
| | - Masafumi Nozawa
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0397, Japan
- Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0397, Japan
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3
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Behrens KA, Koblmueller S, Kocher TD. Diversity of Sex Chromosomes in Vertebrates: Six Novel Sex Chromosomes in Basal Haplochromines (Teleostei: Cichlidae). Genome Biol Evol 2024; 16:evae152. [PMID: 39073759 DOI: 10.1093/gbe/evae152] [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] [Accepted: 07/12/2024] [Indexed: 07/30/2024] Open
Abstract
African cichlid fishes are known for their high rates of phenotypic evolution. A rapid rate of diversification is apparent also in the diversity of their sex chromosomes. To date, sex determiners have been identified on 18 of 22 chromosomes in the standard karyotype. Here, we use whole-genome sequencing to characterize the sex chromosomes of seven populations of basal haplochromines, focusing on the genus Pseudocrenilabrus. We identify six new sex chromosome systems, including the first report of a cichlid sex-determining system on linkage group 12. We then quantify the rates and patterns of sex chromosome turnover in this clade. Finally, we test whether some autosomes become sex chromosomes in East African cichlids more often than expected by chance.
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Affiliation(s)
- Kristen A Behrens
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | | | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD 20742, USA
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4
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Kess T, Lehnert SJ, Bentzen P, Duffy S, Messmer A, Dempson JB, Newport J, Whidden C, Robertson MJ, Chaput G, Breau C, April J, Gillis C, Kent M, Nugent CM, Bradbury IR. Variable parallelism in the genomic basis of age at maturity across spatial scales in Atlantic Salmon. Ecol Evol 2024; 14:e11068. [PMID: 38584771 PMCID: PMC10995719 DOI: 10.1002/ece3.11068] [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: 01/06/2024] [Accepted: 01/31/2024] [Indexed: 04/09/2024] Open
Abstract
Complex traits often exhibit complex underlying genetic architectures resulting from a combination of evolution from standing variation, hard and soft sweeps, and alleles of varying effect size. Increasingly, studies implicate both large-effect loci and polygenic patterns underpinning adaptation, but the extent that common genetic architectures are utilized during repeated adaptation is not well understood. Sea age or age at maturation represents a significant life history trait in Atlantic Salmon (Salmo salar), the genetic basis of which has been studied extensively in European Atlantic populations, with repeated identification of large-effect loci. However, the genetic basis of sea age within North American Atlantic Salmon populations remains unclear, as does the potential for a parallel trans-Atlantic genomic basis to sea age. Here, we used a large single-nucleotide polymorphism (SNP) array and low-coverage whole-genome resequencing to explore the genomic basis of sea age variation in North American Atlantic Salmon. We found significant associations at the gene and SNP level with a large-effect locus (vgll3) previously identified in European populations, indicating genetic parallelism, but found that this pattern varied based on both sex and geographic region. We also identified nonrepeated sets of highly predictive loci associated with sea age among populations and sexes within North America, indicating polygenicity and low rates of genomic parallelism. Despite low genome-wide parallelism, we uncovered a set of conserved molecular pathways associated with sea age that were consistently enriched among comparisons, including calcium signaling, MapK signaling, focal adhesion, and phosphatidylinositol signaling. Together, our results indicate parallelism of the molecular basis of sea age in North American Atlantic Salmon across large-effect genes and molecular pathways despite population-specific patterns of polygenicity. These findings reveal roles for both contingency and repeated adaptation at the molecular level in the evolution of life history variation.
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Affiliation(s)
- Tony Kess
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Sarah J. Lehnert
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Paul Bentzen
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Steven Duffy
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Amber Messmer
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - J. Brian Dempson
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Jason Newport
- Marine Environmental Research Infrastructure for Data Integration and Application NetworkHalifaxNova ScotiaCanada
| | | | - Martha J. Robertson
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Gerald Chaput
- Fisheries and Oceans CanadaGulf Fisheries CentreMonctonNew BrunswickCanada
| | - Cindy Breau
- Fisheries and Oceans CanadaGulf Fisheries CentreMonctonNew BrunswickCanada
| | - Julien April
- Ministère des Forêts de la Faune et des ParcsQuebecQuebecCanada
| | - Carole‐Anne Gillis
- Gespe'gewa'gi, Mi'gma'qi, ListugujGespe'gewa'gi Institute of Natural UnderstandingQuebecQuebecCanada
| | - Matthew Kent
- Centre for Integrative GeneticsNorwegian University of Life SciencesÅsNorway
| | - Cameron M. Nugent
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Ian R. Bradbury
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
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5
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Miettinen A, Romakkaniemi A, Dannewitz J, Pakarinen T, Palm S, Persson L, Östergren J, Primmer CR, Pritchard VL. Temporal allele frequency changes in large-effect loci reveal potential fishing impacts on salmon life-history diversity. Evol Appl 2024; 17:e13690. [PMID: 38681510 PMCID: PMC11046039 DOI: 10.1111/eva.13690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/26/2024] [Accepted: 03/27/2024] [Indexed: 05/01/2024] Open
Abstract
Fishing has the potential to influence the life-history traits of exploited populations. However, our understanding of how fisheries can induce evolutionary genetic changes remains incomplete. The discovery of large-effect loci linked with ecologically important life-history traits, such as age at maturity in Atlantic salmon (Salmo salar), provides an opportunity to study the impacts of temporally varying fishing pressures on these traits. A 93-year archive of fish scales from wild Atlantic salmon catches from the northern Baltic Sea region allowed us to monitor variation in adaptive genetic diversity linked with age at maturity of wild Atlantic salmon populations. The dataset consisted of samples from both commercial and recreational fisheries that target salmon on their spawning migration. Using a genotyping-by-sequencing approach (GT-seq), we discovered strong within-season allele frequency changes at the vgll3 locus linked with Atlantic salmon age at maturity: fishing in the early season preferentially targeted the vgll3 variant linked with older maturation. We also found within-season temporal variation in catch proportions of different wild Atlantic salmon subpopulations. Therefore, selective pressures of harvesting may vary depending on the seasonal timing of fishing, which has the potential to cause evolutionary changes in key life-history traits and their diversity. This knowledge can be used to guide fisheries management to reduce the effects of fishing practices on salmon life-history diversity. Thus, this study provides a tangible example of using genomic approaches to infer, monitor and help mitigate human impacts on adaptively important genetic variation in nature.
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Affiliation(s)
- Antti Miettinen
- Organismal & Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
| | | | - Johan Dannewitz
- Department of Aquatic Resources, Institute of Freshwater ResearchSwedish University of Agricultural SciencesDrottningholmSweden
| | | | - Stefan Palm
- Department of Aquatic Resources, Institute of Freshwater ResearchSwedish University of Agricultural SciencesDrottningholmSweden
| | - Lo Persson
- Department of Wildlife, Fish and Environmental StudiesSwedish University of Agricultural SciencesUmeåSweden
| | - Johan Östergren
- Department of Aquatic Resources, Institute of Freshwater ResearchSwedish University of Agricultural SciencesDrottningholmSweden
| | - Craig R. Primmer
- Organismal & Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
| | - Victoria L. Pritchard
- Institute for Biodiversity & Freshwater ConservationUniversity of the Highlands & IslandsInvernessUK
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6
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Prokkola JM, Chew KK, Anttila K, Maamela KS, Yildiz A, Åsheim ER, Primmer CR, Aykanat T. Tissue-specific metabolic enzyme levels covary with whole-animal metabolic rates and life-history loci via epistatic effects. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220482. [PMID: 38186275 PMCID: PMC10772610 DOI: 10.1098/rstb.2022.0482] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/03/2023] [Indexed: 01/09/2024] Open
Abstract
Metabolic rates, including standard (SMR) and maximum (MMR) metabolic rate have often been linked with life-history strategies. Variation in context- and tissue-level metabolism underlying SMR and MMR may thus provide a physiological basis for life-history variation. This raises a hypothesis that tissue-specific metabolism covaries with whole-animal metabolic rates and is genetically linked to life history. In Atlantic salmon (Salmo salar), variation in two loci, vgll3 and six6, affects life history via age-at-maturity as well as MMR. Here, using individuals with known SMR and MMR with different vgll3 and six6 genotype combinations, we measured proxies of mitochondrial density and anaerobic metabolism, i.e. maximal activities of the mitochondrial citrate synthase (CS) and lactate dehydrogenase (LDH) enzymes, in four tissues (heart, intestine, liver, white muscle) across low- and high-food regimes. We found enzymatic activities were related to metabolic rates, mainly SMR, in the intestine and heart. Individual loci were not associated with the enzymatic activities, but we found epistatic effects and genotype-by-environment interactions in CS activity in the heart and epistasis in LDH activity in the intestine. These effects suggest that mitochondrial density and anaerobic capacity in the heart and intestine may partly mediate variation in metabolic rates and life history via age-at-maturity. This article is part of the theme issue 'The evolutionary significance of variation in metabolic rates'.
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Affiliation(s)
- Jenni M. Prokkola
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
- Natural Resources Institute Finland (Luke), Paavo Havaksen tie 3, 90570 Oulu, Finland
- Lammi Biological Station, University of Helsinki, Pääjärventie 320, 16900 Lammi, Finland
| | - Kuan Kiat Chew
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | - Katja Anttila
- Department of Biology, University of Turku, 20014 Turku, Finland
| | - Katja S. Maamela
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
- Lammi Biological Station, University of Helsinki, Pääjärventie 320, 16900 Lammi, Finland
- Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, 00014 Helsinki, Finland
| | - Atakan Yildiz
- Biotechnology Institute, Ankara University, Ankara 06135, Turkey
| | - Eirik R. Åsheim
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
- Lammi Biological Station, University of Helsinki, Pääjärventie 320, 16900 Lammi, Finland
- Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, 00014 Helsinki, Finland
| | - Craig R. Primmer
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
- Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, 00014 Helsinki, Finland
| | - Tutku Aykanat
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
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7
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Kitano J, Ansai S, Takehana Y, Yamamoto Y. Diversity and Convergence of Sex-Determination Mechanisms in Teleost Fish. Annu Rev Anim Biosci 2024; 12:233-259. [PMID: 37863090 DOI: 10.1146/annurev-animal-021122-113935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
Sexual reproduction is prevalent across diverse taxa. However, sex-determination mechanisms are so diverse that even closely related species often differ in sex-determination systems. Teleost fish is a taxonomic group with frequent turnovers of sex-determining mechanisms and thus provides us with great opportunities to investigate the molecular and evolutionary mechanisms underlying the turnover of sex-determining systems. Here, we compile recent studies on the diversity of sex-determination mechanisms in fish. We demonstrate that genes in the TGF-β signaling pathway are frequently used for master sex-determining (MSD) genes. MSD genes arise via two main mechanisms, duplication-and-transposition and allelic mutations, with a few exceptions. We also demonstrate that temperature influences sex determination in many fish species, even those with sex chromosomes, with higher temperatures inducing differentiation into males in most cases. Finally, we review theoretical models for the turnover of sex-determining mechanisms and discuss what questions remain elusive.
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Affiliation(s)
- Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan;
| | - Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan;
| | - Yusuke Takehana
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan;
| | - Yoji Yamamoto
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan;
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8
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Colihueque N, Parraguez M. Assessing the Effectiveness of Sex-Linked Molecular Markers to Identify Neomale Breeders for the Production of All-Female Progenies of Rainbow Trout. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:199-204. [PMID: 38227175 DOI: 10.1007/s10126-024-10288-x] [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: 10/28/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024]
Abstract
A cultured stock of masculinized rainbow trout was diagnosed with Y-linked markers (sdY and OmyY1) aiming to detect neomales before their use at the production level. To achieve a reliable diagnosis, the following steps were considered: (1) PCR amplification of the housekeeping β-actin gene to determine the DNA quality of samples, (2) validation of the Y-linked markers by their PCR amplification in male and female samples with known sex, and (3) molecular sexing of the masculinized juveniles based on male-specific (XY genotype) and neomale-specific (XX genotype) PCR product band patterns visualized on agarose gel. The validity and concordance of the markers were assessed. The housekeeping gene identified samples with negative PCR amplification revealing a poor DNA quality. The OmyY1 marker presented a more distinctive PCR product band pattern between males and females than the sdY marker and identified a higher proportion of true males (sensitivity = 1.0 and 0.91, respectively). The OmyY1 marker accurately identified 105 neomales of the 198 masculinized individuals on account their consistent and distinctive PCR product band pattern. Among both markers, there was a medium high positive concordance (γ index = 0.7). It is concluded that the OmyY1 marker shows the best performance to reliably detect neomales, a step that is essential to have certified breeders for the production of all-female progenies in fish farming.
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Affiliation(s)
- Nelson Colihueque
- Laboratorio de Biología Molecular y Citogenética, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile.
| | - Margarita Parraguez
- Laboratorio de Biología, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
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9
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Brekke C, Johnston SE, Knutsen TM, Berg P. Genetic architecture of individual meiotic crossover rate and distribution in Atlantic Salmon. Sci Rep 2023; 13:20481. [PMID: 37993527 PMCID: PMC10665409 DOI: 10.1038/s41598-023-47208-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023] Open
Abstract
Meiotic recombination through chromosomal crossovers ensures proper segregation of homologous chromosomes during meiosis, while also breaking down linkage disequilibrium and shuffling alleles at loci located on the same chromosome. Rates of recombination can vary between species, but also between and within individuals, sex and chromosomes within species. Indeed, the Atlantic salmon genome is known to have clear sex differences in recombination with female biased heterochiasmy and markedly different landscapes of crossovers between males and females. In male meiosis, crossovers occur strictly in the telomeric regions, whereas in female meiosis crossovers tend to occur closer to the centromeres. However, little is known about the genetic control of these patterns and how this differs at the individual level. Here, we investigate genetic variation in individual measures of recombination in > 5000 large full-sib families of a Norwegian Atlantic salmon breeding population with high-density SNP genotypes. We show that females had 1.6 × higher crossover counts (CC) than males, with autosomal linkage maps spanning a total of 2174 cM in females and 1483 cM in males. However, because of the extreme telomeric bias of male crossovers, female recombination is much more important for generation of new haplotypes with 8 × higher intra-chromosomal genetic shuffling than males. CC was heritable in females (h2 = 0.11) and males (h2 = 0.10), and shuffling was also heritable in both sex but with a lower heritability in females (h2 = 0.06) than in males (h2 = 0.11). Inter-sex genetic correlations for both traits were close to zero, suggesting that rates and distribution of crossovers are genetically distinct traits in males and females, and that there is a potential for independent genetic change in both sexes in the Atlantic Salmon. Together, these findings give novel insights into the genetic architecture of recombination in salmonids and contribute to a better understanding of how rates and distribution of recombination may evolve in eukaryotes more broadly.
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Affiliation(s)
- Cathrine Brekke
- Institute of Ecology and Evolution, School of Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK.
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Post Box 5003, 1433, Ås, Norway.
| | - Susan E Johnston
- Institute of Ecology and Evolution, School of Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | | | - Peer Berg
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Post Box 5003, 1433, Ås, Norway
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10
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Kuhl H, Euclide PT, Klopp C, Cabau C, Zahm M, Roques C, Iampietro C, Kuchly C, Donnadieu C, Feron R, Parrinello H, Poncet C, Jaffrelo L, Confolent C, Wen M, Herpin A, Jouanno E, Bestin A, Haffray P, Morvezen R, de Almeida TR, Lecocq T, Schaerlinger B, Chardard D, Żarski D, Larson W, Postlethwait JH, Timirkhanov S, Kloas W, Wuertz S, Stöck M, Guiguen Y. Multi-genome comparisons reveal gain-and-loss evolution of the anti-Mullerian hormone receptor type 2 gene, an old master sex determining gene, in Percidae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566804. [PMID: 38014084 PMCID: PMC10680665 DOI: 10.1101/2023.11.13.566804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplications (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19-27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome-18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variants (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in testis than ovary. Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.
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Affiliation(s)
- Heiner Kuhl
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries – IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587 Berlin, Germany
| | - Peter T Euclide
- Department of Forestry and Natural Resources | Illinois-Indiana Sea Grant, Purdue University, West Lafayette, Indiana, USA
| | - Christophe Klopp
- Sigenae, Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Cedric Cabau
- Sigenae, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Margot Zahm
- Sigenae, Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Céline Roques
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | | | - Claire Kuchly
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | | | - Romain Feron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Hugues Parrinello
- Montpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, 34094, Montpellier Cedex 05, France
| | - Charles Poncet
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Lydia Jaffrelo
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Carole Confolent
- GDEC Gentyane, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ming Wen
- INRAE, LPGP, 35000, Rennes, France
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | | | | | - Anastasia Bestin
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes cedex, France
| | - Pierrick Haffray
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes cedex, France
| | - Romain Morvezen
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes cedex, France
| | | | - Thomas Lecocq
- University of Lorraine, INRAE, UR AFPA, Nancy, France
| | | | | | - Daniel Żarski
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, ul. Tuwima 10, 10-748, Olsztyn, Poland
| | - Wes Larson
- National Oceanographic and Atmospheric Administration, National Marine Fisheries Service, Alaska Fisheries Science Center, Auke Bay Laboratories, 17109 Point Lena Loop Road, Juneau, AK, 99801, USA
| | | | | | - Werner Kloas
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries – IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587 Berlin, Germany
| | - Sven Wuertz
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries – IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587 Berlin, Germany
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries – IGB (Forschungsverbund Berlin), Müggelseedamm 301/310, D-12587 Berlin, Germany
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11
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Shen X, Yan H, Li W, Zhou H, Wang J, Zhang Q, Zhang L, Liu Q, Liu Y. Estrodiol-17β and aromatase inhibitor treatment induced alternations of genome-wide DNA methylation pattern in Takifugu rubripes gonads. Gene 2023; 882:147641. [PMID: 37460000 DOI: 10.1016/j.gene.2023.147641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/12/2023] [Accepted: 07/12/2023] [Indexed: 07/28/2023]
Abstract
Estradiol-17β (E2) and aromatase inhibitor (AI) exposure can change the phenotypic sex of fish gonads. To investigated whether alterations in DNA methylation is involved in this process, the level of genome-wide DNA methylation in Takifugu rubripes gonads was quantitatively analyzed during the E2-induced feminization and AI-induced masculinization processes in this study. The methylation levels of the total cytosine (C) in control-XX(C-XX), control-XY (C-XY), E2-treated-XY (E-XY) and AI-treated-XX (AI-XX) were 9.11%, 9.19%, 8.63% and 9.23%, respectively. In the C-XX vs C-XY comparison, 4,196 differentially methylated regions (DMRs) overlapped with the gene body of 2,497 genes and 608 DMRs overlapped with the promoter of 575 genes. In the E-XY vs C-XY comparison, 6,539 DMRs overlapped with the gene body of 3,416 genes and 856 DMRs overlapped with the promoter of 776 genes. In the AI-XX vs C-XX comparison, 2,843 DMRs overlapped with the gene body of 1,831 genes and 461 DMRs overlapped with the promoter of 421 genes. Gonadal genomic methylation mainly occurred at CG sites and the genes that overlapped with DMRs on CG context were most enriched in the signaling pathways related to gonad differentiation, such as the Wnt, TGF-β, MAPK, CAM and GnRH pathways. The DNA methylation levels of steroid synthesis genes and estrogen receptor genes promoter or gene body were negative correlated with their expression. After bisulfite sequencing verification, the DNA methylation level of the amhr2 promoter in XY was increased after E2 treatment, which consistent with the data from the genome-wide DNA methylation sequencing. In C-XY group, the expression of amhr2 was significantly higher than that in E-XY (p < 0.05). Additionally, dnmt1, which is responsible for methylation maintenance, expressed at similar level in four groups (p > 0.05). dnmt3, tet2, and setd1b, which were responsible for methylation modification, expressed at significantly higher levels in E-XY compared to the C-XY (p < 0.05). Dnmt3 and tet2 were expressed at significantly higher levels in AI-XX than that in C-XX (p < 0.05). These results indicated that E2 and AI treatment lead to the aberrant genome-wide DNA methylation level and expression level of dnmt3, tet2, and setd1b in T. rubripes gonad.
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Affiliation(s)
- Xufang Shen
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Life Sciences, Liaoning Normal University, Dalian, Liaoning 116029, China
| | - Hongwei Yan
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning 116023, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, 116023 Dalian, Liaoning, China.
| | - Weiyuan Li
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Marine Science and Environment Engineering, Dalian Ocean University, 116023 Dalian, Liaoning, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, 116023 Dalian, Liaoning, China
| | - Huiting Zhou
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning 116023, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, 116023 Dalian, Liaoning, China
| | - Jia Wang
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning 116023, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, 116023 Dalian, Liaoning, China
| | - Qi Zhang
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning 116023, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, 116023 Dalian, Liaoning, China
| | - Lei Zhang
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Marine Science and Environment Engineering, Dalian Ocean University, 116023 Dalian, Liaoning, China
| | - Qi Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Marine Science and Environment Engineering, Dalian Ocean University, 116023 Dalian, Liaoning, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, 116023 Dalian, Liaoning, China.
| | - Ying Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China
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12
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Nusbaumer D, Garaud L, de Guttry C, Ançay L, Wedekind C. Sperm of more colourful males are better adapted to ovarian fluids in lake char (Salmonidae). Mol Ecol 2023; 32:5369-5381. [PMID: 37602965 DOI: 10.1111/mec.17103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 07/11/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023]
Abstract
Fish often spawn eggs with ovarian fluids that have been hypothesized to support the sperm of some males over others (cryptic female choice). Alternatively, sperm reactions to ovarian fluids could reveal male strategies. We used wild-caught lake char (Salvelinus umbla) to experimentally test whether sperm react differently to the presence of ovarian fluid, and whether any differential sperm reaction could be predicted by male breeding coloration, male inbreeding coefficients (based of 4150 SNPs) or the kinship coefficients between males and females. Male coloration was positively linked to body size and current health (based on lymphocytosis and thrombocytosis) but was a poor predictor of inbreeding or kinship coefficients. We found that sperm of more colourful males were faster in diluted ovarian fluids than in water only, while sperm of paler males were faster in water than in ovarian fluids. We then let equal numbers of sperm compete for fertilizations in the presence or absence of ovarian fluids and genetically assigned 1464 embryos (from 70 experimental trials) to their fathers. The presence of ovarian fluids significantly increased the success of the more colourful competitors. Sperm of less inbred competitors were more successful when tested in water only than in diluted ovarian fluids. The kinship coefficients had no significant effects on sperm traits or fertilization success in the presence of ovarian fluids, although parallel stress tests on embryos had revealed that females would profit more from mating with least related males rather than most coloured ones. We conclude that sperm of more colourful males are best adapted to ovarian fluids, and that the observed reaction norms suggest male strategies rather than cryptic female choice.
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Affiliation(s)
- David Nusbaumer
- Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland
| | - Laura Garaud
- Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland
| | - Christian de Guttry
- Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland
| | - Laurie Ançay
- Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland
| | - Claus Wedekind
- Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland
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13
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Rondeau EB, Christensen KA, Johnson HA, Sakhrani D, Biagi CA, Wetklo M, Despins CA, Leggatt RA, Minkley DR, Withler RE, Beacham TD, Koop BF, Devlin RH. Insights from a chum salmon (Oncorhynchus keta) genome assembly regarding whole-genome duplication and nucleotide variation influencing gene function. G3 (BETHESDA, MD.) 2023; 13:jkad127. [PMID: 37293843 PMCID: PMC10411575 DOI: 10.1093/g3journal/jkad127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/30/2023] [Accepted: 06/04/2023] [Indexed: 06/10/2023]
Abstract
Chum salmon are ecologically important to Pacific Ocean ecosystems and commercially important to fisheries. To improve the genetic resources available for this species, we sequenced and assembled the genome of a male chum salmon using Oxford Nanopore read technology and the Flye genome assembly software (contig N50: ∼2 Mbp, complete BUSCOs: ∼98.1%). We also resequenced the genomes of 59 chum salmon from hatchery sources to better characterize the genome assembly and the diversity of nucleotide variants impacting phenotype variation. With genomic sequences from a doubled haploid individual, we were able to identify regions of the genome assembly that have been collapsed due to high sequence similarity between homeologous (duplicated) chromosomes. The homeologous chromosomes are relics of an ancient salmonid-specific genome duplication. These regions were enriched with genes whose functions are related to the immune system and responses to toxins. From analyzing nucleotide variant annotations of the resequenced genomes, we were also able to identify genes that have increased levels of variants thought to moderately impact gene function. Genes related to the immune system and the detection of chemical stimuli (olfaction) had increased levels of these variants based on a gene ontology enrichment analysis. The tandem organization of many of the enriched genes raises the question of why they have this organization.
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Affiliation(s)
- Eric B Rondeau
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Kris A Christensen
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
| | - Hollie A Johnson
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
| | - Dionne Sakhrani
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
| | - Carlo A Biagi
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
| | - Mike Wetklo
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Cody A Despins
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
| | - Rosalind A Leggatt
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
| | - David R Minkley
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
| | - Ruth E Withler
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Terry D Beacham
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada
| | - Robert H Devlin
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC V7V 1N6, Canada
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14
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Müller S, Du K, Guiguen Y, Pichler M, Nakagawa S, Stöck M, Schartl M, Lamatsch DK. Massive expansion of sex-specific SNPs, transposon-related elements, and neocentromere formation shape the young W-chromosome from the mosquitofish Gambusia affinis. BMC Biol 2023; 21:109. [PMID: 37189152 DOI: 10.1186/s12915-023-01607-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/27/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND The Western mosquitofish, Gambusia affinis, is a model for sex chromosome organization and evolution of female heterogamety. We previously identified a G. affinis female-specific marker, orthologous to the aminomethyl transferase (amt) gene of the related platyfish (Xiphophorus maculatus). Here, we have analyzed the structure and differentiation of the G. affinis W-chromosome, using a cytogenomics and bioinformatics approach. RESULTS The long arm of the G. affinis W-chromosome (Wq) is highly enriched in dispersed repetitive sequences, but neither heterochromatic nor epigenetically silenced by hypermethylation. In line with this, Wq sequences are highly transcribed, including an active nucleolus organizing region (NOR). Female-specific SNPs and evolutionary young transposable elements were highly enriched and dispersed along the W-chromosome long arm, suggesting constrained recombination. Wq copy number expanded elements also include female-specific transcribed sequences from the amt locus with homology to TE. Collectively, the G. affinis W-chromosome is actively differentiating by sex-specific copy number expansion of transcribed TE-related elements, but not (yet) by extensive sequence divergence or gene decay. CONCLUSIONS The G. affinis W-chromosome exhibits characteristic genomic properties of an evolutionary young sex chromosome. Strikingly, the observed sex-specific changes in the genomic landscape are confined to the W long arm, which is separated from the rest of the W-chromosome by a neocentromere acquired during sex chromosome evolution and may thus have become functionally insulated. In contrast, W short arm sequences were apparently shielded from repeat-driven differentiation, retained Z-chromosome like genomic features, and may have preserved pseudo-autosomal properties.
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Affiliation(s)
- Stefan Müller
- Institute of Human Genetics, Munich University Hospital, Ludwig Maximilians University, Munich, Germany.
| | - Kang Du
- Department of Chemistry and Biochemistry, The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA
| | | | - Maria Pichler
- Universität Innsbruck, Research Department for Limnology, Mondsee, Mondsee, Austria
| | - Shinichi Nakagawa
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Matthias Stöck
- Leibniz-Institute for Freshwater Ecology and Inland Fisheries (IGB), Department of Ecophysiology and Aquaculture, Berlin, Germany
- Amphibian Research Center, Hiroshima University, Higashihiroshima, 739-8526, Japan
| | - Manfred Schartl
- Department of Chemistry and Biochemistry, The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA
- Developmental Biochemistry, University of Würzburg, BiozentrumWürzburg, Germany
| | - Dunja K Lamatsch
- Universität Innsbruck, Research Department for Limnology, Mondsee, Mondsee, Austria.
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15
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Balogh RE, Csorbai B, Guti C, Keszte S, Urbányi B, Orbán L, Kovács B. Validation of a male-specific DNA marker confirms XX/XY-type sex determination in several Hungarian strains of African catfish (Clarias gariepinus). Theriogenology 2023; 205:106-113. [PMID: 37116410 DOI: 10.1016/j.theriogenology.2023.04.017] [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: 12/19/2022] [Revised: 03/24/2023] [Accepted: 04/15/2023] [Indexed: 04/30/2023]
Abstract
African catfish (Clarias gariepinus) is a promising food fish species with significant potential and growing mass of production in freshwater aquaculture. Male African catfish possess improved production characteristics over females, therefore the use of monosex populations could be advantageous for aquaculture production. However, our knowledge about the sex determination mechanism of this species is still limited and controversial. A previously isolated male-specific DNA marker (CgaY1) was validated using offspring groups from targeted crosses (n = 630) and it was found to predict the sex of 608 individuals correctly (96.43% accuracy). Using the proportion of recombinants, we estimated the average genetic distance between the potential sex determination locus and the sex-specific marker to be 3.57 cM. As an earlier study suggested that both XX/XY and ZZ/ZW systems coexist in this species, we tested the applicability of their putative 'moderately sex-linked loci' and found that no sex-specific amplification could be detected for any of them. In addition, temperature-induced masculinization suggested by others was also tested, but no such effect was detected in our stocks when the published parameters were used for heat treatment. Altogether, our results support an exclusive XX/XY sex determination system in our African catfish stock and indicate a good potential for the future use of this male-specific DNA marker in research and commercial production.
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Affiliation(s)
- Réka Enikő Balogh
- Institute of Aquaculture and Environmental Safety, Szent István Campus, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Balázs Csorbai
- Institute of Aquaculture and Environmental Safety, Szent István Campus, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Csaba Guti
- The Hungarian National Fishing Association, Budapest, Hungary
| | - Szilvia Keszte
- Institute of Aquaculture and Environmental Safety, Szent István Campus, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Béla Urbányi
- Institute of Aquaculture and Environmental Safety, Szent István Campus, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - László Orbán
- Frontline Fish Genomics Research Group, Department of Applied Fish Biology, Institute of Aquaculture and Environmental Safety, Georgikon Campus, Hungarian University of Agriculture and Life Sciences, Keszthely, Hungary.
| | - Balázs Kovács
- Institute of Aquaculture and Environmental Safety, Szent István Campus, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary.
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16
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XY sex determination in a cnidarian. BMC Biol 2023; 21:32. [PMID: 36782149 PMCID: PMC9926710 DOI: 10.1186/s12915-023-01532-2] [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: 06/07/2022] [Accepted: 01/31/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Sex determination occurs across animal species, but most of our knowledge about its mechanisms comes from only a handful of bilaterian taxa. This limits our ability to infer the evolutionary history of sex determination within animals. RESULTS In this study, we generated a linkage map of the genome of the colonial cnidarian Hydractinia symbiolongicarpus and used it to demonstrate that this species has an XX/XY sex determination system. We demonstrate that the X and Y chromosomes have pseudoautosomal and non-recombining regions. We then use the linkage map and a method based on the depth of sequencing coverage to identify genes encoded in the non-recombining region and show that many of them have male gonad-specific expression. In addition, we demonstrate that recombination rates are enhanced in the female genome and that the haploid chromosome number in Hydractinia is n = 15. CONCLUSIONS These findings establish Hydractinia as a tractable non-bilaterian model system for the study of sex determination and the evolution of sex chromosomes.
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17
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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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18
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de la Herrán R, Hermida M, Rubiolo JA, Gómez-Garrido J, Cruz F, Robles F, Navajas-Pérez R, Blanco A, Villamayor PR, Torres D, Sánchez-Quinteiro P, Ramirez D, Rodríguez ME, Arias-Pérez A, Cross I, Duncan N, Martínez-Peña T, Riaza A, Millán A, De Rosa MC, Pirolli D, Gut M, Bouza C, Robledo D, Rebordinos L, Alioto T, Ruíz-Rejón C, Martínez P. A chromosome-level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex-determining gene in the flatfish Solea senegalensis. Mol Ecol Resour 2023; 23:886-904. [PMID: 36587276 DOI: 10.1111/1755-0998.13750] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/23/2022] [Accepted: 12/28/2022] [Indexed: 01/02/2023]
Abstract
Sex determination (SD) shows huge variation among fish and a high evolutionary rate, as illustrated by the Pleuronectiformes (flatfishes). This order is characterized by its adaptation to demersal life, compact genomes and diversity of SD mechanisms. Here, we assembled the Solea senegalensis genome, a flatfish of great commercial value, into 82 contigs (614 Mb) combining long- and short-read sequencing, which were next scaffolded using a highly dense genetic map (28,838 markers, 21 linkage groups), representing 98.9% of the assembly. Further, we established the correspondence between the assembly and the 21 chromosomes by using BAC-FISH. Whole genome resequencing of six males and six females enabled the identification of 41 single nucleotide polymorphism variants in the follicle stimulating hormone receptor (fshr) consistent with an XX/XY SD system. The observed sex association was validated in a broader independent sample, providing a novel molecular sexing tool. The fshr gene displayed differential expression between male and female gonads from 86 days post-fertilization, when the gonad is still an undifferentiated primordium, concomitant with the activation of amh and cyp19a1a, testis and ovary marker genes, respectively, in males and females. The Y-linked fshr allele, which included 24 nonsynonymous variants and showed a highly divergent 3D protein structure, was overexpressed in males compared to the X-linked allele at all stages of gonadal differentiation. We hypothesize a mechanism hampering the action of the follicle stimulating hormone driving the undifferentiated gonad toward testis.
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Affiliation(s)
- Roberto de la Herrán
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Miguel Hermida
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Juan Andres Rubiolo
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Jèssica Gómez-Garrido
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona, Spain
| | - Fernando Cruz
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona, Spain
| | - Francisca Robles
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Rafael Navajas-Pérez
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Andres Blanco
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Paula Rodriguez Villamayor
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Dorinda Torres
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Pablo Sánchez-Quinteiro
- Departamento de Anatomía, Producción Animal y Ciencias Clínicas Veterinarias Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Daniel Ramirez
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Maria Esther Rodríguez
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Alberto Arias-Pérez
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Ismael Cross
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Neil Duncan
- IRTA Sant Carles de la Rapita, Tarragona, Spain
| | | | - Ana Riaza
- Stolt Sea Farm SA, Departamento I+D, A Coruña, Spain
| | | | - M Cristina De Rosa
- Institute of Chemical Sciences and Technologies "Giulio Natta" (SCITEC) - CNR c/o Catholic University of Rome, Rome, Italy
| | - Davide Pirolli
- Institute of Chemical Sciences and Technologies "Giulio Natta" (SCITEC) - CNR c/o Catholic University of Rome, Rome, Italy
| | - Marta Gut
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona, Spain
| | - Carmen Bouza
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Laureana Rebordinos
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Tyler Alioto
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carmelo Ruíz-Rejón
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Paulino Martínez
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
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Valette T, Leitwein M, Lascaux JM, Desmarais E, Berrebi P, Guinand B. Redundancy analysis, genome-wide association studies and the pigmentation of brown trout (Salmo trutta L.). JOURNAL OF FISH BIOLOGY 2023; 102:96-118. [PMID: 36218076 DOI: 10.1111/jfb.15243] [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: 09/26/2021] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
The association of molecular variants with phenotypic variation is a main issue in biology, often tackled with genome-wide association studies (GWAS). GWAS are challenging, with increasing, but still limited, use in evolutionary biology. We used redundancy analysis (RDA) as a complimentary ordination approach to single- and multitrait GWAS to explore the molecular basis of pigmentation variation in brown trout (Salmo trutta) belonging to wild populations impacted by hatchery fish. Based on 75,684 single nucleotide polymorphic (SNP) markers, RDA, single- and multitrait GWAS allowed the extraction of 337 independent colour patterning loci (CPLs) associated with trout pigmentation traits, such as the number of red and black spots on flanks. Collectively, these CPLs (i) mapped onto 35 out of 40 brown trout linkage groups indicating a polygenic genomic architecture of pigmentation, (ii) were found to be associated with 218 candidate genes, including 197 genes formerly mentioned in the literature associated to skin pigmentation, skin patterning, differentiation or structure notably in a close relative, the rainbow trout (Onchorhynchus mykiss), and (iii) related to functions relevant to pigmentation variation (e.g., calcium- and ion-binding, cell adhesion). Annotated CPLs include genes with well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also markers associated with genes formerly found expressed in rainbow or brown trout skins. RDA was also shown to be useful to investigate management issues, especially the dynamics of trout pigmentation submitted to several generations of hatchery introgression.
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20
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Dysin AP, Shcherbakov YS, Nikolaeva OA, Terletskii VP, Tyshchenko VI, Dementieva NV. Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics. Genes (Basel) 2022; 13:genes13122221. [PMID: 36553488 PMCID: PMC9778375 DOI: 10.3390/genes13122221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/19/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic salmon (Salmo salar L.), was not without reason one of the first fish species for which a high-quality reference genome assembly was produced and published. Genomic advancements are becoming increasingly essential in both the genetic enhancement of farmed salmon and the conservation of wild salmon stocks. The salmon genome has also played a significant role in influencing our comprehension of the evolutionary and functional ramifications of the ancestral whole-genome duplication event shared by all Salmonidae species. Here we provide an overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species, focusing on those studies that aim to advance our understanding of salmonid ecology, physiology, and evolution, particularly for the purpose of improving aquaculture production. This review should make potential researchers pay attention to the current state of research on the salmonid genome, which should potentially attract interest in this important problem, and hence the application of new technologies (such as genome editing) in uncovering the genetic and evolutionary features of salmoniforms that underlie functional variation in traits of commercial and scientific importance.
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Affiliation(s)
- Artem P. Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
- Correspondence:
| | - Yuri S. Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Olga A. Nikolaeva
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Valerii P. Terletskii
- All-Russian Research Veterinary Institute of Poultry Science-Branch of the Federal Scientific Center, All-Russian Research and Technological Poultry Institute (ARRVIPS), Lomonosov, 198412 St. Petersburg, Russia
| | - Valentina I. Tyshchenko
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Natalia V. Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
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21
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Liu Z, Zhou T, Gao D. Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture. Front Genet 2022; 13:994471. [PMID: 36406125 PMCID: PMC9666392 DOI: 10.3389/fgene.2022.994471] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/20/2022] [Indexed: 11/25/2022] Open
Abstract
Major progress has been made with genomic and genetic studies in aquaculture in the last decade. However, research on epigenetic regulation of aquaculture traits is still at an early stage. It is apparent that most, if not all, aquaculture traits are regulated at both genetic and epigenetic levels. This paper reviews recent progress in understanding of genetic and epigenetic regulation of important aquaculture traits such as growth, reproduction, disease resistance, and stress responses. Although it is challenging to make generalized statements, DNA methylation is mostly correlated with down-regulation of gene expression, especially when at promoters and enhancers. As such, methylation of growth factors and their receptors is negatively correlated with growth; hypomethylation of genes important for stress tolerance is correlated with increased stress tolerance; hypomethylation of genes important for male or female sex differentiation leads to sex differentiation into males or females, respectively. It is apparent that environmental regulation of aquaculture traits is mediated at the level of epigenetic regulation, and such environment-induced epigenetic changes appeared to be intergenerationally inherited, but evidences for transgenerational inheritance are still limited.
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Affiliation(s)
- Zhanjiang Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States,*Correspondence: Zhanjiang Liu,
| | - Tao Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Dongya Gao
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States
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22
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Hattori RS, Kumazawa K, Nakamoto M, Nakano Y, Yamaguchi T, Kitano T, Yamamoto E, Fuji K, Sakamoto T. Y-specific amh allele, amhy, is the master sex-determining gene in Japanese flounder Paralichthys olivaceus. Front Genet 2022; 13:1007548. [PMID: 36186422 PMCID: PMC9523440 DOI: 10.3389/fgene.2022.1007548] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 08/25/2022] [Indexed: 01/12/2023] Open
Abstract
Japanese flounder (Paralichthys olivaceus) is an important marine fish species of both fisheries and aquaculture in Northeast Asia. The commercial interest for all-female progenies due to several sex-related traits has prompted basic research on the mechanisms of sex determination in this species. By conducting a linkage analysis of the sex-determining locus, we initially identified 12 microsatellite markers linked to sex in 11 scaffolds, whose localization was restricted to a specific region of linkage group 9. Sequence analysis of this region identified 181 genes based on the UniProt database annotations. Among them, the amh gene was considered a potential candidate for sex determination because this gene is known to have taken over the role of sex determination in many teleosts. An in-depth sequence analysis of both the coding and non-coding regions of amh in XX and XY individuals detected nine SNPs linked with maleness. However, because these substitutions were synonymous, the upstream and downstream regions of amh were also investigated and a male-specific variant with deletions in the promoter region was detected. This truncated Y-specific amh variant was named amhy, and the amh shared by both sexes was named amhx. The association analysis using both females and males of the genotypic sex inferred by the presence/absence of amhy found complete association with phenotypic sex and genotype. Gene expression analysis in larvae derived from a single-pair progeny by quantitative real-time PCR detected amhy transcripts in the larval trunks between 20 and 100 days after hatching only in XY larvae. Localization of amhy by in situ hybridization was detected in presumptive Sertoli cells of XY gonads. Expression of amhx was almost undetectable in both XX and XY genotypes. Loss of Amh function by CRISPR-Cas9 induced male-to-female sex reversal, indicating that this gene was necessary for the masculinization of XY individuals. In conclusion, the complete linkage of amhy with males, its early expression in XY gonads before testicular differentiation, and the induction of sex reversal by loss-of-function mutation support the view that amhy is the sex-determining gene in this species.
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Affiliation(s)
- Ricardo Shohei Hattori
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Keiichiro Kumazawa
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Masatoshi Nakamoto
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Yuki Nakano
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Toshiya Yamaguchi
- Nansei Field Station, National Research and Development Agency, Japan Fisheries Research and Education Agency, Mie, Japan
| | - Takeshi Kitano
- Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Eiichi Yamamoto
- Tottori Prefectural Fisheries Experimental Station, Tottori, Japan
| | - Kanako Fuji
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Takashi Sakamoto
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
- *Correspondence: Takashi Sakamoto,
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Yu Y, Chen M, Lu ZY, Liu Y, Li B, Gao ZX, Shen ZG. High-temperature stress will put the thermo-sensitive teleost yellow catfish (Tachysurus fulvidraco) in danger through reducing reproductivity. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 239:113638. [PMID: 35597142 DOI: 10.1016/j.ecoenv.2022.113638] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/28/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Recently, concerns for species that sex differentiation is influenced by temperature in the context of global warming have increased because disrupted operational sex ratios could threaten population maintenance. In contrast, little attention has been given to the reproductive ability of populations that experienced elevated temperatures. In this study, we demonstrated that high temperature (HT) would decrease population size via three different aspects of reproductive ability for the first time. We show that, in a thermo-sensitive teleost yellow catfish, a short period of HT (+3 °C) exposure during the critical period of sex differentiation leads to a different percentage of masculinization of XX genotypic females (1-23%) in wet-lab and natural water bodies. Combining the results of gonadal appearance, histology, sperm parameters, and fertilization rate, we found that XX pseudo-males induced by HT display significantly discounted fertility and reproductive performance compared to XY normal males. We demonstrate that the survival of the XY genotype is lower than XX genotype under environmental stress, including HT, hypoxia, and parasite infection, and the differential survival seems unrelated to male-biased sexual size dimorphism. The mathematical model predicts that the phenotypic female percent will be stabilized at 50% and the population will be sustainably maintained when masculinizing force is less than 0.5, while HT will put the population in danger when the masculinizing force exceeds 0.5. However, when we combine the real-world data of reproductive ability and mathematic model, our results suggest the population size decreases and the long-term survival of the studied species are threatened under the projected pace of increasing temperature. These findings will be useful for understanding the long-term effects of increasing temperature on sex ratio, reproduction and population maintenance in teleost.
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Affiliation(s)
- Yue Yu
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Huazhong Agricultural University, Wuhan, PR China
| | - Min Chen
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Huazhong Agricultural University, Wuhan, PR China
| | - Zi-Yi Lu
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Huazhong Agricultural University, Wuhan, PR China
| | - Ya Liu
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Huazhong Agricultural University, Wuhan, PR China
| | - Bo Li
- Institute of Fisheries, Wuhan Academy of Agricultural Sciences, Wuhan, PR China
| | - Ze-Xia Gao
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Huazhong Agricultural University, Wuhan, PR China
| | - Zhi-Gang Shen
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Huazhong Agricultural University, Wuhan, PR China.
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24
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Zhu C, Liu H, Pan Z, Cheng L, Sun Y, Wang H, Chang G, Wu N, Ding H, Zhao H, Zhang L, Yu X. Insights into chromosomal evolution and sex determination of Pseudobagrus ussuriensis (Bagridae, Siluriformes) based on a chromosome-level genome. DNA Res 2022; 29:6647841. [PMID: 35861402 PMCID: PMC9358014 DOI: 10.1093/dnares/dsac028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/20/2022] [Indexed: 12/01/2022] Open
Abstract
Pseudobagrus ussuriensis is an aquaculture catfish with significant sexual dimorphism. In this study, a chromosome-level genome with a size of 741.97 Mb was assembled for female P. ussuriensis. A total of 26 chromosome-level contigs covering 97.34% of the whole-genome assembly were obtained with an N50 of 28.53 Mb and an L50 of 11. A total of 24,075 protein-coding genes were identified, with 91.54% (22,039) genes being functionally annotated. Based on the genome assembly, four chromosome evolution clusters of catfishes were identified and the formation process of P. ussuriensis chromosomes was predicted. A total of 55 sex-related quantitative trait loci (QTLs) with a phenotypic variance explained value of 100% were located on chromosome 8 (chr08). The QTLs and other previously identified sex-specific markers were located in a sex-determining region of 16.83 Mb (from 6.90 to 23.73 Mb) on chr08, which was predicted as the X chromosome. The sex-determining region comprised 554 genes, with 135 of which being differently expressed between males and females/pseudofemales, and 16 candidate sex-determining genes were screened out. The results of this study provided a useful chromosome-level genome for genetic, genomic and evolutionary studies of P. ussuriensis, and also be useful for further studies on sex-determination mechanism analysis and sex-control breeding of this fish.
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Affiliation(s)
- Chuankun Zhu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Haiyang Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou 510380, China
| | - Zhengjun Pan
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Lei Cheng
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences , Harbin 150070, China
| | - Yanhong Sun
- Wuhan Aquaculture Science Research Institute , Wuhan 430207, China
| | - Hui Wang
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Guoliang Chang
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Nan Wu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Huaiyu Ding
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Haitao Zhao
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Lei Zhang
- Key Laboratory of Fishery Sustainable Development and Water Environment Protection of Huai’an City, Huai’an Sub Center of the Institute of Hydrobiology, Chinese Academy of Sciences , Huai’an 223002, China
| | - Xiangsheng Yu
- Huai’an Fisheries Technical Guidance Station , Huai’an 223001, China
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25
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Jordan-Ward R, von Hippel FA, Zheng G, Salamova A, Dillon D, Gologergen J, Immingan T, Dominguez E, Miller P, Carpenter D, Postlethwait JH, Byrne S, Buck CL. Elevated mercury and PCB concentrations in Dolly Varden (Salvelinus malma) collected near a formerly used defense site on Sivuqaq, Alaska. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 826:154067. [PMID: 35217049 PMCID: PMC9078153 DOI: 10.1016/j.scitotenv.2022.154067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/11/2022] [Accepted: 02/17/2022] [Indexed: 04/13/2023]
Abstract
Environmental pollution causes adverse health effects in many organisms and contributes to health disparities for Arctic communities that depend on subsistence foods, including the Yupik residents of Sivuqaq (St. Lawrence Island), Alaska. Sivuqaq's proximity to Russia made it a strategic location for U.S. military defense sites during the Cold War. Two radar surveillance stations were installed on Sivuqaq, including at the Northeast Cape. High levels of persistent organic pollutants and toxic metals continue to leach from the Northeast Cape formerly used defense (FUD) site despite remediation efforts. We quantified total mercury (Hg) and polychlorinated biphenyl (PCB) concentrations, and carbon and nitrogen stable isotope signatures, in skin and muscle samples from Dolly Varden (Salvelinus malma), an important subsistence species. We found that Hg and PCB concentrations significantly differed across locations, with the highest concentrations found in fish collected near the FUD site. We found that 89% of fish collected from near the FUD site had Hg concentrations that exceeded the U.S. Environmental Protection Agency's (EPA) unlimited Hg-contaminated fish consumption screening level for subsistence fishers (0.049 μg/g). All fish sampled near the FUD site exceeded the EPA's PCB guidelines for cancer risk for unrestricted human consumption (0.0015 μg/g ww). Both Hg and PCB concentrations had a significant negative correlation with δ13C when sites receiving input from the FUD site were included in the analysis, but these relationships were insignificant when input sites were excluded. δ15N had a significant negative correlation with Hg concentration, but not with PCB concentration. These results suggest that the Northeast Cape FUD site remains a point source of Hg and PCB pollution and contributes to higher concentrations in resident fish, including subsistence species. Moreover, elevated Hg and PCB levels in fish near the FUD site may pose a health risk for Sivuqaq residents.
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Affiliation(s)
- Renee Jordan-Ward
- Department of Biological Sciences, Northern Arizona University, 617 S. Beaver St., Flagstaff, AZ 86011, USA
| | - Frank A von Hippel
- Department of Community, Environment and Policy, Mel & Enid Zuckerman College of Public Health, University of Arizona, 1295 N. Martin Ave., P.O. Box 245210, Tucson, AZ 85724, USA.
| | - Guomao Zheng
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Amina Salamova
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Danielle Dillon
- Department of Biological Sciences, Northern Arizona University, 617 S. Beaver St., Flagstaff, AZ 86011, USA
| | - Jesse Gologergen
- Alaska Community Action on Toxics, 1225 E. International Airport Road, Suite 220, Anchorage, AK 99518, USA
| | - Tiffany Immingan
- Alaska Community Action on Toxics, 1225 E. International Airport Road, Suite 220, Anchorage, AK 99518, USA
| | - Elliott Dominguez
- Department of Biological Sciences, Northern Arizona University, 617 S. Beaver St., Flagstaff, AZ 86011, USA
| | - Pamela Miller
- Alaska Community Action on Toxics, 1225 E. International Airport Road, Suite 220, Anchorage, AK 99518, USA
| | - David Carpenter
- Institute for Health and the Environment, University at Albany, 5 University Place, Rensselaer, NY 12144, USA
| | - John H Postlethwait
- Institute of Neuroscience, University of Oregon, 1254 University of Oregon, Eugene, OR 97403, USA
| | - Samuel Byrne
- Middlebury College, Department of Biology and Global Health Program, 14 Old Chapel Rd, Middlebury, VT 05753, USA
| | - C Loren Buck
- Department of Biological Sciences, Northern Arizona University, 617 S. Beaver St., Flagstaff, AZ 86011, USA
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26
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Gabián M, Morán P, Saura M, Carvajal-Rodríguez A. Detecting Local Adaptation between North and South European Atlantic Salmon Populations. BIOLOGY 2022; 11:933. [PMID: 35741456 PMCID: PMC9219887 DOI: 10.3390/biology11060933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/09/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Pollution and other anthropogenic effects have driven a decrease in Atlantic salmon (Salmo salar) in the Iberian Peninsula. The restocking effort carried out in the 1980s, with salmon from northern latitudes with the aim of mitigating the decline of native populations, failed, probably due to the deficiency in adaptation of foreign salmon from northern Europe to the warm waters of the Iberian Peninsula. This result would imply that the Iberian populations of Atlantic salmon have experienced local adaptation in their past evolutionary history, as has been described for other populations of this species and other salmonids. Local adaptation can occur by divergent selections between environments, favoring the fixation of alleles that increase the fitness of a population in the environment it inhabits relative to other alleles favored in another population. In this work, we compared the genomes of different populations from the Iberian Peninsula (Atlantic and Cantabric basins) and Scotland in order to provide tentative evidence of candidate SNPs responsible for the adaptive differences between populations, which may explain the failures of restocking carried out during the 1980s. For this purpose, the samples were genotyped with a 220,000 high-density SNP array (Affymetrix) specific to Atlantic salmon. Our results revealed potential evidence of local adaptation for North Spanish and Scottish populations. As expected, most differences concerned the comparison of the Iberian Peninsula with Scotland, although there were also differences between Atlantic and Cantabric populations. A high proportion of the genes identified are related to development and cellular metabolism, DNA transcription and anatomical structure. A particular SNP was identified within the NADP-dependent malic enzyme-2 (mMEP-2*), previously reported by independent studies as a candidate for local adaptation in salmon from the Iberian Peninsula. Interestingly, the corresponding SNP within the mMEP-2* region was consistent with a genomic pattern of divergent selection.
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Affiliation(s)
- María Gabián
- Centro de Investigación Mariña (CIM), Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310 Vigo, Spain; (M.G.); (P.M.)
| | - Paloma Morán
- Centro de Investigación Mariña (CIM), Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310 Vigo, Spain; (M.G.); (P.M.)
| | - María Saura
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), 28040 Madrid, Spain;
| | - Antonio Carvajal-Rodríguez
- Centro de Investigación Mariña (CIM), Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310 Vigo, Spain; (M.G.); (P.M.)
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27
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Repeated translocation of a supergene underlying rapid sex chromosome turnover in Takifugu pufferfish. Proc Natl Acad Sci U S A 2022; 119:e2121469119. [PMID: 35658077 DOI: 10.1073/pnas.2121469119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceAlthough turnover of sex chromosomes is very common in many vertebrate lineages, the transition process is still elusive. We studied the sex-determining region (SDR) of 12 congeneric fish species of Takifugu fish that compose an important model for the study of genomics and sex determination. We found that while nine species retained their ancestral SDR, three species had acquired derived SDRs. Although the derived SDRs resided in three different chromosomes, they harbored a shared supergene flanked by two putative transposable elements. The results highlight the underestimated role of a mobile supergene in turnover of sex chromosomes in vertebrates.
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28
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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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Venney CJ, Wellband KW, Normandeau E, Houle C, Garant D, Audet C, Bernatchez L. Thermal regime during parental sexual maturation, but not during offspring rearing, modulates DNA methylation in brook charr ( Salvelinus fontinalis). Proc Biol Sci 2022; 289:20220670. [PMID: 35506232 PMCID: PMC9065957 DOI: 10.1098/rspb.2022.0670] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 01/04/2023] Open
Abstract
Epigenetic inheritance can result in plastic responses to changing environments being faithfully transmitted to offspring. However, it remains unclear how epigenetic mechanisms such as DNA methylation can contribute to multigenerational acclimation and adaptation to environmental stressors. Brook charr (Salvelinus fontinalis), an economically important salmonid, is highly sensitive to thermal stress and is of conservation concern in the context of climate change. We studied the effects of temperature during parental sexual maturation and offspring rearing on whole-genome DNA methylation in brook charr juveniles (fry). Parents were split between warm and cold temperatures during sexual maturation, mated in controlled breeding designs, then offspring from each family were split between warm (8°C) and cold (5°C) rearing environments. Using whole-genome bisulfite sequencing, we found 188 differentially methylated regions (DMRs) due to parental maturation temperature after controlling for family structure. By contrast, offspring rearing temperature had a negligible effect on offspring methylation. Stable intergenerational inheritance of DNA methylation and minimal plasticity in progeny could result in the transmission of acclimatory epigenetic states to offspring, priming them for a warming environment. Our findings have implications pertaining to the role of intergenerational epigenetic inheritance in response to ongoing climate change.
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Affiliation(s)
- Clare J. Venney
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada G1 V 0A6
| | - Kyle W. Wellband
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada G1 V 0A6
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada G1 V 0A6
| | - Carolyne Houle
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1 K 2R1
| | - Dany Garant
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1 K 2R1
| | - Céline Audet
- Institut des sciences de la mer de Rimouski (ISMER), Université du Québec à Rimouski (UQAR), Rimouski, QC, Canada G5 L 2Z9
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada G1 V 0A6
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30
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Palejowski H, Bylemans J, Ammann V, Marques da Cunha L, Nusbaumer D, Castro I, Uppal A, Mobley KB, Knörr S, Wedekind C. Sex-Specific Life History Affected by Stocking in Juvenile Brown Trout. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.869925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Salmonids are a socioeconomically and ecologically important group of fish that are often managed by stocking. Little is known about potential sex-specific effects of stocking, but recent studies found that the sexes differ in their stress tolerances already at late embryonic stage, i.e., before hatchery-born larvae are released into the wild and long before morphological gonad formation. It has also been speculated that sex-specific life histories can affect juvenile growth and mortality, and that a resulting sex-biassed demography can reduce population growth. Here we test whether juvenile brown trout (Salmo trutta) show sex-specific life histories and whether such sex effects differ in hatchery- and wild-born fish. We modified a genetic sexing protocol to reduce false assignment rates and used it to study the timing of sex differentiation in a laboratory setting, and in a large-scale field experiment to study growth and mortality of hatchery- and wild-born fish in different environments. We found no sex-specific mortality in any of the environments we studied. However, females started sex differentiation earlier than males, and while growth rates were similar in the laboratory, they differed significantly in the field depending on location and origin of fish. Overall, hatchery-born males grew larger than hatchery-born females while wild-born fish showed the reverse pattern. Whether males or females grew larger was location-specific. We conclude that juvenile brown trout show sex-specific growth that is affected by stocking and by other environmental factors that remain to be identified.
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31
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Wen M, Pan Q, Jouanno E, Montfort J, Zahm M, Cabau C, Klopp C, Iampietro C, Roques C, Bouchez O, Castinel A, Donnadieu C, Parrinello H, Poncet C, Belmonte E, Gautier V, Avarre J, Dugue R, Gustiano R, Hà TTT, Campet M, Sriphairoj K, Ribolli J, de Almeida FL, Desvignes T, Postlethwait JH, Floi Bucao C, Robinson‐Rechavi M, Bobe J, Herpin A, Guiguen Y. An ancient truncated duplication of the anti‐Mullerian hormone receptor type 2 gene is a potential conserved master sex determinant in the Pangasiidae catfish family. Mol Ecol Resour 2022; 22:2411-2428. [PMID: 35429227 PMCID: PMC9555307 DOI: 10.1111/1755-0998.13620] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/29/2022] [Accepted: 04/11/2022] [Indexed: 11/30/2022]
Abstract
The evolution of sex determination (SD) in teleosts is amazingly dynamic, as reflected by the variety of different master sex-determining genes identified. Pangasiids are economically important catfishes in South Asian countries, but little is known about their SD system. Here, we generated novel genomic resources for 12 Pangasiids and characterized their SD system. Based on a Pangasianodon hypophthalmus chromosome-scale genome assembly, we identified an anti-Müllerian hormone receptor type Ⅱ gene (amhr2) duplication, which was further characterized as being sex-linked in males and expressed only in testes. These results point to a Y chromosome male-specific duplication (amhr2by) of the autosomal amhr2a. Sequence annotation revealed that the P. hypophthalmus Amhr2by is truncated in its N-terminal domain, lacking the cysteine-rich extracellular part of the receptor that is crucial for ligand binding, suggesting a potential route for its neofunctionalization. Reference-guided assembly of 11 additional Pangasiids, along with sex-linkage studies, revealed that this truncated amhr2by duplication is a male-specific conserved gene in Pangasiids. Reconstructions of the amhr2 phylogeny suggested that amhr2by arose from an ancient duplication/insertion event at the root of the Siluroidei radiation that is dated to ~100 million years ago. Together these results bring multiple lines of evidence supporting that amhr2by is an ancient and conserved master sex-determining gene in Pangasiids, a finding that highlights the recurrent use of the transforming growth factor β pathway, which is often used for the recruitment of teleost master SD genes, and provides another empirical case towards firther understanding of dynamics of SD systems.
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Affiliation(s)
- Ming Wen
- State Key Laboratory of Developmental Biology of Freshwater Fish College of Life Science Hunan Normal University Changsha China
- INRAE LPGP 35000 Rennes France
| | - Qiaowei Pan
- INRAE LPGP 35000 Rennes France
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
| | | | | | - Margot Zahm
- Plate‐forme bio‐informatique Genotoul Mathématiques et Informatique Appliquées de Toulouse INRAE Castanet Tolosan France
| | - Cédric Cabau
- SIGENAE, GenPhySE Université de Toulouse INRAE ENVT Castanet Tolosan France
| | - Christophe Klopp
- Plate‐forme bio‐informatique Genotoul Mathématiques et Informatique Appliquées de Toulouse INRAE Castanet Tolosan France
- SIGENAE, GenPhySE Université de Toulouse INRAE ENVT Castanet Tolosan France
| | | | - Céline Roques
- INRAE, US 1426, GeT‐PlaGe Genotoul, Castanet‐Tolosan France
| | | | | | | | - Hugues Parrinello
- Montpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle 141 rue de la Cardonille 34094 Montpellier Cedex France
| | - Charles Poncet
- GDEC Gentyane INRAE Université Clermont Auvergne Clermont‐Ferrand France
| | - Elodie Belmonte
- GDEC Gentyane INRAE Université Clermont Auvergne Clermont‐Ferrand France
| | - Véronique Gautier
- GDEC Gentyane INRAE Université Clermont Auvergne Clermont‐Ferrand France
| | | | - Remi Dugue
- ISEM Univ Montpellier CNRS IRD Montpellier France
| | - Rudhy Gustiano
- Research Institute of Freshwater Fisheries (CRIFI‐RIFF) Instalasi Penelitian Perikanan Air Tawar Jalan Ragunan‐Pasar Minggu P.O. Box 7220/jkspm Jakarta 12540 Indonesia
| | - Trần Thị Thúy Hà
- Research Institute for Aquaculture No.1. Dinh Bang Tu Son, Bac Ninh Viet Nam
| | | | - Kednapat Sriphairoj
- Faculty of Natural Resources and Agro‐Industry Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus Sakon Nakhon Thailand
| | - Josiane Ribolli
- Laboratório de Biologia e Cultivo de Peixes de Água Doce Universidade Federal de Santa Catarina Florianópolis SC Brasil
| | | | - Thomas Desvignes
- Institute of Neuroscience University of Oregon Eugene OR 97403 USA
| | | | - Christabel Floi Bucao
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- SIB Swiss Institute of Bioinformatics 1015 Lausanne Switzerland
| | - Marc Robinson‐Rechavi
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- SIB Swiss Institute of Bioinformatics 1015 Lausanne Switzerland
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32
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Dynamics of sexual development in teleosts with a note on Mugil cephalus. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2022.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Do Ty3/Gypsy Transposable Elements Play Preferential Roles in Sex Chromosome Differentiation? Life (Basel) 2022; 12:life12040522. [PMID: 35455013 PMCID: PMC9025612 DOI: 10.3390/life12040522] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/13/2022] [Accepted: 03/30/2022] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) comprise a substantial portion of eukaryotic genomes. They have the unique ability to integrate into new locations and serve as the main source of genomic novelties by mediating chromosomal rearrangements and regulating portions of functional genes. Recent studies have revealed that TEs are abundant in sex chromosomes. In this review, we propose evolutionary relationships between specific TEs, such as Ty3/Gypsy, and sex chromosomes in different lineages based on the hypothesis that these elements contributed to sex chromosome differentiation processes. We highlight how TEs can drive the dynamics of sex-determining regions via suppression recombination under a selective force to affect the organization and structural evolution of sex chromosomes. The abundance of TEs in the sex-determining regions originates from TE-poor genomic regions, suggesting a link between TE accumulation and the emergence of the sex-determining regions. TEs are generally considered to be a hallmark of chromosome degeneration. Finally, we outline recent approaches to identify TEs and study their sex-related roles and effects in the differentiation and evolution of sex chromosomes.
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34
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Collins EE, Romero N, Zendt JS, Narum SR. Whole-Genome Resequencing to Evaluate Life History Variation in Anadromous Migration of Oncorhynchus mykiss. Front Genet 2022; 13:795850. [PMID: 35368705 PMCID: PMC8964970 DOI: 10.3389/fgene.2022.795850] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/24/2022] [Indexed: 12/04/2022] Open
Abstract
Anadromous fish experience physiological modifications necessary to migrate between vastly different freshwater and marine environments, but some species such as Oncorhynchus mykiss demonstrate variation in life history strategies with some individuals remaining exclusively resident in freshwater, whereas others undergo anadromous migration. Because there is limited understanding of genes involved in this life history variation across populations of this species, we evaluated the genomic difference between known anadromous (n = 39) and resident (n = 78) Oncorhynchus mykiss collected from the Klickitat River, WA, USA, with whole-genome resequencing methods. Sequencing of these collections yielded 5.64 million single-nucleotide polymorphisms that were tested for significant differences between resident and anadromous groups along with previously identified candidate gene regions. Although a few regions of the genome were marginally significant, there was one region on chromosome Omy12 that provided the most consistent signal of association with anadromy near two annotated genes in the reference assembly: COP9 signalosome complex subunit 6 (CSN6) and NACHT, LRR, and PYD domain–containing protein 3 (NLRP3). Previously identified candidate genes for anadromy within the inversion region of chromosome Omy05 in coastal steelhead and rainbow trout were not informative for this population as shown in previous studies. Results indicate that the significant region on chromosome Omy12 may represent a minor effect gene for male anadromy and suggests that this life history variation in Oncorhynchus mykiss is more strongly driven by other mechanisms related to environmental rearing such as epigenetic modification, gene expression, and phenotypic plasticity. Further studies into regulatory mechanisms of this trait are needed to understand drivers of anadromy in populations of this protected species.
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Affiliation(s)
- Erin E. Collins
- Hagerman Genetics Laboratory, Columbia River Inter-Tribal Fish Commission, Hagerman, ID, United States
- *Correspondence: Erin E. Collins,
| | - Nicolas Romero
- Yakama Nation Fisheries, Yakima/Klickitat Fisheries Project, Klickitat, WA, United States
| | - Joseph S. Zendt
- Yakama Nation Fisheries, Yakima/Klickitat Fisheries Project, Klickitat, WA, United States
| | - Shawn R. Narum
- Hagerman Genetics Laboratory, Columbia River Inter-Tribal Fish Commission, Hagerman, ID, United States
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Bertho S, Herpin A, Jouanno E, Yano A, Bobe J, Parrinello H, Journot L, Guyomard R, Muller T, Swanson P, McKinney G, Williamson K, Meek M, Schartl M, Guiguen Y. A nonfunctional copy of the salmonid sex-determining gene ( sdY) is responsible for the “apparent” XY females in Chinook salmon, Oncorhynchus tshawytscha. G3 GENES|GENOMES|GENETICS 2022; 12:6493265. [PMID: 35100376 PMCID: PMC8824802 DOI: 10.1093/g3journal/jkab451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/03/2021] [Indexed: 11/14/2022]
Abstract
Abstract
Many salmonids have a male heterogametic (XX/XY) sex determination system, and they are supposed to have a conserved master sex-determining gene (sdY) that interacts at the protein level with Foxl2 leading to the blockage of the synergistic induction of Foxl2 and Nr5a1 of the cyp19a1a promoter. However, this hypothesis of a conserved master sex-determining role of sdY in salmonids is challenged by a few exceptions, one of them being the presence of naturally occurring “apparent” XY Chinook salmon, Oncorhynchus tshawytscha, females. Here, we show that some XY Chinook salmon females have a sdY gene (sdY-N183), with 1 missense mutation leading to a substitution of a conserved isoleucine to an asparagine (I183N). In contrast, Chinook salmon males have both a nonmutated sdY-I183 gene and the missense mutation sdY-N183 gene. The 3-dimensional model of SdY-I183N predicts that the I183N hydrophobic to hydrophilic amino acid change leads to a modification in the SdY β-sandwich structure. Using in vitro cell transfection assays, we found that SdY-I183N, like the wild-type SdY, is preferentially localized in the cytoplasm. However, compared to wild-type SdY, SdY-I183N is more prone to degradation, its nuclear translocation by Foxl2 is reduced, and SdY-I183N is unable to significantly repress the synergistic Foxl2/Nr5a1 induction of the cyp19a1a promoter. Altogether, our results suggest that the sdY-N183 gene of XY Chinook females is nonfunctional and that SdY-I183N is no longer able to promote testicular differentiation by impairing the synthesis of estrogens in the early differentiating gonads of wild Chinook salmon XY females.
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Affiliation(s)
- Sylvain Bertho
- INRAE, LPGP, Rennes 35000, France
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg 97074, Germany
| | | | | | | | | | - Hugues Parrinello
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, Montpellier 34094, France
| | - Laurent Journot
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, Montpellier 34094, France
| | - René Guyomard
- GABI, INRAE, AgroParisTech, Université Paris-Saclay, Paris 75005, France
| | - Thomas Muller
- Julius-von-Sachs-Institute, Department of Molecular Plant Physiology and Biophysics, University of Wuerzburg, Wuerzburg 97082, Germany
| | - Penny Swanson
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98112, USA
| | - Garrett McKinney
- Molecular Genetics Laboratory, Washington Department of Fish & Wildlife, Olympia, WA 98501, USA
| | | | - Mariah Meek
- Dept. of Integrative Biology, AgBio Research, and Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
- Department of Developmental Biochemistry, Biocenter, University of Wüerzburg, Wuerzburg 97074, Germany
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Christensen KA, Rondeau EB, Sakhrani D, Biagi CA, Johnson H, Joshi J, Flores AM, Leelakumari S, Moore R, Pandoh PK, Withler RE, Beacham TD, Leggatt RA, Tarpey CM, Seeb LW, Seeb JE, Jones SJM, Devlin RH, Koop BF. The pink salmon genome: Uncovering the genomic consequences of a two-year life cycle. PLoS One 2021; 16:e0255752. [PMID: 34919547 PMCID: PMC8682878 DOI: 10.1371/journal.pone.0255752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/02/2021] [Indexed: 12/30/2022] Open
Abstract
Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to the western Pacific Ocean. Pink salmon are also the most abundant of these species and account for a large proportion of the commercial value of the salmon fishery worldwide. A two-year life history of pink salmon generates temporally isolated populations that spawn either in even-years or odd-years. To uncover the influence of this genetic isolation, reference genome assemblies were generated for each year-class and whole genome re-sequencing data was collected from salmon of both year-classes. The salmon were sampled from six Canadian rivers and one Japanese river. At multiple centromeres we identified peaks of Fst between year-classes that were millions of base-pairs long. The largest Fst peak was also associated with a million base-pair chromosomal polymorphism found in the odd-year genome near a centromere. These Fst peaks may be the result of a centromere drive or a combination of reduced recombination and genetic drift, and they could influence speciation. Other regions of the genome influenced by odd-year and even-year temporal isolation and tentatively under selection were mostly associated with genes related to immune function, organ development/maintenance, and behaviour.
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Affiliation(s)
- Kris A. Christensen
- West Vancouver, Fisheries and Oceans Canada, British Columbia, Canada
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
- * E-mail: (KAC); (BFK)
| | - Eric B. Rondeau
- West Vancouver, Fisheries and Oceans Canada, British Columbia, Canada
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Dionne Sakhrani
- West Vancouver, Fisheries and Oceans Canada, British Columbia, Canada
| | - Carlo A. Biagi
- West Vancouver, Fisheries and Oceans Canada, British Columbia, Canada
| | - Hollie Johnson
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Jay Joshi
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Anne-Marie Flores
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Sreeja Leelakumari
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Richard Moore
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Pawan K. Pandoh
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Ruth E. Withler
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Terry D. Beacham
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | | | - Carolyn M. Tarpey
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Lisa W. Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - James E. Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Steven J. M. Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Robert H. Devlin
- West Vancouver, Fisheries and Oceans Canada, British Columbia, Canada
| | - Ben F. Koop
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
- * E-mail: (KAC); (BFK)
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Geffroy B, Besson M, Sánchez-Baizán N, Clota F, Goikoetxea A, Sadoul B, Ruelle F, Blanc MO, Parrinello H, Hermet S, Blondeau-Bidet E, Pratlong M, Piferrer F, Vandeputte M, Allal F. Unraveling the genotype by environment interaction in a thermosensitive fish with a polygenic sex determination system. Proc Natl Acad Sci U S A 2021; 118:e2112660118. [PMID: 34880131 PMCID: PMC8685686 DOI: 10.1073/pnas.2112660118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2021] [Indexed: 01/03/2023] Open
Abstract
In most animals, sex determination occurs at conception, when sex chromosomes are segregated following Mendelian laws. However, in multiple reptiles and fishes, this genetic sex can be overridden by external factors after fertilization or birth. In some species, the genetic sex may also be governed by multiple genes, further limiting our understanding of sex determination in such species. We used the European sea bass (Dicentrarchus labrax) as a model and combined genomic (using a single nucleotide polymorphism chip) and transcriptomic (RNA-Sequencing) approaches to thoroughly depict this polygenic sex determination system and its interaction with temperature. We estimated genetic sex tendency (eGST), defined as the estimated genetic liability to become a given sex under a liability threshold model for sex determination, which accurately predicts the future phenotypic sex. We found evidence that energetic pathways, concerning the regulation of lipids and glucose, are involved in sex determination and could explain why females tend to exhibit higher energy levels and improved growth compared to males. Besides, early exposure to high-temperature up-regulated sox3, followed by sox9a in individuals with intermediate eGST, but not in individuals showing highly female-biased eGST, providing the most parsimonious explanation for temperature-induced masculinization. This gonadal state was maintained likely by DNA methylation and the up-regulation of several genes involved in histone modifications, including jmjd1c Overall, we describe a sex determination system resulting from continuous genetic and environmental influences in an animal. Our results provide significant progress in our understanding of the mechanisms underlying temperature-induced masculinization in fish.
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Affiliation(s)
- Benjamin Geffroy
- MARBEC Université de Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France;
| | - Mathieu Besson
- SYSAAF, Station LPGP/INRAE, 35042 Rennes, France
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - Núria Sánchez-Baizán
- Institut de Ciències del Mar, Spanish National Research Council, Barcelona, Spain
| | - Frederic Clota
- MARBEC Université de Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | | | - Bastien Sadoul
- MARBEC Université de Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, France
| | - François Ruelle
- Laboratoire Service d'Expérimentations Aquacoles, Ifremer, Palavas-les-Flots, France
| | - Marie-Odile Blanc
- Laboratoire Service d'Expérimentations Aquacoles, Ifremer, Palavas-les-Flots, France
| | - Hugues Parrinello
- MGX, BCM, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Sophie Hermet
- MARBEC Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Eva Blondeau-Bidet
- MARBEC Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Marine Pratlong
- MGX, BCM, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Francesc Piferrer
- Institut de Ciències del Mar, Spanish National Research Council, Barcelona, Spain
| | - Marc Vandeputte
- MARBEC Université de Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - François Allal
- MARBEC Université de Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France
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Nusbaumer D, Garaud L, Ançay L, Wedekind C. Sex-Specific Stress Tolerance in Embryos of Lake Char (Salvelinus umbla). Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.768263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Salmonid fish have become important models in evolution and ecology, but possible effects of embryo or larval sex are mostly ignored, probably because morphological gonad formation starts only months after hatching and sexual maturation years later. However, recent gene expression studies and first observations in domestic strains suggest that sex-specific life histories could already start at an embryonic stage. Here we test this hypothesis in embryos and larvae of lake char (Salvelinus umbla). We sampled wild char and used their gametes to produce embryos of 40 different families. Embryos were raised singly in a stress or a non-stress environment until a late larval stage (stress was induced by allowing remainders of ovarian fluids to support microbial growth). Genetic markers were then used to sex the fish and reconstruct paternity (N = 1,463, including dead embryos). Primary sex ratio did not differ among families and was about 1:1. Female embryos hatched on average later and showed lower stress tolerance than male embryos. There were significant parental effects on offspring growth and mortality, but the sex differences in embryo performance were not family specific. We conclude that the sexes differ in their life history and susceptibilities to environmental stress already at embryonic stages. Environmental stress during incubation can therefore affect population sex ratio and hence population growth and genetics.
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Ferchaud AL, Mérot C, Normandeau E, Ragoussis J, Babin C, Djambazian H, Bérubé P, Audet C, Treble M, Walkusz W, Bernatchez L. Chromosome-level assembly reveals a putative Y-autosomal fusion in the sex determination system of the Greenland Halibut (Reinhardtius hippoglossoides). G3-GENES GENOMES GENETICS 2021; 12:6428537. [PMID: 34791178 DOI: 10.1093/g3journal/jkab376] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 10/21/2021] [Indexed: 11/13/2022]
Abstract
Despite the commercial importance of Greenland Halibut (Reinhardtius hippoglossoides), important gaps still persist in our knowledge of this species, including its reproductive biology and sex determination mechanism. Here, we combined single-molecule sequencing of long reads (Pacific Sciences) with chromatin conformation capture sequencing (Hi-C) data to assemble the first chromosome-level reference genome for this species. The high-quality assembly encompassed more than 598 Megabases (Mb) assigned to 1 594 scaffolds (scaffold N50 = 25 Mb) with 96% of its total length distributed among 24 chromosomes. Investigation of the syntenic relationship with other economically important flatfish species revealed a high conservation of synteny blocks among members of this phylogenetic clade. Sex determination analysis revealed that, similar to other teleost fishes, flatfishes also exhibit a high level of plasticity and turnover in sex-determination mechanisms. A low-coverage whole-genome sequence analysis of 198 individuals revealed that Greenland Halibut possesses a male heterogametic XY system and several putative candidate genes implied in the sex determination of this species. Our study also suggests for the first time in flatfishes that a putative Y-autosomal fusion could be associated with a reduction of recombination typical of the early steps of sex chromosome evolution.
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Affiliation(s)
- Anne-Laure Ferchaud
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
| | - Claire Mérot
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
| | - Jiannis Ragoussis
- McGill Genome Centre and Department for Human Genetics, McGill University, Montreal, Quebec, H3A 0G1, Canada
| | - Charles Babin
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
| | - Haig Djambazian
- McGill Genome Centre and Department for Human Genetics, McGill University, Montreal, Quebec, H3A 0G1, Canada
| | - Pierre Bérubé
- McGill Genome Centre and Department for Human Genetics, McGill University, Montreal, Quebec, H3A 0G1, Canada
| | - Céline Audet
- Institut des sciences de la mer de Rimouski, Université du Québec à Rimouski, 310 allée des Ursulines, Rimouski, QC G5L 3A1, Canada
| | - Margaret Treble
- Fisheries and Oceans Canada, Winnipeg Department, Arctic Aquatic Research Division, Freshwater Institute Winnipeg, Manitoba, R3T2N6, Canada
| | - Wocjciech Walkusz
- Fisheries and Oceans Canada, Winnipeg Department, Arctic Aquatic Research Division, Freshwater Institute Winnipeg, Manitoba, R3T2N6, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada
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40
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Morin J, Royle TCA, Zhang H, Speller C, Alcaide M, Morin R, Ritchie M, Cannon A, George M, George M, Yang D. Indigenous sex-selective salmon harvesting demonstrates pre-contact marine resource management in Burrard Inlet, British Columbia, Canada. Sci Rep 2021; 11:21160. [PMID: 34759290 PMCID: PMC8581006 DOI: 10.1038/s41598-021-00154-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 10/07/2021] [Indexed: 11/30/2022] Open
Abstract
To gain insight into pre-contact Coast Salish fishing practices, we used new palaeogenetic analytical techniques to assign sex identifications to salmonid bones from four archaeological sites in Burrard Inlet (Tsleil-Waut), British Columbia, Canada, dating between about 2300-1000 BP (ca. 400 BCE-CE 1200). Our results indicate that male chum salmon (Oncorhynchus keta) were preferentially targeted at two of the four sampled archaeological sites. Because a single male salmon can mate with several females, selectively harvesting male salmon can increase a fishery's maximum sustainable harvest. We suggest such selective harvesting of visually distinctive male spawning chum salmon was a common practice, most effectively undertaken at wooden weirs spanning small salmon rivers and streams. We argue that this selective harvesting of males is indicative of an ancient and probably geographically widespread practice for ensuring sustainable salmon populations. The archaeological data presented here confirms earlier ethnographic accounts describing the selective harvest of male salmon.
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Affiliation(s)
- Jesse Morin
- grid.17091.3e0000 0001 2288 9830Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC Canada
| | - Thomas C. A. Royle
- grid.61971.380000 0004 1936 7494Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, BC Canada
| | - Hua Zhang
- grid.61971.380000 0004 1936 7494Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, BC Canada
| | - Camilla Speller
- grid.17091.3e0000 0001 2288 9830Department of Anthropology, University of British Columbia, Vancouver, BC Canada
| | - Miguel Alcaide
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC Canada
| | - Ryan Morin
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC Canada
| | - Morgan Ritchie
- grid.17091.3e0000 0001 2288 9830Department of Anthropology, University of British Columbia, Vancouver, BC Canada
| | - Aubrey Cannon
- grid.25073.330000 0004 1936 8227Department of Anthropology, McMaster University, Hamilton, ON Canada
| | | | | | - Dongya Yang
- grid.61971.380000 0004 1936 7494Ancient DNA Laboratory, Department of Archaeology, Simon Fraser University, Burnaby, BC Canada
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41
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Lin CJ, Jeng SR, Lei ZY, Yueh WS, Dufour S, Wu GC, Chang CF. Involvement of Transforming Growth Factor Beta Family Genes in Gonadal Differentiation in Japanese Eel, Anguilla japonica, According to Sex-Related Gene Expressions. Cells 2021; 10:cells10113007. [PMID: 34831230 PMCID: PMC8616510 DOI: 10.3390/cells10113007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/20/2021] [Accepted: 11/01/2021] [Indexed: 11/18/2022] Open
Abstract
The gonochoristic feature with environmental sex determination that occurs during the yellow stage in the eel provides an interesting model to investigate the mechanisms of gonadal development. We previously studied various sex-related genes during gonadal sex differentiation in Japanese eels. In the present study, the members of transforming growth factor beta (TGF-β) superfamily were investigated. Transcript levels of anti-Müllerian hormone, its receptor, gonadal soma-derived factor (amh, amhr2, and gsdf, respectively) measured by real-time polymerase chain reaction (qPCR) showed a strong sexual dimorphism. Transcripts were dominantly expressed in the testis, and their levels significantly increased with testicular differentiation. In contrast, the expressions of amh, amhr2, and gsdf transcripts were low in the ovary of E2-feminized female eels. In situ hybridization detected gsdf (but not amh) transcript signals in undifferentiated gonads. amh and gsdf signals were localized to Sertoli cells and had increased significantly with testicular differentiation. Weak gsdf and no amh signals were detected in early ovaries of E2-feminized female eels. Transcript levels of amh and gsdf (not amhr2) decreased during human chorionic gonadotropin (HCG)-induced spermatogenesis in males. This study suggests that amh, amhr2, and especially gsdf might be involved in the gene pathway regulating testicular differentiation of Japanese eels.
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Affiliation(s)
- Chien-Ju Lin
- Department of Aquaculture, National Pingtung University of Science and Technology, Pingtung 912, Taiwan;
| | - Shan-Ru Jeng
- Department of Aquaculture, National Kaohsiung University of Science and Technology, Kaohsiung 811, Taiwan; (Z.-Y.L.); (W.-S.Y.)
- Correspondence: (S.-R.J.); (G.-C.W.); (C.-F.C.)
| | - Zhen-Yuan Lei
- Department of Aquaculture, National Kaohsiung University of Science and Technology, Kaohsiung 811, Taiwan; (Z.-Y.L.); (W.-S.Y.)
| | - Wen-Shiun Yueh
- Department of Aquaculture, National Kaohsiung University of Science and Technology, Kaohsiung 811, Taiwan; (Z.-Y.L.); (W.-S.Y.)
| | - Sylvie Dufour
- Laboratory Biology of Aquatic Organisms and Ecosystems (BOREA), Muséum National d’Histoire Naturelle, CNRS, IRD, Sorbonne Université, CEDEX 05, 75231 Paris, France;
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202, Taiwan
| | - Guan-Chung Wu
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202, Taiwan
- Department of Aquaculture, National Taiwan Ocean University, Keelung 202, Taiwan
- Correspondence: (S.-R.J.); (G.-C.W.); (C.-F.C.)
| | - Ching-Fong Chang
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202, Taiwan
- Department of Aquaculture, National Taiwan Ocean University, Keelung 202, Taiwan
- Correspondence: (S.-R.J.); (G.-C.W.); (C.-F.C.)
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42
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Folio DM, Gil J, Caudron A, Labonne J. Genotype-by-environment interactions drive the maintenance of genetic variation in a Salmo trutta L. hybrid zone. Evol Appl 2021; 14:2698-2711. [PMID: 34815748 PMCID: PMC8591331 DOI: 10.1111/eva.13307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 08/18/2021] [Accepted: 09/15/2021] [Indexed: 11/28/2022] Open
Abstract
Allopatric gene pools can evolve in different directions through adaptive and nonadaptive processes and are therefore a source of intraspecific diversity. The connection of these previously isolated gene pools through human intervention can lead to intraspecific diversity loss, through extirpation of native populations or hybridization. However, the mechanisms leading to these situations are not always explicitly documented and are thus rarely used to manage intraspecific diversity. In particular, genotype-by-environment (GxE) interactions can drive postzygotic reproductive isolation mechanisms that may result in a mosaic of diversity patterns, depending on the local environment. We test this hypothesis using a salmonid species (Salmo trutta) in the Mediterranean (MED) area, where intensive stocking from non-native Atlantic (ATL) origins has led to various outcomes of hybridization with the native MED lineage, going from MED resilience to total extirpation via full hybridization. We investigate patterns of offspring survival at egg stage in natural environments, based on parental genotypes in interaction with river temperature, to detect potential GxE interactions. Our results show a strong influence of maternal GxE interaction on embryonic survival, mediated by maternal effect through egg size, and a weak influence of paternal GxE interaction. In particular, when egg size is large and temperature is cold, the survival rate of offspring originating from MED females is three times higher than that of ATL females' offspring. Because river temperatures show contrast at small scale, this cold adaptation for MED females' offspring constitutes a potent postzygotic mechanism to explain small-scale spatial heterogeneity in diversity observed in MED areas where ATL fish have been stocked. It also indicates that management efforts could be specifically targeted at the environments that actively favor native intraspecific diversity through eco-evolutionary processes such as postzygotic selection.
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Affiliation(s)
- Dorinda Marie Folio
- Université de Pau et des Pays de l’AdourUMR INRAE‐UPPAEcobiopSaint‐Pée‐sur‐NivelleFrance
- SCIMABIO InterfaceThonon‐les‐BainsFrance
| | - Jordi Gil
- UMR CARRTELINRAEUSMBThonon‐les‐BainsFrance
- Conservatoire des Espaces Naturels Rhône‐AlpesVogüeFrance
| | | | - Jacques Labonne
- Université de Pau et des Pays de l’AdourUMR INRAE‐UPPAEcobiopSaint‐Pée‐sur‐NivelleFrance
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43
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Sinclair-Waters M, Piavchenko N, Ruokolainen A, Aykanat T, Erkinaro J, Primmer CR. Refining the genomic location of single nucleotide polymorphism variation affecting Atlantic salmon maturation timing at a key large-effect locus. Mol Ecol 2021; 31:562-570. [PMID: 34716945 DOI: 10.1111/mec.16256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 12/14/2022]
Abstract
Efforts to understand the genetic underpinnings of phenotypic variation are becoming more and more frequent in molecular ecology. Such efforts often lead to the identification of candidate regions showing signals of association and/or selection. These regions may contain multiple genes and therefore validation of which genes are actually responsible for the signal is required. In Atlantic salmon (Salmo salar), a large-effect locus for maturation timing, an ecologically important trait, occurs in a genomic region including two genes, vgll3 and akap11, but data for clearly determining which of the genes (or both) contribute to the association have been lacking. Here, we take advantage of natural recombination events detected between the two candidate genes in a salmon broodstock to reduce linkage disequilibrium at the locus, thus enabling delineation of the influence of variation at these two genes on early maturation. By rearing 5,895 males to maturation age, of which 81% had recombinant vgll3/akap11 allelic combinations, we found that vgll3 single nucleotide polymorphism (SNP) variation was strongly associated with early maturation, whereas there was little or no association between akap11 SNP variation and early maturation. These findings provide strong evidence supporting vgll3 as the primary candidate gene in the chromosome 25 locus for influencing early maturation. This will help guide future research for understanding the genetic processes controlling early maturation. This also exemplifies the utility of natural recombinants to more precisely map causal variation underlying ecologically important phenotypic diversity.
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Affiliation(s)
- Marion Sinclair-Waters
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Nikolai Piavchenko
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Annukka Ruokolainen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | - Tutku Aykanat
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
| | | | - Craig R Primmer
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
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44
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Callet T, Li H, Surget A, Terrier F, Sandres F, Lanuque A, Panserat S, Marandel L. No adverse effect of a maternal high carbohydrate diet on their offspring, in rainbow trout ( Oncorhynchus mykiss). PeerJ 2021; 9:e12102. [PMID: 34589301 PMCID: PMC8434805 DOI: 10.7717/peerj.12102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/11/2021] [Indexed: 01/09/2023] Open
Abstract
In order to develop a sustainable salmonid aquaculture, it is essential to continue to reduce the use of the protein-rich fishmeal. One promising solution to do so is the use of plant-derived carbohydrates in diet destined to broodstock. However, in mammals, the reduction of protein content (replaced by carbohydrates) in parental diet is known to have strong adverse effects on offspring phenotypes and metabolism. For the first time, the effect of a paternal and a maternal high carbohydrate-low protein diet was assessed on progeny at long term in the rainbow trout. A 30% protein diminution in both males and females broodstock diet during 10 month and 5 months, respectively, did not trigger adverse consequences on their offspring. At the molecular level, offspring transcriptomes were not significantly altered, emphasizing no effect on metabolism. Tenuous differences in the biochemical composition of the liver and the viscera were observed. The recorded effects remained in the normal range of value and accordingly offspring growth were not negatively affected over the long term. Overall, we demonstrated here that a 30% protein diminution during gametogenesis is feasible, confirming the possibility to increase the proportion of plant-derived carbohydrates in female broodstock diets to replace fishmeal proteins.
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Affiliation(s)
- Therese Callet
- Institut National de la Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Saint-Pée-sur-Nivelle, France
| | - Hongyan Li
- Institut National de la Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Saint-Pée-sur-Nivelle, France.,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Anne Surget
- Institut National de la Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Saint-Pée-sur-Nivelle, France
| | - Frederic Terrier
- Institut National de la Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Saint-Pée-sur-Nivelle, France
| | - Franck Sandres
- Institut National de la Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Saint-Pée-sur-Nivelle, France
| | - Anthony Lanuque
- Institut National de la Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Saint-Pée-sur-Nivelle, France
| | - Stephane Panserat
- Institut National de la Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Saint-Pée-sur-Nivelle, France
| | - Lucie Marandel
- Institut National de la Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Saint-Pée-sur-Nivelle, France
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45
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Sex Determination and Differentiation in Teleost: Roles of Genetics, Environment, and Brain. BIOLOGY 2021; 10:biology10100973. [PMID: 34681072 PMCID: PMC8533387 DOI: 10.3390/biology10100973] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/19/2021] [Accepted: 09/20/2021] [Indexed: 01/19/2023]
Abstract
The fish reproductive system is a complex biological system. Nonetheless, reproductive organ development is conserved, which starts with sex determination and then sex differentiation. The sex of a teleost is determined and differentiated from bipotential primordium by genetics, environmental factors, or both. These two processes are species-specific. There are several prominent genes and environmental factors involved during sex determination and differentiation. At the cellular level, most of the sex-determining genes suppress the female pathway. For environmental factors, there are temperature, density, hypoxia, pH, and social interaction. Once the sexual fate is determined, sex differentiation takes over the gonadal developmental process. Environmental factors involve activation and suppression of various male and female pathways depending on the sexual fate. Alongside these factors, the role of the brain during sex determination and differentiation remains elusive. Nonetheless, GnRH III knockout has promoted a male sex-biased population, which shows brain involvement during sex determination. During sex differentiation, LH and FSH might not affect the gonadal differentiation, but are required for regulating sex differentiation. This review discusses the role of prominent genes, environmental factors, and the brain in sex determination and differentiation across a few teleost species.
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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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Duan W, Gao FX, Chen ZW, Gao Y, Gui JF, Zhao Z, Shi Y. A sex-linked SNP mutation in amhr2 is responsible for male differentiation in obscure puffer (Takifugu obscurus). Mol Biol Rep 2021; 48:6035-6046. [PMID: 34341900 DOI: 10.1007/s11033-021-06606-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/27/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Anti-Mullerian hormone receptor type II (Amhr2) is a key receptor of Amh signaling in regulating gonad development. The amhr2 gene has been identified in numerous species, including a few teleost fishes. However, the roles of Amhr2 in Amh signaling in fish are poorly studied. METHODS AND RESULTS In this study, an amhr2 homolog from obscure puffer (Takifugu obscurus) was identified, and its molecular characteristics were systematically analyzed. Expression analysis revealed that amhr2 was highly expressed in the gonads of adult pufferfish and significantly upregulated during sex differentiation. Significantly, a sex-linked SNP site was verified in obscure puffer amhr2. Females exhibited a homozygous genotype (C/C), while males possessed a heterozygous genotype (C/G), resulting in an amino acid variation (His/Asp384) in the kinase domain of Amhr2. Then, the functions of the different Amhr2 genotypes were further investigated. The male genotype protein (Amhr2D384) showed an enhanced ability to interact with the type I receptor (Bmpr1a) compared to the female genotype (Amhr2H384). The phosphorylation levels of Smads and activity of the target gene (id3) induced by the male genotype were also much higher than those induced by the female genotype. These results confirmed that the male genotype had an enhanced effect on the Amh signaling pathway compared with the female genotype. CONCLUSIONS This study provides direct experimental evidence for the roles of different Amhr2 genotypes in pufferfish and suggests that amhr2 is responsible for male sex differentiation in obscure puffer.
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Affiliation(s)
- Wen Duan
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Fan-Xiang Gao
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China.,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zi-Wei Chen
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Yang Gao
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Jian-Fang Gui
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China.,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zhe Zhao
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Yan Shi
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China.
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Hale MC, McLaughlin R, Wilson C, Mackereth R, Nichols KM. Differential gene expression associated with behavioral variation in ecotypes of Lake Superior brook trout (Salvelinus fontinalis). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 40:100884. [PMID: 34303261 DOI: 10.1016/j.cbd.2021.100884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/06/2021] [Accepted: 07/10/2021] [Indexed: 11/17/2022]
Abstract
Associations between behaviors and the development of different life history tactics have been documented in several species of salmon, trout, and charr. While it is well known that such behaviors are heritable the genes and molecular pathways connected to these behaviors remain unknown. We used an RNA-seq approach to identify genes and molecular pathways differentially regulated in brain tissue between "shy" and "bold" brook trout (Salvelinus fontinalis). A small number of genes were differentially expressed between the behavioral types at several months after hatching and two years of age. Pathway analysis revealed that EIF2 signaling differed consistently between shy and bold individuals suggesting large-scale differences in protein synthesis between behavioral types in the brain. Additionally, the RNA-seq data were used to find polymorphisms within the brook trout genome and a GWAS approach was used to test for statistical associations between genetic variants and behavior type. One allele located in a transcription factor (TSHZ3) contained a protein-coding non-synonymous SNP suggesting that functional variation within TSHZ3 is connected to the development of different behaviors. These results suggest that the molecular basis of behavioral development is complex and due to the differential expression of many genes involved in a wide-range of different molecular pathways.
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Affiliation(s)
- Matthew C Hale
- Department of Biology, Texas Christian University, Fort Worth, TX 76129, United States of America.
| | - Robert McLaughlin
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Chris Wilson
- Aquatic Biodiversity and Conservation Unit, Ontario Ministry of Natural Resources, Trent University, Peterborough, ON K9J 7B8, Canada
| | - Robert Mackereth
- Department of Biology, Lakehead University, Thunder Bay, ON P7B 5E1, Canada
| | - Krista M Nichols
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98112, United States of America
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Duval E, Skaala Ø, Quintela M, Dahle G, Delaval A, Wennevik V, Glover KA, Hansen MM. Long-term monitoring of a brown trout (Salmo trutta) population reveals kin-associated migration patterns and contributions by resident trout to the anadromous run. BMC Ecol Evol 2021; 21:143. [PMID: 34256705 PMCID: PMC8276402 DOI: 10.1186/s12862-021-01876-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/02/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND In species showing partial migration, as is the case for many salmonid fishes, it is important to assess how anthropogenic pressure experienced by migrating individuals affects the total population. We focused on brown trout (Salmo trutta) from the Guddal River in the Norwegian Hardanger Fjord system, which encompasses both resident and anadromous individuals. Aquaculture has led to increased anthropogenic pressure on brown trout during the marine phase in this region. Fish traps in the Guddal River allow for sampling all ascending anadromous spawners and descending smolts. We analyzed microsatellite DNA markers from all individuals ascending in 2006-2016, along with all emigrating smolts in 2017. We investigated (1) if there was evidence for declines in census numbers and effective population size during that period, (2) if there was association between kinship and migration timing in smolts and anadromous adults, and (3) to what extent resident trout were parents of outmigrating smolts. RESULTS Census counts of anadromous spawners showed no evidence for a decline from 2006 to 2016, but were lower than in 2000-2005. Estimates of effective population size also showed no trends of declines during the study period. Sibship reconstruction of the 2017 smolt run showed significant association between kinship and migration timing, and a similar association was indicated in anadromous spawners. Parentage assignment of 2017 smolts with ascending anadromous trout as candidate parents, and assuming that unknown parents represented resident trout, showed that 70% of smolts had at least one resident parent and 24% had two resident parents. CONCLUSIONS The results bear evidence of a population that after an initial decline has stabilized at a lower number of anadromous spawners. The significant association between kinship and migration timing in smolts suggests that specific episodes of elevated mortality in the sea could disproportionally affect some families and reduce overall effective population size. Finally, the results based on parentage assignment demonstrate a strong buffering effect of resident trout in case of elevated marine mortality affecting anadromous trout, but also highlight that increased mortality of anadromous trout, most of which are females, may lower overall production in the system.
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Affiliation(s)
- Eloïse Duval
- Department of Biology, Aarhus University, Ny Munkegade 114, 8000, Aarhus C, Denmark.
- Theoretical and Experimental Ecology Station, UMR-5321, CNRS, University of Toulouse III Paul Sabatier, 2 route du CNRS, 09200, Moulis, France.
| | - Øystein Skaala
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway.
| | - María Quintela
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
| | - Geir Dahle
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
| | - Aurélien Delaval
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
- Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Vidar Wennevik
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
| | - Kevin A Glover
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
- Institute of Biology, University of Bergen, Bergen, Norway
| | - Michael M Hansen
- Department of Biology, Aarhus University, Ny Munkegade 114, 8000, Aarhus C, Denmark.
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway.
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50
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Kuhl H, Guiguen Y, Höhne C, Kreuz E, Du K, Klopp C, Lopez-Roques C, Yebra-Pimentel ES, Ciorpac M, Gessner J, Holostenco D, Kleiner W, Kohlmann K, Lamatsch DK, Prokopov D, Bestin A, Bonpunt E, Debeuf B, Haffray P, Morvezen R, Patrice P, Suciu R, Dirks R, Wuertz S, Kloas W, Schartl M, Stöck M. A 180 Myr-old female-specific genome region in sturgeon reveals the oldest known vertebrate sex determining system with undifferentiated sex chromosomes. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200089. [PMID: 34247507 PMCID: PMC8273502 DOI: 10.1098/rstb.2020.0089] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Several hypotheses explain the prevalence of undifferentiated sex chromosomes in poikilothermic vertebrates. Turnovers change the master sex determination gene, the sex chromosome or the sex determination system (e.g. XY to WZ). Jumping master genes stay main triggers but translocate to other chromosomes. Occasional recombination (e.g. in sex-reversed females) prevents sex chromosome degeneration. Recent research has uncovered conserved heteromorphic or even homomorphic sex chromosomes in several clades of non-avian and non-mammalian vertebrates. Sex determination in sturgeons (Acipenseridae) has been a long-standing basic biological question, linked to economical demands by the caviar-producing aquaculture. Here, we report the discovery of a sex-specific sequence from sterlet (Acipenser ruthenus). Using chromosome-scale assemblies and pool-sequencing, we first identified an approximately 16 kb female-specific region. We developed a PCR-genotyping test, yielding female-specific products in six species, spanning the entire phylogeny with the most divergent extant lineages (A. sturio, A. oxyrinchus versus A. ruthenus, Huso huso), stemming from an ancient tetraploidization. Similar results were obtained in two octoploid species (A. gueldenstaedtii, A. baerii). Conservation of a female-specific sequence for a long period, representing 180 Myr of sturgeon evolution, and across at least one polyploidization event, raises many interesting biological questions. We discuss a conserved undifferentiated sex chromosome system with a ZZ/ZW-mode of sex determination and potential alternatives. 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)
- Heiner Kuhl
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 and 310, 12587 Berlin, Germany
| | | | - Christin Höhne
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 and 310, 12587 Berlin, Germany
| | - Eva Kreuz
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 and 310, 12587 Berlin, Germany
| | - Kang Du
- 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
| | - Christophe Klopp
- SIGENAE, Plate-forme Bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRAe, 31326 Castanet-Tolosan, France
| | | | | | - Mitica Ciorpac
- Danube Delta National Institute for Research and Development, Tulcea 820112, Romania.,Genetic Improvement Laboratory, Research Station for Cattle Breeding Dancu - Iasi (SCDCB Dancu), Academy of Agricultural and Forestry Sciences 'Gheorghe Ionescu-Sisesti', Iasi-Ungheni Street, No. 9, Holboca, Iași county 707252, Romania
| | - Jörn Gessner
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 and 310, 12587 Berlin, Germany
| | - Daniela Holostenco
- Danube Delta National Institute for Research and Development, Tulcea 820112, Romania
| | - Wibke Kleiner
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 and 310, 12587 Berlin, Germany
| | - Klaus Kohlmann
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 and 310, 12587 Berlin, Germany
| | - Dunja K Lamatsch
- Research Department for Limnology, University of Innsbruck, A-5310 Mondsee, Austria
| | - Dmitry Prokopov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Anastasia Bestin
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042 Rennes cedex, France
| | | | - Bastien Debeuf
- SCEA Sturgeon, 29 rue du Carillon, 17240 Saint Fort sur Gironde, France
| | - Pierrick Haffray
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042 Rennes cedex, France
| | - Romain Morvezen
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042 Rennes cedex, France
| | - Pierre Patrice
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042 Rennes cedex, France
| | - Radu Suciu
- Danube Delta National Institute for Research and Development, Tulcea 820112, Romania
| | - Ron Dirks
- Future Genomics Technologies B.V., Sylviusweg 74, 2333 BD, Leiden, The Netherlands
| | - Sven Wuertz
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 and 310, 12587 Berlin, Germany
| | - Werner Kloas
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 and 310, 12587 Berlin, Germany
| | - 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
| | - Matthias Stöck
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 and 310, 12587 Berlin, Germany
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