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He L, Wang Y, Wang Y, Zhang RG, Wang Y, Hörandl E, Ma T, Mao YF, Mank JE, Ming R. Allopolyploidization from two dioecious ancestors leads to recurrent evolution of sex chromosomes. Nat Commun 2024; 15:6893. [PMID: 39134553 PMCID: PMC11319354 DOI: 10.1038/s41467-024-51158-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 07/31/2024] [Indexed: 08/15/2024] Open
Abstract
Polyploidization presents an unusual challenge for species with sex chromosomes, as it can lead to complex combinations of sex chromosomes that disrupt reproductive development. This is particularly true for allopolyploidization between species with different sex chromosome systems. Here, we assemble haplotype-resolved chromosome-level genomes of a female allotetraploid weeping willow (Salix babylonica) and a male diploid S. dunnii. We show that weeping willow arose from crosses between a female ancestor from the Salix-clade, which has XY sex chromosomes on chromosome 7, and a male ancestor from the Vetrix-clade, which has ancestral XY sex chromosomes on chromosome 15. We find that weeping willow has one pair of sex chromosomes, ZW on chromosome 15, that derived from the ancestral XY sex chromosomes in the male ancestor of the Vetrix-clade. Moreover, the ancestral 7X chromosomes from the female ancestor of the Salix-clade have reverted to autosomal inheritance. Duplicated intact ARR17-like genes on the four homologous chromosomes 19 likely have contributed to the maintenance of dioecy during polyploidization and sex chromosome turnover. Taken together, our results suggest the rapid evolution and reversion of sex chromosomes following allopolyploidization in weeping willow.
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Affiliation(s)
- Li He
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
| | - Yuàn Wang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yi Wang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Ren-Gang Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Yuán Wang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Göttingen, Göttingen, Germany
| | - Tao Ma
- Key Laboratory for Bio‑Resource and Eco‑Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yan-Fei Mao
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Judith E Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Ray Ming
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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2
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Cecalev D, Viçoso B, Galupa R. Compensation of gene dosage on the mammalian X. Development 2024; 151:dev202891. [PMID: 39140247 DOI: 10.1242/dev.202891] [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] [Indexed: 08/15/2024]
Abstract
Changes in gene dosage can have tremendous evolutionary potential (e.g. whole-genome duplications), but without compensatory mechanisms, they can also lead to gene dysregulation and pathologies. Sex chromosomes are a paradigmatic example of naturally occurring gene dosage differences and their compensation. In species with chromosome-based sex determination, individuals within the same population necessarily show 'natural' differences in gene dosage for the sex chromosomes. In this Review, we focus on the mammalian X chromosome and discuss recent new insights into the dosage-compensation mechanisms that evolved along with the emergence of sex chromosomes, namely X-inactivation and X-upregulation. We also discuss the evolution of the genetic loci and molecular players involved, as well as the regulatory diversity and potentially different requirements for dosage compensation across mammalian species.
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Affiliation(s)
- Daniela Cecalev
- Molecular, Cellular and Developmental Biology (MCD) Unit, Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062, Toulouse, France
| | - Beatriz Viçoso
- Institute of Science and Technology Austria (ISTA), Am Campus 1, Klosterneuburg 3400, Austria
| | - Rafael Galupa
- Molecular, Cellular and Developmental Biology (MCD) Unit, Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062, Toulouse, France
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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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Jay P, Jeffries D, Hartmann FE, Véber A, Giraud T. Why do sex chromosomes progressively lose recombination? Trends Genet 2024; 40:564-579. [PMID: 38677904 DOI: 10.1016/j.tig.2024.03.005] [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: 10/17/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/29/2024]
Abstract
Progressive recombination loss is a common feature of sex chromosomes. Yet, the evolutionary drivers of this phenomenon remain a mystery. For decades, differences in trait optima between sexes (sexual antagonism) have been the favoured hypothesis, but convincing evidence is lacking. Recent years have seen a surge of alternative hypotheses to explain progressive extensions and maintenance of recombination suppression: neutral accumulation of sequence divergence, selection of nonrecombining fragments with fewer deleterious mutations than average, sheltering of recessive deleterious mutations by linkage to heterozygous alleles, early evolution of dosage compensation, and constraints on recombination restoration. Here, we explain these recent hypotheses and dissect their assumptions, mechanisms, and predictions. We also review empirical studies that have brought support to the various hypotheses.
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Affiliation(s)
- Paul Jay
- Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark; Université Paris-Saclay, CNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079, Bâtiment 680, 12 route RD128, 91190 Gif-sur-Yvette, France.
| | - Daniel Jeffries
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Fanny E Hartmann
- Université Paris-Saclay, CNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079, Bâtiment 680, 12 route RD128, 91190 Gif-sur-Yvette, France
| | - Amandine Véber
- Université Paris Cité, CNRS, MAP5, F-75006 Paris, France
| | - Tatiana Giraud
- Université Paris-Saclay, CNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079, Bâtiment 680, 12 route RD128, 91190 Gif-sur-Yvette, France
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Balini LC, Fernandes CA, Portela-Castro ALDB, Melo RFD, Zawadzki CH, Borin-Carvalho LA. Initial Steps of XY Sex Chromosome Differentiation in the Armored Catfish Hypostomus albopunctatus (Siluriformes: Loricariidae) Revealed by Heterochromatin Accumulation. Zebrafish 2024; 21:265-273. [PMID: 38386543 DOI: 10.1089/zeb.2023.0100] [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: 02/24/2024] Open
Abstract
In fish species, heterochromatinization is one process that could trigger sex chromosome differentiation. The present article describes a nascent XX/XY sex chromosome system evidenced by heterochromatin accumulation and microsatellite (GATA)8 in Hypostomus albopunctatus from two populations of the Paraná River basin. The specimens of H. albopunctatus from the Campo and Bossi Rivers share the same karyotype. The species exhibits 74 chromosomes (8m+14sm +16st +36a, fundamental number = 112). The C-banding technique suggests male heterogamety in H. albopunctatus, where the Y-chromosome is morphologically like the X-chromosome but differs from it for having long arms that are entirely heterochromatic. Double fluorescence in situ hybridization (FISH) with 18S and 5S rDNA probes confirmed the Ag-nucleolus organizer region sites in a single pair for both populations, and minor rDNA clusters showed interpopulational variation. FISH with the microsatellite (GATA)8 probe showed a dispersed pattern in the karyotype, accumulating these sequences of sex chromosomes of both populations. FISH with microsatellite (CGC)10 probe showed interpopulational variation. The absence of differentiated sex chromosomes in H. albopunctatus is described previously, and a new variant is documented herein where XY chromosomes can be seen in an early stage of differentiation.
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Affiliation(s)
- Ligia Carla Balini
- Department of Biotechnology, Genetics, and Cell Biology, State University of Maringá, Maringá, Paraná, Brazil
| | - Carlos Alexandre Fernandes
- Department of Biotechnology, Genetics, and Cell Biology, State University of Maringá, Maringá, Paraná, Brazil
- Limnology, Ichthyology and Aquaculture Research Nucleus (NUPELIA), Biological Sciences Center, State University of Maringá, Maringá, Paraná, Brazil
| | - Ana Luiza de Brito Portela-Castro
- Department of Biotechnology, Genetics, and Cell Biology, State University of Maringá, Maringá, Paraná, Brazil
- Limnology, Ichthyology and Aquaculture Research Nucleus (NUPELIA), Biological Sciences Center, State University of Maringá, Maringá, Paraná, Brazil
| | - Rafael Fernando de Melo
- Department of Biotechnology, Genetics, and Cell Biology, State University of Maringá, Maringá, Paraná, Brazil
| | - Cláudio Henrique Zawadzki
- Limnology, Ichthyology and Aquaculture Research Nucleus (NUPELIA), Biological Sciences Center, State University of Maringá, Maringá, Paraná, Brazil
- Department of Biology, State University of Maringá, Maringá, Paraná, Brazil
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Crepaldi C, Cabral-de-Mello DC, Parise-Maltempi PP. Comparative analysis of transposable elements dynamics in fish with different sex chromosome systems. Genome 2024. [PMID: 38739948 DOI: 10.1139/gen-2023-0134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Transposable elements (TEs) are widespread genomic components with substantial roles in genome evolution and sex chromosome differentiation. In this study, we compared the TE composition of three closely related fish with different sex chromosome systems: Megaleporinus elongatus (Z1Z1Z2Z2/Z1W1Z2W2), Megaleporinus macrocephalus (ZZ/ZW) (both with highly differentiated W sex chromosomes), and Leporinus friderici (without heteromorphic sex chromosomes). We created custom TE libraries for each species using clustering methods and manual annotation and prediction, and we predicted TE temporal dynamics through divergence-based analysis. The TE abundance ranged from 16% to 21% in the three mobilomes, with L. friderici having the lowest overall. Despite the recent amplification of TEs in all three species, we observed differing expansion activities, particularly between the two genera. Both Megaleporinus recently experienced high retrotransposon activity, with a reduction in DNA TEs, which could have implications in sex chromosome composition. In contrast, L. friderici showed the opposite pattern. Therefore, despite having similar TE compositions, Megaleporinus and Leporinus exhibit distinct TE histories that likely evolved after their separation, highlighting a rapid TE expansion over short evolutionary periods.
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Affiliation(s)
- Carolina Crepaldi
- Universidade Estadual Paulista (UNESP) "Júlio de Mesquita Filho", Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Rio Claro, Brazil
| | - Diogo Cavalcanti Cabral-de-Mello
- Universidade Estadual Paulista (UNESP) "Júlio de Mesquita Filho", Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Rio Claro, Brazil
| | - Patricia Pasquali Parise-Maltempi
- Universidade Estadual Paulista (UNESP) "Júlio de Mesquita Filho", Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Rio Claro, Brazil
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Dos Santos GE, Crepaldi C, da Silva MJ, Parise-Maltempi PP. Revealing the Satellite DNA Content in Ancistrus sp. (Siluriformes: Loricariidae) by Genomic and Bioinformatic Analysis. Cytogenet Genome Res 2024; 164:52-59. [PMID: 38631304 DOI: 10.1159/000538926] [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: 01/23/2024] [Accepted: 04/12/2024] [Indexed: 04/19/2024] Open
Abstract
INTRODUCTION Eukaryotic genomes are composed of simple, repetitive sequences, including satellite DNAs (satDNA), which are noncoding sequences arranged in tandem arrays. These sequences play a crucial role in genomic functions and innovations, influencing processes such as the maintenance of nuclear material, the formation of heterochromatin and the differentiation of sex chromosomes. In this genomic era, advances in next-generation sequencing and bioinformatics tools have facilitated the exhaustive cataloging of repetitive elements in genomes, particularly in non-model species. This study focuses on the satDNA content of Ancistrus sp., a diverse species of fish from the Loricariidae family. The genus Ancistrus shows significant karyotypic evolution, with extensive variability from the ancestral diploid number. METHODS By means of bioinformatic approaches, 40 satDNA families in Ancistrus sp., constituting 5.19% of the genome were identified. Analysis of the abundance and divergence landscape revealed diverse profiles, indicating recent amplification and homogenization of these satDNA sequences. RESULTS The most abundant satellite, AnSat1-142, constitutes 2.1% of the genome, while the least abundant, AnSat40-52, represents 0.0034%. The length of the monomer repeat varies from 16 to 142 base pairs, with an average length of 61 bp. These results contribute to understanding the genomic dynamics and evolution of satDNAs in Ancistrus sp. CONCLUSION The study underscores the variability of satDNAs between fish species and provides valuable information on chromosome organization and the evolution of repetitive elements in non-model organisms.
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Affiliation(s)
- Gabriel Esbrisse Dos Santos
- General and Applied Biology Department, Bioscience Institute/São Paulo State University (UNESP), Rio Claro, Brazil
| | - Carolina Crepaldi
- General and Applied Biology Department, Bioscience Institute/São Paulo State University (UNESP), Rio Claro, Brazil
| | - Marcelo João da Silva
- General and Applied Biology Department, Bioscience Institute/São Paulo State University (UNESP), Rio Claro, Brazil
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Amorim KDJ, Costa GWWF, Motta-Neto CC, Soares RX, Borges AT, Benetti DD, Cioffi MB, Bertollo LAC, Tanomtong A, Molina WF. Karyotypic changes and diversification time in Epinephelidae groupers (Perciformes). Implications on reproductive isolation. AN ACAD BRAS CIENC 2024; 96:e20221011. [PMID: 38597487 DOI: 10.1590/0001-3765202420221011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 06/26/2023] [Indexed: 04/11/2024] Open
Abstract
Groupers (Epinephelidae and Serranidae) have attracted special attention to fish farming, and their species offer good opportunities for successful hybridizations. Cytogenetic data allow a better understanding of the role of karyotypic diversification in the acquisition of post-zygotic reproductive isolation (RI). Thus, chromosomal analyses were performed on E. striatus (Caribbean Sea), E. coioides and E. tauvina (Indo-Pacific Region), using standard procedures and mapping of six repetitive DNA classes by the in situ hybridization. The three species have 2n=48 chromosomes. The karyotypes of E. coioides and E. striatus are composed only of acrocentric chromosomes (FN=48), while E. tauvina has 8 submetacentric chromosomes (FN=56). Heterochromatin has a preferential centromeric distribution, and the microsatellite repeats are dispersed throughout the chromosomes of all species. The 18S and 5S rDNA sites are unique but show a colocalization arrangement in E. tauvina and E. striatus. The chromosomal organization suggests that the three species still maintain a significant amount of syntenic regions. The range of the karyotype divergence and the RI levels showed low, but goes turn proportionally greater in relation to the divergence time between the parental species. The slow acquisition of postzygotic RI is consistent with the high karyotype homogeneity presented by Epinephelidae family.
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Affiliation(s)
- Karlla Danielle J Amorim
- Universidade Federal do Rio Grande do Norte, Centro de Biociências, Departamento de Biologia Celular e Genética, Av. Senador Salgado Filho, s/n, Campus Universitário, Lagoa Nova, 59078-970 Natal, RN, Brazil
| | - Gideão W W F Costa
- Universidade Federal do Rio Grande do Norte, Centro de Biociências, Departamento de Biologia Celular e Genética, Av. Senador Salgado Filho, s/n, Campus Universitário, Lagoa Nova, 59078-970 Natal, RN, Brazil
| | - Clóvis C Motta-Neto
- Universidade Federal do Rio Grande do Norte, Centro de Biociências, Departamento de Biologia Celular e Genética, Av. Senador Salgado Filho, s/n, Campus Universitário, Lagoa Nova, 59078-970 Natal, RN, Brazil
| | - Rodrigo X Soares
- Universidade Federal do Rio Grande do Norte, Centro de Biociências, Departamento de Biologia Celular e Genética, Av. Senador Salgado Filho, s/n, Campus Universitário, Lagoa Nova, 59078-970 Natal, RN, Brazil
| | - Amanda T Borges
- Universidade Federal do Rio Grande do Norte, Centro de Biociências, Departamento de Biologia Celular e Genética, Av. Senador Salgado Filho, s/n, Campus Universitário, Lagoa Nova, 59078-970 Natal, RN, Brazil
| | - Daniel D Benetti
- University of Miami, Rosenstiel School of Marine and Atmospheric Science (RSMAS), 4600 Rickenbacker Causeway, Miami, FL 33149, USA
| | - Marcelo B Cioffi
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Laboratório de Citogenética de Peixes, Caixa Postal 676, 13565-905 São Carlos, SP, Brazil
| | - Luiz A C Bertollo
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Laboratório de Citogenética de Peixes, Caixa Postal 676, 13565-905 São Carlos, SP, Brazil
| | - Alongklod Tanomtong
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen, 40002,Thailand
- Toxic Substances in Livestock and Aquatic Animals Research Group, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
| | - Wagner F Molina
- Universidade Federal do Rio Grande do Norte, Centro de Biociências, Departamento de Biologia Celular e Genética, Av. Senador Salgado Filho, s/n, Campus Universitário, Lagoa Nova, 59078-970 Natal, RN, Brazil
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Filipović I, Marshall JM, Rašić G. Finding divergent sequences of homomorphic sex chromosomes via diploidized nanopore-based assembly from a single male. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582759. [PMID: 38464271 PMCID: PMC10925256 DOI: 10.1101/2024.02.29.582759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Although homomorphic sex chromosomes can have non-recombining regions with elevated sequence divergence between its complements, such divergence signals can be difficult to detect bioinformatically. If found in genomes of e.g. insect pests, these sequences could be targeted by the engineered genetic sexing and control systems. Here, we report an approach that can leverage long-read nanopore sequencing of a single XY male to identify divergent regions of homomorphic sex chromosomes. Long-read data are used for de novo genome assembly that is diploidized in a way that maximizes sex-specific differences between its haploid complements. We show that the correct assembly phasing is supported by the mapping of nanopore reads from the male's haploid Y-bearing sperm cells. The approach revealed a highly divergent region (HDR) near the centromere of the homomorphic sex chromosome of Aedes aegypti, the most important arboviral vector, for which there is a great interest in creating new genetic control tools. HDR is located ~5Mb downstream of the known male-determining locus on chromosome 1 and is significantly enriched for ovary-biased genes. While recombination in HDR ceased relatively recently (~1.4 MYA), HDR gametologs have divergent exons and introns of protein coding genes, and most lncRNA genes became X-specific. Megabases of previously invisible sex-linked sequences provide new putative targets for engineering the genetic systems to control this deadly mosquito. Broadly, our approach expands the toolbox for studying cryptic structure of sex chromosomes.
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Affiliation(s)
- Igor Filipović
- Mosquito Genomics, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Australia
- The University of Queensland, School of Biological Sciences, St Lucia, QLD, Australia
| | - John M Marshall
- Divisions of Biostatistics and Epidemiology, School of Public Health, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Gordana Rašić
- Mosquito Genomics, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Australia
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Guo L, Malara D, Battaglia P, Waiho K, Davis DA, Deng Y, Shen Z, Rao K. Turnovers of Sex-Determining Mutation in the Golden Pompano and Related Species Provide Insights into Microevolution of Undifferentiated Sex Chromosome. Genome Biol Evol 2024; 16:evae037. [PMID: 38408866 PMCID: PMC10919887 DOI: 10.1093/gbe/evae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 02/28/2024] Open
Abstract
The suppression of recombination is considered a hallmark of sex chromosome evolution. However, previous research has identified undifferentiated sex chromosomes and sex determination by single SNP in the greater amberjack (Seriola dumerili). We observed the same phenomena in the golden pompano (Trachinotus ovatus) of the same family Carangidae and discovered a different sex-determining SNP within the same gene Hsd17b1. We propose an evolutionary model elucidating the turnover of sex-determining mutations by highlighting the contrasting dynamics between purifying selection, responsible for maintaining W-linked Hsd17b1, and neutral evolution, which drives Z-linked Hsd17b1. Additionally, sporadic loss-of-function mutations in W-linked Hsd17b1 contribute to the conversion of W chromosomes into Z chromosomes. This model was directly supported by simulations, closely related species, and indirectly by zebrafish mutants. These findings shed new light on the early stages of sex chromosome evolution.
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Affiliation(s)
- Liang Guo
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan Province 410081, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong Province 510300, China
| | - Danilo Malara
- Stazione Zoologica Anton Dohrn, Integrated Marine Ecology Department, CRIMAC, Calabria Marine Centre, Amendolara 87071, Italy
| | - Pietro Battaglia
- Integrated Marine Ecology Department, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina 98168, Italy
| | - Khor Waiho
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu 21300, Malaysia
- Centre for Chemical Biology, Universiti Sains Malaysia, Minden 11900, Malaysia
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - D Allen Davis
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36830, USA
| | - Yu Deng
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan Province 410081, China
| | - Zhongyuan Shen
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan Province 410081, China
| | - Ke Rao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan Province 410081, China
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11
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Filatov DA. Evolution of a plant sex chromosome driven by expanding pericentromeric recombination suppression. Sci Rep 2024; 14:1373. [PMID: 38228625 DOI: 10.1038/s41598-024-51153-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/01/2024] [Indexed: 01/18/2024] Open
Abstract
Recombination suppression around sex-determining gene(s) is a key step in evolution of sex chromosomes, but it is not well understood how it evolves. Recently evolved sex-linked regions offer an opportunity to understand the mechanisms of recombination cessation. This paper analyses such a region on Silene latifolia (Caryophyllaceae) sex chromosomes, where recombination was suppressed in the last 120 thousand years ("stratum 3"). Locating the boundaries of the stratum 3 in S. latifolia genome sequence revealed that this region is far larger than assumed previously-it is about 14 Mb long and includes 202 annotated genes. A gradient of X:Y divergence detected in the stratum 3, with divergence increasing proximally, indicates gradual recombination cessation, possibly caused by expansion of pericentromeric recombination suppression (PRS) into the pseudoautosomal region. Expansion of PRS was also the likely cause for the formation of the older stratum 2 on S. latifolia sex chromosomes. The role of PRS in sex chromosome evolution has been underappreciated, but it may be a significant factor, especially in the species with large chromosomes where PRS is often extensive.
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Affiliation(s)
- Dmitry A Filatov
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK.
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12
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Mora P, Hospodářská M, Voleníková AC, Koutecký P, Štundlová J, Dalíková M, Walters JR, Nguyen P. Sex-biased gene content is associated with sex chromosome turnover in Danaini butterflies. Mol Ecol 2024:e17256. [PMID: 38180347 DOI: 10.1111/mec.17256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/01/2023] [Accepted: 12/13/2023] [Indexed: 01/06/2024]
Abstract
Sex chromosomes play an outsized role in adaptation and speciation, and thus deserve particular attention in evolutionary genomics. In particular, fusions between sex chromosomes and autosomes can produce neo-sex chromosomes, which offer important insights into the evolutionary dynamics of sex chromosomes. Here, we investigate the evolutionary origin of the previously reported Danaus neo-sex chromosome within the tribe Danaini. We assembled and annotated genomes of Tirumala septentrionis (subtribe Danaina), Ideopsis similis (Amaurina), Idea leuconoe (Euploeina) and Lycorea halia (Itunina) and identified their Z-linked scaffolds. We found that the Danaus neo-sex chromosome resulting from the fusion between a Z chromosome and an autosome corresponding to the Melitaea cinxia chromosome (McChr) 21 arose in a common ancestor of Danaina, Amaurina and Euploina. We also identified two additional fusions as the W chromosome further fused with the synteny block McChr31 in I. similis and independent fusion occurred between ancestral Z chromosome and McChr12 in L. halia. We further tested a possible role of sexually antagonistic selection in sex chromosome turnover by analysing the genomic distribution of sex-biased genes in I. leuconoe and L. halia. The autosomes corresponding to McChr21 and McChr31 involved in the fusions are significantly enriched in female- and male-biased genes, respectively, which could have hypothetically facilitated fixation of the neo-sex chromosomes. This suggests a role of sexual antagonism in sex chromosome turnover in Lepidoptera. The neo-Z chromosomes of both I. leuconoe and L. halia appear fully compensated in somatic tissues, but the extent of dosage compensation for the ancestral Z varies across tissues and species.
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Affiliation(s)
- Pablo Mora
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Monika Hospodářská
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | | | - Petr Koutecký
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Jana Štundlová
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Martina Dalíková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - James R Walters
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Petr Nguyen
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
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13
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Xu XW, Sun P, Gao C, Zheng W, Chen S. Assembly of the poorly differentiated Verasper variegatus W chromosome by different sequencing technologies. Sci Data 2023; 10:893. [PMID: 38092799 PMCID: PMC10719390 DOI: 10.1038/s41597-023-02790-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 11/24/2023] [Indexed: 12/17/2023] Open
Abstract
The assembly of W and Y chromosomes poses significant challenges in vertebrate genome sequencing and assembly. Here, we successfully assembled the W chromosome of Verasper variegatus with a length of 20.48 Mb by combining population and PacBio HiFi sequencing data. It was identified as a young sex chromosome and showed signs of expansion in repetitive sequences. The major component of the expansion was Ty3/Gypsy. The ancestral Osteichthyes karyotype consists of 24 protochromosomes. The sex chromosomes in four Pleuronectiformes species derived from a pair of homologous protochromosomes resulting from a whole-genome duplication event in teleost fish, yet with different sex-determination systems. V. variegatus and Cynoglossus semilaevis adhere to the ZZ/ZW system, while Hippoglossus stenolepis and H. hippoglossus follow the XX/XY system. Interestingly, V. variegatus and H. hippoglossus derived from one protochromosome, while C. semilaevis and H. stenolepis derived from another protochromosome. Our study provides valuable insights into the evolution of sex chromosomes in flatfish and sheds light on the important role of whole-genome duplication in shaping the evolution of sex chromosomes.
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Affiliation(s)
- Xi-Wen Xu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, 266237, China
| | - Pengchuan Sun
- Key Laboratory for Bio-resources and Eco-environment & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Chengbin Gao
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Weiwei Zheng
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Songlin Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, 266237, China.
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14
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Zhang X, Xiang J, Yuan J, Li F. Penaeid Shrimp Chromosome Studies Entering the Post-Genomic Era. Genes (Basel) 2023; 14:2050. [PMID: 38002993 PMCID: PMC10671375 DOI: 10.3390/genes14112050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Chromosome studies provide the foundation for comprehending inheritance, variation, systematics, and evolution. Penaeid shrimps are a group of crustaceans with great economic importance. Basic cytogenetic information obtained from these shrimps can be used to study their genome structure, chromosome relationships, chromosome variation, polyploidy manipulation, and breeding. The study of shrimp chromosomes experienced significant growth in the 1990s and has been closely linked to the progress of genome research since the application of next-generation sequencing technology. To date, the genome sequences of five penaeid shrimp species have been published. The availability of these genomes has ushered the study of shrimp chromosomes into the post-genomic era. Currently, research on shrimp cytogenetics not only involves chromosome counting and karyotyping, but also extends to investigating submicroscopic changes; exploring genome structure and regulation during various cell divisions; and contributing to the understanding of mechanisms related to growth, sexual control, stress resistance, and genome evolution. In this article, we provide an overview of the progress made in chromosome research on penaeid shrimp. We emphasize the mutual promotion between studies on chromosome structure and genome research and highlight the impact of chromosome-level assembly on studies of genome structure and function. Additionally, we summarize the emerging trends in post-genomic-era shrimp chromosome research.
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Affiliation(s)
- Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (J.Y.)
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianhai Xiang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (J.Y.)
| | - Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (J.Y.)
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Z.); (J.X.); (J.Y.)
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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15
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Rasoarahona R, Wattanadilokchatkun P, Panthum T, Jaisamut K, Lisachov A, Thong T, Singchat W, Ahmad SF, Han K, Kraichak E, Muangmai N, Koga A, Duengkae P, Antunes A, Srikulnath K. MicrosatNavigator: exploring nonrandom distribution and lineage-specificity of microsatellite repeat motifs on vertebrate sex chromosomes across 186 whole genomes. Chromosome Res 2023; 31:29. [PMID: 37775555 DOI: 10.1007/s10577-023-09738-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/11/2023] [Accepted: 09/05/2023] [Indexed: 10/01/2023]
Abstract
Microsatellites are short tandem DNA repeats, ubiquitous in genomes. They are believed to be under selection pressure, considering their high distribution and abundance beyond chance or random accumulation. However, limited analysis of microsatellites in single taxonomic groups makes it challenging to understand their evolutionary significance across taxonomic boundaries. Despite abundant genomic information, microsatellites have been studied in limited contexts and within a few species, warranting an unbiased examination of their genome-wide distribution in distinct versus closely related-clades. Large-scale comparisons have revealed relevant trends, especially in vertebrates. Here, "MicrosatNavigator", a new tool that allows quick and reliable investigation of perfect microsatellites in DNA sequences, was developed. This tool can identify microsatellites across the entire genome sequences. Using this tool, microsatellite repeat motifs were identified in the genome sequences of 186 vertebrates. A significant positive correlation was noted between the abundance, density, length, and GC bias of microsatellites and specific lineages. The (AC)n motif is the most prevalent in vertebrate genomes, showing distinct patterns in closely related species. Longer microsatellites were observed on sex chromosomes in birds and mammals but not on autosomes. Microsatellites on sex chromosomes of non-fish vertebrates have the lowest GC content, whereas high-GC microsatellites (≥ 50 M% GC) are preferred in bony and cartilaginous fishes. Thus, similar selective forces and mutational processes may constrain GC-rich microsatellites to different clades. These findings should facilitate investigations into the roles of microsatellites in sex chromosome differentiation and provide candidate microsatellites for functional analysis across the vertebrate evolutionary spectrum.
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Affiliation(s)
- Ryan Rasoarahona
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Pish Wattanadilokchatkun
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Kitipong Jaisamut
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Artem Lisachov
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan, 31116, Republic of Korea
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea
| | - Ekaphan Kraichak
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Botany, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Akihiko Koga
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros Do Porto de Leixes, Av. General Norton de Matos, S/N, 4450-208, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, S/N, 4169-007, Porto, Portugal
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, (CASTNAR, NRU-KU, Thailand), Bangkok, 10900, Thailand.
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok, 10900, Thailand.
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16
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Arnqvist G, Rowe L. Ecology, the pace-of-life, epistatic selection and the maintenance of genetic variation in life-history genes. Mol Ecol 2023; 32:4713-4724. [PMID: 37386734 DOI: 10.1111/mec.17062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 06/09/2023] [Accepted: 06/19/2023] [Indexed: 07/01/2023]
Abstract
Evolutionary genetics has long struggled with understanding how functional genes under selection remain polymorphic in natural populations. Taking as a starting point that natural selection is ultimately a manifestation of ecological processes, we spotlight an underemphasized and potentially ubiquitous ecological effect that may have fundamental effects on the maintenance of genetic variation. Negative frequency dependency is a well-established emergent property of density dependence in ecology, because the relative profitability of different modes of exploiting or utilizing limiting resources tends to be inversely proportional to their frequency in a population. We suggest that this may often generate negative frequency-dependent selection (NFDS) on major effect loci that affect rate-dependent physiological processes, such as metabolic rate, that are phenotypically manifested as polymorphism in pace-of-life syndromes. When such a locus under NFDS shows stable intermediate frequency polymorphism, this should generate epistatic selection potentially involving large numbers of loci with more minor effects on life-history (LH) traits. When alternative alleles at such loci show sign epistasis with a major effect locus, this associative NFDS will promote the maintenance of polygenic variation in LH genes. We provide examples of the kind of major effect loci that could be involved and suggest empirical avenues that may better inform us on the importance and reach of this process.
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Affiliation(s)
- Göran Arnqvist
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Locke Rowe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Swedish Collegium of Advanced Study, Uppsala, Sweden
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17
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Sykes NTB, Kolora SRR, Sudmant PH, Owens GL. Rapid turnover and evolution of sex-determining regions in Sebastes rockfishes. Mol Ecol 2023; 32:5013-5027. [PMID: 37548650 DOI: 10.1111/mec.17090] [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: 01/31/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/08/2023]
Abstract
Nature has evolved a wealth of sex determination (SD) mechanisms, driven by both genetic and environmental factors. Recent studies of SD in fishes have shown that not all taxa fit the classic paradigm of sex chromosome evolution and diverse SD methods can be found even among closely related species. Here, we apply a suite of genomic approaches to investigate sex-biased genomic variation in eight species of Sebastes rockfish found in the northeast Pacific Ocean. Using recently assembled chromosome-level rockfish genomes, we leverage published sequence data to identify disparate sex chromosomes and sex-biased loci in five species. We identify two putative male sex chromosomes in S. diaconus, a single putative sex chromosome in the sibling species S. carnatus and S. chrysomelas, and an unplaced sex determining contig in the sibling species S. miniatus and S. crocotulus. Our study provides evidence for disparate means of sex determination within a recently diverged set of species and sheds light on the diverse origins of sex determination mechanisms present in the animal kingdom.
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Affiliation(s)
- Nathan T B Sykes
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Sree Rohit Raj Kolora
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Peter H Sudmant
- Department of Integrative Biology, University of California, Berkeley, California, USA
- Center for Computational Biology, University of California, Berkeley, California, USA
| | - Gregory L Owens
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
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18
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de Oliveira MPB, Kretschmer R, Deon GA, Toma GA, Ezaz T, Goes CAG, Porto-Foresti F, Liehr T, Utsunomia R, Cioffi MDB. Following the Pathway of W Chromosome Differentiation in Triportheus (Teleostei: Characiformes). BIOLOGY 2023; 12:1114. [PMID: 37626998 PMCID: PMC10452202 DOI: 10.3390/biology12081114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/04/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023]
Abstract
In this work, we trace the dynamics of satellite DNAs (SatDNAs) accumulation and elimination along the pathway of W chromosome differentiation using the well-known Triportheus fish model. Triportheus stands out due to a conserved ZZ/ZW sex chromosome system present in all examined species. While the Z chromosome is conserved in all species, the W chromosome is invariably smaller and exhibits differences in size and morphology. The presumed ancestral W chromosome is comparable to that of T. auritus, and contains 19 different SatDNA families. Here, by examining five additional Triportheus species, we showed that the majority of these repetitive sequences were eliminated as speciation was taking place. The W chromosomes continued degeneration, while the Z chromosomes of some species began to accumulate some TauSatDNAs. Additional species-specific SatDNAs that made up the heterochromatic region of both Z and W chromosomes were most likely amplified in each species. Therefore, the W chromosomes of the various Triportheus species have undergone significant evolutionary changes in a short period of time (15-25 Myr) after their divergence.
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Affiliation(s)
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas 96010-610, Brazil;
| | - Geize Aparecida Deon
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Sao Carlos 13565-905, Brazil; (M.P.B.d.O.); (G.A.D.); (G.A.T.); (M.d.B.C.)
| | - Gustavo Akira Toma
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Sao Carlos 13565-905, Brazil; (M.P.B.d.O.); (G.A.D.); (G.A.T.); (M.d.B.C.)
| | - Tariq Ezaz
- Faculty of Science and Technology, Centre for Conservation Ecology and Genomics, University of Canberra, Canberra 2617, Australia;
| | - Caio Augusto Gomes Goes
- Faculdade de Ciências, Universidade Estadual Paulista, Bauru 13506-900, Brazil; (C.A.G.G.); (F.P.-F.); (R.U.)
| | - Fábio Porto-Foresti
- Faculdade de Ciências, Universidade Estadual Paulista, Bauru 13506-900, Brazil; (C.A.G.G.); (F.P.-F.); (R.U.)
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany
| | - Ricardo Utsunomia
- Faculdade de Ciências, Universidade Estadual Paulista, Bauru 13506-900, Brazil; (C.A.G.G.); (F.P.-F.); (R.U.)
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Sao Carlos 13565-905, Brazil; (M.P.B.d.O.); (G.A.D.); (G.A.T.); (M.d.B.C.)
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19
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Zhou Y, Zhan X, Jin J, Zhou L, Bergman J, Li X, Rousselle MMC, Belles MR, Zhao L, Fang M, Chen J, Fang Q, Kuderna L, Marques-Bonet T, Kitayama H, Hayakawa T, Yao YG, Yang H, Cooper DN, Qi X, Wu DD, Schierup MH, Zhang G. Eighty million years of rapid evolution of the primate Y chromosome. Nat Ecol Evol 2023; 7:1114-1130. [PMID: 37268856 DOI: 10.1038/s41559-022-01974-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 12/15/2022] [Indexed: 06/04/2023]
Abstract
The Y chromosome usually plays a critical role in determining male sex and comprises sequence classes that have experienced unique evolutionary trajectories. Here we generated 19 new primate sex chromosome assemblies, analysed them with 10 existing assemblies and report rapid evolution of the Y chromosome across primates. The pseudoautosomal boundary has shifted at least six times during primate evolution, leading to the formation of a Simiiformes-specific evolutionary stratum and to the independent start of young strata in Catarrhini and Platyrrhini. Different primate lineages experienced different rates of gene loss and structural and chromatin change on their Y chromosomes. Selection on several Y-linked genes has contributed to the evolution of male developmental traits across the primates. Additionally, lineage-specific expansions of ampliconic regions have further increased the diversification of the structure and gene composition of the Y chromosome. Overall, our comprehensive analysis has broadened our knowledge of the evolution of the primate Y chromosome.
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Affiliation(s)
| | | | | | - Long Zhou
- Centre for Evolutionary & Organismal Biology, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Juraj Bergman
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University, Aarhus C., Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus C., Denmark
| | - Xuemei Li
- BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | | | - Lan Zhao
- College of Life Sciences, Northwest University, Xi'an, China
| | | | | | - Qi Fang
- BGI-Shenzhen, Shenzhen, China
| | - Lukas Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Haruka Kitayama
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
- Japan Monkey Centre, Inuyama, Japan
| | - Yong-Gang Yao
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- James D. Watson Institute of Genome Sciences, Hangzhou, China
- Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Xiaoguang Qi
- College of Life Sciences, Northwest University, Xi'an, China
| | - Dong-Dong Wu
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | | | - Guojie Zhang
- Centre for Evolutionary & Organismal Biology, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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20
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Yue J, Krasovec M, Kazama Y, Zhang X, Xie W, Zhang S, Xu X, Kan B, Ming R, Filatov DA. The origin and evolution of sex chromosomes, revealed by sequencing of the Silene latifolia female genome. Curr Biol 2023:S0960-9822(23)00678-4. [PMID: 37290443 DOI: 10.1016/j.cub.2023.05.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/07/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
White campion (Silene latifolia, Caryophyllaceae) was the first vascular plant where sex chromosomes were discovered. This species is a classic model for studies on plant sex chromosomes due to presence of large, clearly distinguishable X and Y chromosomes that originated de novo about 11 million years ago (mya), but lack of genomic resources for this relatively large genome (∼2.8 Gb) remains a significant hurdle. Here we report S. latifolia female genome assembly integrated with sex-specific genetic maps of this species, focusing on sex chromosomes and their evolution. The analysis reveals a highly heterogeneous recombination landscape with strong reduction in recombination rate in the central parts of all chromosomes. Recombination on the X chromosome in female meiosis primarily occurs at the very ends, and over 85% of the X chromosome length is located in a massive (∼330 Mb) gene-poor, rarely recombining pericentromeric region (Xpr). The results indicate that the non-recombining region on the Y chromosome (NRY) initially evolved in a relatively small (∼15 Mb), actively recombining region at the end of the q-arm, possibly as a result of inversion on the nascent X chromosome. The NRY expanded about 6 mya via linkage between the Xpr and the sex-determining region, which may have been caused by expanding pericentromeric recombination suppression on the X chromosome. These findings shed light on the origin of sex chromosomes in S. latifolia and yield genomic resources to assist ongoing and future investigations into sex chromosome evolution.
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Affiliation(s)
- Jingjing Yue
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Marc Krasovec
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK; Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Yusuke Kazama
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Kenjojima, Matsuoka, Eiheiji-cho, Fukui 910-1195, Japan
| | - Xingtan Zhang
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518100, China
| | - Wangyang Xie
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shencheng Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518100, China
| | - Xiuming Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361100, China
| | - Baolin Kan
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ray Ming
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Dmitry A Filatov
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK.
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21
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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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22
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Richardson JML, Alexander HJ, Anholt BR. Variance components of sex determination in the copepod Tigriopus californicus estimated from a pedigree analysis. Ecol Evol 2023; 13:e9997. [PMID: 37153021 PMCID: PMC10154854 DOI: 10.1002/ece3.9997] [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: 12/20/2022] [Revised: 03/19/2023] [Accepted: 03/24/2023] [Indexed: 05/09/2023] Open
Abstract
Extensive theory exists regarding population sex ratio evolution that predicts equal sex ratio (when parental investment is equal). In most animals, sex chromosomes determine the sex of offspring, and this fixed genotype for sex has made theory difficult to test since genotypic variance for the trait (sex) is lacking. It has long been argued that the genotype has become fixed in most animals due to the strong selection for equal sex ratios. The marine copepod Tigriopus californicus has no sex chromosomes, multiple genes affecting female brood sex ratio, and a brood sex ratio that responds to selection. The species thus provides an opportune system in which to test established sex ratio theory. In this paper, we further our exploration of polygenic sex determination in T. californicus using an incomplete diallel crossing design for analysis of the variance components of sex determination in the species. Our data confirm the presence of extra-binomial variance for sex, further confirming that sex is not determined through simple Mendelian trait inheritance. In addition, our crosses and backcrosses of isofemale lines selected for biased brood sex ratios show intermediate phenotypic means, as expected if sex is a threshold trait determined by an underlying "liability" trait controlled by many genes of small effects. Furthermore, crosses between families from the same selection line had similar increases in phenotypic variance as crosses between families from different selection lines, suggesting families from artificial selection lines responded to selection pressure through different underlying genetic bases. Finally, we estimate heritability of an individual to be male or female on the observed binary scale as 0.09 (95% CI: 0.034-0.14). This work furthers our accumulating evidence for polygenic sex determination in T. californicus laying the foundation for this as a model species in future studies of sex ratio evolution theory.
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Affiliation(s)
- Jean M. L. Richardson
- Bamfield Marine Sciences CentreBamfieldBritish ColumbiaCanadaV0R 1B0
- Department of BiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
| | | | - Bradley R. Anholt
- Bamfield Marine Sciences CentreBamfieldBritish ColumbiaCanadaV0R 1B0
- Department of BiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
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23
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João Da Silva M, Gazoni T, Haddad CFB, Parise-Maltempi PP. Analysis in Proceratophrys boiei genome illuminates the satellite DNA content in a frog from the Brazilian Atlantic forest. Front Genet 2023; 14:1101397. [PMID: 37065500 PMCID: PMC10095563 DOI: 10.3389/fgene.2023.1101397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/13/2023] [Indexed: 03/31/2023] Open
Abstract
Satellite DNAs (satDNAs) are one of the most abundant elements in genomes. Characterized as tandemly organized sequences that can be amplified into multiple copies, mainly in heterochromatic regions. The frog P. boiei (2n = 22, ZZ♂/ZW♀) is found in the Brazilian Atlantic forest and has an atypical pattern of heterochromatin distribution when compared to other anuran amphibians, with large pericentromeric blocks on all chromosomes. In addition, females of Proceratophrys boiei have a metacentric sex chromosome W showing heterochromatin in all chromosomal extension. In this work, we performed high-throughput genomic, bioinformatic, and cytogenetic analyses to characterize the satellite DNA content (satellitome) in P. boiei, mainly due to high amount of C-positive heterochromatin and the highly heterochromatic W sex chromosome. After all the analyses, it is remarkable that the satellitome of P. boiei is composed of a high number of satDNA families (226), making P. boiei the frog species with the highest number of satellites described so far. Consistent with the observation of large centromeric C-positive heterochromatin blocks, the genome of P. boiei is enriched with high copy number of repetitive DNAs, with total satDNA abundance comprising 16.87% of the genome. We successfully mapped via Fluorescence in situ hybridization the two most abundant repeats in the genome, PboSat01-176 and PboSat02-192, highlighting the presence of certain satDNAs sequences in strategic chromosomal regions (e.g., centromere and pericentromeric region), which leads to their participation in crucial processes for genomic organization and maintenance. Our study reveals a great diversity of satellite repeats that are driving genomic organization in this frog species. The characterization and approaches regarding satDNAs in this species of frog allowed the confirmation of some insights from satellite biology and a possible relationship with the evolution of sex chromosomes, especially in anuran amphibians, including P. boiei, for which data were not available.
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Affiliation(s)
- Marcelo João Da Silva
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências (IB), Universidade Estadual Paulista (UNESP), São Paulo, Brazil
| | - Thiago Gazoni
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências (IB), Universidade Estadual Paulista (UNESP), São Paulo, Brazil
| | - Célio Fernando Baptista Haddad
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências (IB), Universidade Estadual Paulista (UNESP), São Paulo, Brazil
| | - Patricia Pasquali Parise-Maltempi
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências (IB), Universidade Estadual Paulista (UNESP), São Paulo, Brazil
- *Correspondence: Patricia Pasquali Parise-Maltempi,
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24
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Heterochiasmy and Sex Chromosome Evolution in Silene. Genes (Basel) 2023; 14:genes14030543. [PMID: 36980816 PMCID: PMC10048291 DOI: 10.3390/genes14030543] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 02/24/2023] Open
Abstract
The evolution of a non-recombining sex-specific region is a key step in sex chromosome evolution. Suppression of recombination between the (proto-) X- and Y-chromosomes in male meiosis creates a non-recombining Y-linked region (NRY), while the X-chromosome continues to recombine in females. Lack of recombination in the NRY defines its main properties—genetic degeneration and accumulation of repetitive DNA, making X and Y chromosomes very different from each other. How and why recombination suppression on sex chromosomes evolves remains controversial. A strong difference in recombination rates between the sexes (heterochiasmy) can facilitate or even cause recombination suppression. In the extreme case—complete lack of recombination in the heterogametic sex (achiasmy)—the entire sex-specific chromosome is automatically non-recombining. In this study, I analyse sex-specific recombination rates in a dioecious plant Silene latifolia (Caryophyllaceae), which evolved separate sexes and sex chromosomes ~11 million years ago. I reconstruct high-density RNAseq-based genetic maps including over five thousand genic markers for the two sexes separately. The comparison of the male and female maps reveals only modest heterochiasmy across the genome, with the exception of the sex chromosomes, where recombination is suppressed in males. This indicates that heterochiasmy likely played only a minor, if any, role in NRY evolution in S. latifolia, as recombination suppression is specific to NRY rather than to the entire genome in males. Other mechanisms such as structural rearrangements and/or epigenetic modifications were likely involved, and comparative genome analysis and genetic mapping in multiple Silene species will help to shed light on the mechanism(s) of recombination suppression that led to the evolution of sex chromosomes.
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25
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Sultanova Z, Downing PA, Carazo P. Genetic sex determination, sex chromosome size and sex-specific lifespans across tetrapods. J Evol Biol 2023; 36:480-494. [PMID: 36537352 PMCID: PMC10107984 DOI: 10.1111/jeb.14130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 12/24/2022]
Abstract
Sex differences in lifespan are ubiquitous across the tree of life and exhibit broad taxonomic patterns that remain a puzzle, such as males living longer than females in birds and vice versa in mammals. The prevailing unguarded X hypothesis explains sex differences in lifespan by differential expression of recessive mutations on the X or Z chromosome of the heterogametic sex, but has only received indirect support to date. An alternative hypothesis is that the accumulation of deleterious mutations and repetitive elements on the Y or W chromosome might lower the survival of the heterogametic sex ('toxic Y' hypothesis). Here, we use a new database to report lower survival of the heterogametic relative to the homogametic sex across 136 species of birds, mammals, reptiles and amphibians, as expected if sex chromosomes shape sex-specific lifespans, and consistent with previous findings. We also found that the relative sizes of both the X and the Y chromosomes in mammals (but not the Z or the W chromosomes in birds) are associated with sex differences in lifespan, as predicted by the unguarded X and the 'toxic Y'. Furthermore, we report that the relative size of the Y is negatively associated with male lifespan in mammals, so that small Y size correlates with increased male lifespan. In theory, toxic Y effects are expected to be particularly strong in mammals, and we did not find similar effects in birds. Our results confirm the role of sex chromosomes in explaining sex differences in lifespan across tetrapods and further suggest that, at least in mammals, 'toxic Y' effects may play an important part in this role.
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Affiliation(s)
- Zahida Sultanova
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Philip A Downing
- Department of Biology, Lund University, Lund, Sweden.,Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Pau Carazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
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26
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Mrnjavac A, Khudiakova KA, Barton NH, Vicoso B. Slower-X: reduced efficiency of selection in the early stages of X chromosome evolution. Evol Lett 2023; 7:4-12. [PMID: 37065438 PMCID: PMC10091493 DOI: 10.1093/evlett/qrac004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/08/2022] [Accepted: 12/17/2022] [Indexed: 02/04/2023] Open
Abstract
Abstract
Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated.
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Affiliation(s)
- Andrea Mrnjavac
- Institute of Science and Technology Austria , Am Campus 1, 3400 Klosterneuburg , Austria
| | - Ksenia A Khudiakova
- Institute of Science and Technology Austria , Am Campus 1, 3400 Klosterneuburg , Austria
| | - Nicholas H Barton
- Institute of Science and Technology Austria , Am Campus 1, 3400 Klosterneuburg , Austria
| | - Beatriz Vicoso
- Institute of Science and Technology Austria , Am Campus 1, 3400 Klosterneuburg , Austria
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27
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Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles. Animals (Basel) 2023; 13:ani13030471. [PMID: 36766360 PMCID: PMC9913427 DOI: 10.3390/ani13030471] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 02/01/2023] Open
Abstract
Non-avian reptiles comprise a large proportion of amniote vertebrate diversity, with squamate reptiles-lizards and snakes-recently overtaking birds as the most species-rich tetrapod radiation. Despite displaying an extraordinary diversity of phenotypic and genomic traits, genomic resources in non-avian reptiles have accumulated more slowly than they have in mammals and birds, the remaining amniotes. Here we review the remarkable natural history of non-avian reptiles, with a focus on the physical traits, genomic characteristics, and sequence compositional patterns that comprise key axes of variation across amniotes. We argue that the high evolutionary diversity of non-avian reptiles can fuel a new generation of whole-genome phylogenomic analyses. A survey of phylogenetic investigations in non-avian reptiles shows that sequence capture-based approaches are the most commonly used, with studies of markers known as ultraconserved elements (UCEs) especially well represented. However, many other types of markers exist and are increasingly being mined from genome assemblies in silico, including some with greater information potential than UCEs for certain investigations. We discuss the importance of high-quality genomic resources and methods for bioinformatically extracting a range of marker sets from genome assemblies. Finally, we encourage herpetologists working in genomics, genetics, evolutionary biology, and other fields to work collectively towards building genomic resources for non-avian reptiles, especially squamates, that rival those already in place for mammals and birds. Overall, the development of this cross-amniote phylogenomic tree of life will contribute to illuminate interesting dimensions of biodiversity across non-avian reptiles and broader amniotes.
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28
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Han W, Liu L, Wang J, Wei H, Li Y, Zhang L, Guo Z, Li Y, Liu T, Zeng Q, Xing Q, Shu Y, Wang T, Yang Y, Zhang M, Li R, Yu J, Pu Z, Lv J, Lian S, Hu J, Hu X, Bao Z, Bao L, Zhang L, Wang S. Ancient homomorphy of molluscan sex chromosomes sustained by reversible sex-biased genes and sex determiner translocation. Nat Ecol Evol 2022; 6:1891-1906. [PMID: 36280781 DOI: 10.1038/s41559-022-01898-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 09/05/2022] [Indexed: 12/15/2022]
Abstract
Contrary to classic theory prediction, sex-chromosome homomorphy is prevalent in the animal kingdom but it is unclear how ancient homomorphic sex chromosomes avoid chromosome-scale degeneration. Molluscs constitute the second largest, Precambrian-originated animal phylum and have ancient, uncharacterized homomorphic sex chromosomes. Here, we profile eight genomes of the bivalve mollusc family of Pectinidae in a phylogenetic context and show 350 million years sex-chromosome homomorphy, which is the oldest known sex-chromosome homomorphy in the animal kingdom, far exceeding the ages of well-known heteromorphic sex chromosomes such as 130-200 million years in mammals, birds and flies. The long-term undifferentiation of molluscan sex chromosomes is potentially sustained by the unexpected intertwined regulation of reversible sex-biased genes, together with the lack of sexual dimorphism and occasional sex chromosome turnover. The pleiotropic constraint of regulation of reversible sex-biased genes is widely present in ancient homomorphic sex chromosomes and might be resolved in heteromorphic sex chromosomes through gene duplication followed by subfunctionalization. The evolutionary dynamics of sex chromosomes suggest a mechanism for 'inheritance' turnover of sex-determining genes that is mediated by translocation of a sex-determining enhancer. On the basis of these findings, we propose an evolutionary model for the long-term preservation of homomorphic sex chromosomes.
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Affiliation(s)
- Wentao Han
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Liangjie Liu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jing Wang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Huilan Wei
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuli Li
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lijing Zhang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhenyi Guo
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yajuan Li
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Tian Liu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qifan Zeng
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Qiang Xing
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ya Shu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Tong Wang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yaxin Yang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Meiwei Zhang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Ruojiao Li
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jiachen Yu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhongqi Pu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jia Lv
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Shanshan Lian
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jingjie Hu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Xiaoli Hu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenmin Bao
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Lisui Bao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China.
| | - Lingling Zhang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Shi Wang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China.
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29
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Ma W, Rovatsos M. Sex chromosome evolution: The remarkable diversity in the evolutionary rates and mechanisms. J Evol Biol 2022; 35:1581-1588. [DOI: 10.1111/jeb.14119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 12/03/2022]
Affiliation(s)
- Wen‐Juan Ma
- Department of Molecular Biosciences University of Kansas Lawrence Kansas USA
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30
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Darolti I, Almeida P, Wright AE, Mank JE. Comparison of methodological approaches to the study of young sex chromosomes: A case study in Poecilia. J Evol Biol 2022; 35:1646-1658. [PMID: 35506576 PMCID: PMC10084049 DOI: 10.1111/jeb.14013] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/21/2022] [Accepted: 04/11/2022] [Indexed: 12/16/2022]
Abstract
Studies of sex chromosome systems at early stages of divergence are key to understanding the initial process and underlying causes of recombination suppression. However, identifying signatures of divergence in homomorphic sex chromosomes can be challenging due to high levels of sequence similarity between the X and the Y. Variations in methodological precision and underlying data can make all the difference between detecting subtle divergence patterns or missing them entirely. Recent efforts to test for X-Y sequence differentiation in the guppy have led to contradictory results. Here, we apply different analytical methodologies to the same data set to test for the accuracy of different approaches in identifying patterns of sex chromosome divergence in the guppy. Our comparative analysis reveals that the most substantial source of variation in the results of the different analyses lies in the reference genome used. Analyses using custom-made genome assemblies for the focal population or species successfully recover a signal of divergence across different methodological approaches. By contrast, using the distantly related Xiphophorus reference genome results in variable patterns, due to both sequence evolution and structural variations on the sex chromosomes between the guppy and Xiphophorus. Changes in mapping and filtering parameters can additionally introduce noise and obscure the signal. Our results illustrate how analytical differences can alter perceived results and we highlight best practices for the study of nascent sex chromosomes.
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Affiliation(s)
- Iulia Darolti
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pedro Almeida
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Alison E Wright
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Judith E Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Cornwall, UK
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31
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Gong G, Xiong Y, Xiao S, Li XY, Huang P, Liao Q, Han Q, Lin Q, Dan C, Zhou L, Ren F, Zhou Q, Gui JF, Mei J. Origin and chromatin remodeling of young X/Y sex chromosomes in catfish with sexual plasticity. Natl Sci Rev 2022; 10:nwac239. [PMID: 36846302 PMCID: PMC9945428 DOI: 10.1093/nsr/nwac239] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 08/22/2022] [Accepted: 10/21/2022] [Indexed: 11/15/2022] Open
Abstract
Assembly of a complete Y chromosome is a significant challenge in animals with an XX/XY sex-determination system. Recently, we created YY-supermale yellow catfish by crossing XY males with sex-reversed XY females, providing a valuable model for Y-chromosome assembly and evolution. Here, we assembled highly homomorphic Y and X chromosomes by sequencing genomes of the YY supermale and XX female in yellow catfish, revealing their nucleotide divergences with only less than 1% and with the same gene compositions. The sex-determining region (SDR) was identified to locate within a physical distance of 0.3 Mb by FST scanning. Strikingly, the incipient sex chromosomes were revealed to originate via autosome-autosome fusion and were characterized by a highly rearranged region with an SDR downstream of the fusion site. We found that the Y chromosome was at a very early stage of differentiation, as no clear evidence of evolutionary strata and classical structure features of recombination suppression for a rather late stage of Y-chromosome evolution were observed. Significantly, a number of sex-antagonistic mutations and the accumulation of repetitive elements were discovered in the SDR, which might be the main driver of the initial establishment of recombination suppression between young X and Y chromosomes. Moreover, distinct three-dimensional chromatin organizations of the Y and X chromosomes were identified in the YY supermales and XX females, as the X chromosome exhibited denser chromatin structure than the Y chromosome, while they respectively have significantly spatial interactions with female- and male-related genes compared with other autosomes. The chromatin configuration of the sex chromosomes as well as the nucleus spatial organization of the XX neomale were remodeled after sex reversal and similar to those in YY supermales, and a male-specific loop containing the SDR was found in the open chromatin region. Our results elucidate the origin of young sex chromosomes and the chromatin remodeling configuration in the catfish sexual plasticity.
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Affiliation(s)
- Gaorui Gong
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Xiong
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Shijun Xiao
- Jiaxing Key Laboratory for New Germplasm Breeding of Economic Mycology, Jiaxing 314000, China
| | - Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Peipei Huang
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China,School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Qian Liao
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingqing Han
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaohong Lin
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China,State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Cheng Dan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Fan Ren
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | | | - Jie Mei
- Corresponding author. E-mail:
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32
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Ansai S, Montenegro J, Masengi KWA, Nagano AJ, Yamahira K, Kitano J. Diversity of sex chromosomes in Sulawesian medaka fishes. J Evol Biol 2022; 35:1751-1764. [DOI: 10.1111/jeb.14076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/30/2022] [Accepted: 07/14/2022] [Indexed: 12/16/2022]
Affiliation(s)
- Satoshi Ansai
- Graduate School of Life Sciences Tohoku University Sendai Japan
| | - Javier Montenegro
- Tropical Biosphere Research Center University of the Ryukyus Nishihara Japan
| | | | - Atsushi J. Nagano
- Faculty of Agriculture Ryukoku University Otsu Japan
- Institute for Advanced Biosciences Keio University Tsuruoka Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research Center University of the Ryukyus Nishihara Japan
| | - Jun Kitano
- Ecological Genetics Laboratory National Institute of Genetics Shizuoka Japan
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33
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Elkrewi M, Khauratovich U, Toups MA, Bett VK, Mrnjavac A, Macon A, Fraisse C, Sax L, Huylmans AK, Hontoria F, Vicoso B. ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. Genetics 2022; 222:6670797. [PMID: 35977389 PMCID: PMC9526061 DOI: 10.1093/genetics/iyac123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.
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Affiliation(s)
- Marwan Elkrewi
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria
| | - Uladzislava Khauratovich
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria.,Department of Chromosome Biology, Max Perutz Labs, University of Vienna, 1030, Austria
| | - Melissa A Toups
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria.,Department of Life and Environmental Sciences, Faculty of Science and Technology, Bournemouth University, BH12 5BB, UK
| | | | - Andrea Mrnjavac
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria
| | - Ariana Macon
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria
| | - Christelle Fraisse
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria.,CNRS, Univ. Lille, UMR 8198-Evo-Eco-Paleo, F-59000 Lille, France
| | - Luca Sax
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria.,Lewis and Clark College, Portland, OR 97219, USA
| | - Ann Kathrin Huylmans
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria.,Institute of Organismic and Molecular Evolution, Johannes Guttenberg Universität Mainz, Mainz, 55122, Germany
| | - Francisco Hontoria
- Instituto de Acuicultura de Torre de la Sal (IATS-CSIC), Ribera de Cabanes, 12595, Spain
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria
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34
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Hearn KE, Koch EL, Stankowski S, Butlin RK, Faria R, Johannesson K, Westram AM. Differing associations between sex determination and sex‐linked inversions in two ecotypes of
Littorina saxatilis. Evol Lett 2022; 6:358-374. [PMID: 36254259 PMCID: PMC9554762 DOI: 10.1002/evl3.295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 07/07/2022] [Accepted: 07/20/2022] [Indexed: 12/14/2022] Open
Abstract
Sexual antagonism is a common hypothesis for driving the evolution of sex chromosomes, whereby recombination suppression is favored between sexually antagonistic loci and the sex‐determining locus to maintain beneficial combinations of alleles. This results in the formation of a sex‐determining region. Chromosomal inversions may contribute to recombination suppression but their precise role in sex chromosome evolution remains unclear. Because local adaptation is frequently facilitated through the suppression of recombination between adaptive loci by chromosomal inversions, there is potential for inversions that cover sex‐determining regions to be involved in local adaptation as well, particularly if habitat variation creates environment‐dependent sexual antagonism. With these processes in mind, we investigated sex determination in a well‐studied example of local adaptation within a species: the intertidal snail, Littorina saxatilis. Using SNP data from a Swedish hybrid zone, we find novel evidence for a female‐heterogametic sex determination system that is restricted to one ecotype. Our results suggest that four putative chromosomal inversions, two previously described and two newly discovered, span the putative sex chromosome pair. We determine their differing associations with sex, which suggest distinct strata of differing ages. The same inversions are found in the second ecotype but do not show any sex association. The striking disparity in inversion‐sex associations between ecotypes that are connected by gene flow across a habitat transition that is just a few meters wide indicates a difference in selective regime that has produced a distinct barrier to the spread of the newly discovered sex‐determining region between ecotypes. Such sex chromosome‐environment interactions have not previously been uncovered in L. saxatilis and are known in few other organisms. A combination of both sex‐specific selection and divergent natural selection is required to explain these highly unusual patterns.
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Affiliation(s)
- Katherine E. Hearn
- Ecology and Evolutionary Biology, School of Biosciences University of Sheffield Sheffield S10 2TN United Kingdom
| | - Eva L. Koch
- Ecology and Evolutionary Biology, School of Biosciences University of Sheffield Sheffield S10 2TN United Kingdom
- Department of Zoology University of Cambridge Cambridge CB2 3EJ United Kingdom
| | - Sean Stankowski
- Ecology and Evolutionary Biology, School of Biosciences University of Sheffield Sheffield S10 2TN United Kingdom
- ISTA (Institute of Science and Technology Austria) Klosterneuburg 3400 Austria
| | - Roger K. Butlin
- Ecology and Evolutionary Biology, School of Biosciences University of Sheffield Sheffield S10 2TN United Kingdom
- Department of Marine Sciences University of Gothenburg Strömstad SE‐45296 Sweden
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado Campus de Vairão, Universidade do Porto Vairão 4485‐661 Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO Campus de Vairão, Universidade do Porto Vairão 4485‐661 Portugal
| | - Kerstin Johannesson
- Department of Marine Sciences University of Gothenburg Strömstad SE‐45296 Sweden
| | - Anja M. Westram
- ISTA (Institute of Science and Technology Austria) Klosterneuburg 3400 Austria
- Faculty of Biosciences and Aquaculture Nord University Bodø 8026 Norway
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35
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First Insights on the Karyotype Diversification of the Endemic Malagasy Leaf-Toed Geckos (Squamata: Gekkonidae: Uroplatus). Animals (Basel) 2022; 12:ani12162054. [PMID: 36009644 PMCID: PMC9404452 DOI: 10.3390/ani12162054] [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: 07/12/2022] [Revised: 08/01/2022] [Accepted: 08/09/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary The geckos of the genus Uroplatus include peculiar endemic species to Madagascar. Even though they have been the subject of several morphological and molecular studies, karyological analyses have been performed only on U. phantasticus, leaving the chromosomal diversity of the genus completely unexplored. In this study, we performed a preliminary molecular analysis and a comparative cytogenetic study providing the first karyotype description of eight species of Uroplatus and an assessment of their karyological variability. We found chromosome diversity in the species studied in terms of total chromosome number (2n = 34–38), localization of loci of Nucleolar Organizer Regions (NORs) (alternatively on the 2nd, 6th, 10th or 16th pair), heterochromatin composition and occurrence of heteromorphic sex chromosome pairs. Adding our newly generated data to those available from the literature, we show that in the genus Uroplatus, as well as in a larger group of phylogenetically related gecko genera, chromosome diversification mainly occurred toward a reduction in the chromosome number by means of chromosome fusions and translocation of NOR-bearing chromosomes. We also hypothesize that the diversification of sex chromosome systems occurred independently in different genera. Abstract We provide here the first karyotype description of eight Uroplatus species and a characterization of their chromosomal diversity. We performed a molecular taxonomic assessment of several Uroplatus samples using the mitochondrial 12S marker and a comparative cytogenetic analysis with standard karyotyping, silver staining (Ag-NOR) and sequential C-banding + Giemsa, +Chromomycin A3 (CMA3), +4′,6-diamidino-2-phenylindole (DAPI). We found chromosomal variability in terms of chromosome number (2n = 34–38), heterochromatin composition and number and localization of loci or Nucleolar Organizer Regions (NORs) (alternatively on the 2nd, 6th, 10th or 16th pair). Chromosome morphology is almost constant, with karyotypes composed of acrocentric chromosomes, gradually decreasing in length. C-banding evidenced a general low content of heterochromatin, mostly localized on pericentromeric and telomeric regions. Centromeric bands varied among the species studied, resulting in CMA3 positive and DAPI negative or positive to both fluorochromes. We also provide evidence of a first putative heteromorphic sex chromosome system in the genus. In fact, in U. alluaudi the 10th pair was highly heteromorphic, with a metacentric, largely heterochromatic W chromosome, which was much bigger than the Z. We propose an evolutionary scenario of chromosome reduction from 2n = 38 to 2n = 34, by means of translocations of microchromosomes on larger chromosomes (often involving the NOR-bearing microchromosomes). Adding our data to those available from the literature, we show that similar processes characterized the evolutionary radiation of a larger gecko clade. Finally, we hypothesize that sex chromosome diversification occurred independently in different genera.
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36
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Meisel RP. Ecology and the evolution of sex chromosomes. J Evol Biol 2022; 35:1601-1618. [PMID: 35950939 DOI: 10.1111/jeb.14074] [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: 12/17/2021] [Revised: 07/15/2022] [Accepted: 07/21/2022] [Indexed: 11/29/2022]
Abstract
Sex chromosomes are common features of animal genomes, often carrying a sex determination gene responsible for initiating the development of sexually dimorphic traits. The specific chromosome that serves as the sex chromosome differs across taxa as a result of fusions between sex chromosomes and autosomes, along with sex chromosome turnover-autosomes becoming sex chromosomes and sex chromosomes 'reverting' back to autosomes. In addition, the types of genes on sex chromosomes frequently differ from the autosomes, and genes on sex chromosomes often evolve faster than autosomal genes. Sex-specific selection pressures, such as sexual antagonism and sexual selection, are hypothesized to be responsible for sex chromosome turnovers, the unique gene content of sex chromosomes and the accelerated evolutionary rates of genes on sex chromosomes. Sex-specific selection has pronounced effects on sex chromosomes because their sex-biased inheritance can tilt the balance of selection in favour of one sex. Despite the general consensus that sex-specific selection affects sex chromosome evolution, most population genetic models are agnostic as to the specific sources of these sex-specific selection pressures, and many of the details about the effects of sex-specific selection remain unresolved. Here, I review the evidence that ecological factors, including variable selection across heterogeneous environments and conflicts between sexual and natural selection, can be important determinants of sex-specific selection pressures that shape sex chromosome evolution. I also explain how studying the ecology of sex chromosome evolution can help us understand important and unresolved aspects of both sex chromosome evolution and sex-specific selection.
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Affiliation(s)
- Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
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37
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Parker DJ, Jaron KS, Dumas Z, Robinson‐Rechavi M, Schwander T. X chromosomes show relaxed selection and complete somatic dosage compensation across
Timema
stick insect species. J Evol Biol 2022; 35:1734-1750. [PMID: 35933721 PMCID: PMC10087215 DOI: 10.1111/jeb.14075] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 05/06/2022] [Accepted: 07/14/2022] [Indexed: 11/29/2022]
Abstract
Sex chromosomes have evolved repeatedly across the tree of life. As they are present in different copy numbers in males and females, they are expected to experience different selection pressures than the autosomes, with consequences including a faster rate of evolution, increased accumulation of sexually antagonistic alleles and the evolution of dosage compensation. Whether these consequences are general or linked to idiosyncrasies of specific taxa is not clear as relatively few taxa have been studied thus far. Here, we use whole-genome sequencing to identify and characterize the evolution of the X chromosome in five species of Timema stick insects with XX:X0 sex determination. The X chromosome had a similar size (approximately 12% of the genome) and gene content across all five species, suggesting that the X chromosome originated prior to the diversification of the genus. Genes on the X showed evidence of relaxed selection (elevated dN/dS) and a slower evolutionary rate (dN + dS) than genes on the autosomes, likely due to sex-biased mutation rates. Genes on the X also showed almost complete dosage compensation in somatic tissues (heads and legs), but dosage compensation was absent in the reproductive tracts. Contrary to prediction, sex-biased genes showed little enrichment on the X, suggesting that the advantage X-linkage provides to the accumulation of sexually antagonistic alleles is weak. Overall, we found the consequences of X-linkage on gene sequences and expression to be similar across Timema species, showing the characteristics of the X chromosome are surprisingly consistent over 30 million years of evolution.
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Affiliation(s)
- Darren J. Parker
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
- School of Natural Sciences Bangor University Bangor UK
| | - Kamil S. Jaron
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
- School of Biological Sciences Institute of Evolutionary Biology University of Edinburgh Edinburgh UK
| | - Zoé Dumas
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
| | - Marc Robinson‐Rechavi
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
| | - Tanja Schwander
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
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38
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Cauret CMS, Mortimer SME, Roberti MC, Ashman TL, Liston A. Chromosome-scale assembly with a phased sex-determining region resolves features of early Z and W chromosome differentiation in a wild octoploid strawberry. G3 (BETHESDA, MD.) 2022; 12:6603112. [PMID: 35666193 PMCID: PMC9339316 DOI: 10.1093/g3journal/jkac139] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/19/2022] [Indexed: 01/07/2023]
Abstract
When sex chromosomes stop recombining, they start to accumulate differences. The sex-limited chromosome (Y or W) especially is expected to degenerate via the loss of nucleotide sequence and the accumulation of repetitive sequences. However, how early signs of degeneration can be detected in a new sex chromosome is still unclear. The sex-determining region of the octoploid strawberries is young, small, and dynamic. Using PacBio HiFi reads, we obtained a chromosome-scale assembly of a female (ZW) Fragaria chiloensis plant carrying the youngest and largest of the known sex-determining region on the W in strawberries. We fully characterized the previously incomplete sex-determining region, confirming its gene content, genomic location, and evolutionary history. Resolution of gaps in the previous characterization of the sex-determining region added 10 kb of sequence including a noncanonical long terminal repeat-retrotransposon; whereas the Z sequence revealed a Harbinger transposable element adjoining the sex-determining region insertion site. Limited genetic differentiation of the sex chromosomes coupled with structural variation may indicate an early stage of W degeneration. The sex chromosomes have a similar percentage of repeats but differ in their repeat distribution. Differences in the pattern of repeats (transposable element polymorphism) apparently precede sex chromosome differentiation, thus potentially contributing to recombination cessation as opposed to being a consequence of it.
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Affiliation(s)
- Caroline M S Cauret
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sebastian M E Mortimer
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Marcelina C Roberti
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
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39
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Zhang H, Sigeman H, Hansson B. Assessment of phylogenetic approaches to study the timing of recombination cessation on sex chromosomes. J Evol Biol 2022; 35:1721-1733. [PMID: 35895083 PMCID: PMC10086819 DOI: 10.1111/jeb.14068] [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: 01/28/2022] [Revised: 06/18/2022] [Accepted: 06/26/2022] [Indexed: 12/01/2022]
Abstract
The evolution of sex chromosomes is hypothesized to be punctuated by consecutive recombination cessation events, forming "evolutionary strata" that ceased to recombine at different time points. The demarcation of evolutionary strata is often assessed by estimates of the timing of recombination cessation (tRC ) along the sex chromosomes, commonly inferred from the level of synonymous divergence or with species phylogenies at gametologous (X-Y or Z-W) sequence data. However, drift and selection affect sequences unpredictably and introduce uncertainty when inferring tRC . Here, we assess two alternative phylogenetic approaches to estimate tRC ; (i) the expected likelihood weight (ELW) approach that finds the most likely topology among a set of hypothetical topologies and (ii) the BEAST approach that estimates tRC with specified calibration priors on a reference species topology. By using Z and W gametologs of an old and a young evolutionary stratum on the neo-sex chromosome of Sylvioidea songbirds, we show that the ELW and BEAST approaches yield similar tRC estimates, and that both outperform two frequently applied approaches utilizing synonymous substitution rates (dS) and maximum likelihood (ML) trees, respectively. Moreover, we demonstrate that both ELW and BEAST provide more precise tRC estimates when sequences of multiple species are included in the analyses.
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Affiliation(s)
- Hongkai Zhang
- Department of Biology, Lund University, Lund, Sweden
| | - Hanna Sigeman
- Department of Biology, Lund University, Lund, Sweden
| | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
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40
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Schield DR, Perry BW, Card DC, Pasquesi GIM, Westfall AK, Mackessy SP, Castoe TA. The rattlesnake W chromosome: A GC-rich retroelement refugium with retained gene function across ancient evolutionary strata. Genome Biol Evol 2022; 14:6648526. [PMID: 35867356 PMCID: PMC9447483 DOI: 10.1093/gbe/evac116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2022] [Indexed: 11/18/2022] Open
Abstract
Sex chromosomes diverge after the establishment of recombination suppression, resulting in differential sex-linkage of genes involved in genetic sex determination and dimorphic traits. This process produces systems of male or female heterogamety wherein the Y and W chromosomes are only present in one sex and are often highly degenerated. Sex-limited Y and W chromosomes contain valuable information about the evolutionary transition from autosomes to sex chromosomes, yet detailed characterizations of the structure, composition, and gene content of sex-limited chromosomes are lacking for many species. In this study, we characterize the female-specific W chromosome of the prairie rattlesnake (Crotalus viridis) and evaluate how recombination suppression and other processes have shaped sex chromosome evolution in ZW snakes. Our analyses indicate that the rattlesnake W chromosome is over 80% repetitive and that an abundance of GC-rich mdg4 elements has driven an overall high degree of GC-richness despite a lack of recombination. The W chromosome is also highly enriched for repeat sequences derived from endogenous retroviruses and likely acts as a “refugium” for these and other retroelements. We annotated 219 putatively functional W-linked genes across at least two evolutionary strata identified based on estimates of sequence divergence between Z and W gametologs. The youngest of these strata is relatively gene-rich, however gene expression across strata suggests retained gene function amidst a greater degree of degeneration following ancient recombination suppression. Functional annotation of W-linked genes indicates a specialization of the W chromosome for reproductive and developmental function since recombination suppression from the Z chromosome.
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Affiliation(s)
- Drew R Schield
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Daren C Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Giulia I M Pasquesi
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Aundrea K Westfall
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
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41
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Filatov DA. Recent expansion of the non-recombining sex-linked region on Silene latifolia sex chromosomes. J Evol Biol 2022; 35:1696-1708. [PMID: 35834179 PMCID: PMC10083954 DOI: 10.1111/jeb.14063] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/19/2022] [Accepted: 06/21/2022] [Indexed: 11/27/2022]
Abstract
Evolution of a non-recombining sex-specific region on the Y (or W) chromosome (NRY) is a key step in sex chromosome evolution, but how recombination suppression evolves is not well understood. Studies in many different organisms indicated that NRY evolution often involves several expansion steps. Why such NRY expansions occur remains unclear, although it is though that they are likely driven by sexually antagonistic selection. This paper describes a recent NRY expansion due to shift of the pseudoautosomal boundary on the sex chromosomes of a dioecious plant Silene latifolia. The shift resulted in inclusion of at least 16 pseudoautosomal genes into the NRY. This region is pseudoautosomal in closely related Silene dioica and Silene diclinis, indicating that the NRY expansion occurred in S. latifolia after it speciated from the other species ~120 thousand years ago. As S. latifolia and S. dioica actively hybridise across Europe, interspecific gene flow could blur the PAR boundary in these species. The pseudoautosomal genes have significantly elevated genetic diversity (π ~ 3% at synonymous sites), which is consistent with balancing selection maintaining diversity in this region. The recent shift of the PAR boundary in S. latifolia offers an opportunity to study the process of on-going NRY expansion.
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42
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Jay P, Tezenas E, Véber A, Giraud T. Sheltering of deleterious mutations explains the stepwise extension of recombination suppression on sex chromosomes and other supergenes. PLoS Biol 2022; 20:e3001698. [PMID: 35853091 PMCID: PMC9295944 DOI: 10.1371/journal.pbio.3001698] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/03/2022] [Indexed: 12/19/2022] Open
Abstract
Many organisms have sex chromosomes with large nonrecombining regions that have expanded stepwise, generating "evolutionary strata" of differentiation. The reasons for this remain poorly understood, but the principal hypotheses proposed to date are based on antagonistic selection due to differences between sexes. However, it has proved difficult to obtain empirical evidence of a role for sexually antagonistic selection in extending recombination suppression, and antagonistic selection has been shown to be unlikely to account for the evolutionary strata observed on fungal mating-type chromosomes. We show here, by mathematical modeling and stochastic simulation, that recombination suppression on sex chromosomes and around supergenes can expand under a wide range of parameter values simply because it shelters recessive deleterious mutations, which are ubiquitous in genomes. Permanently heterozygous alleles, such as the male-determining allele in XY systems, protect linked chromosomal inversions against the expression of their recessive mutation load, leading to the successive accumulation of inversions around these alleles without antagonistic selection. Similar results were obtained with models assuming recombination-suppressing mechanisms other than chromosomal inversions and for supergenes other than sex chromosomes, including those without XY-like asymmetry, such as fungal mating-type chromosomes. However, inversions capturing a permanently heterozygous allele were found to be less likely to spread when the mutation load segregating in populations was lower (e.g., under large effective population sizes or low mutation rates). This may explain why sex chromosomes remain homomorphic in some organisms but are highly divergent in others. Here, we model a simple and testable hypothesis explaining the stepwise extensions of recombination suppression on sex chromosomes, mating-type chromosomes, and supergenes in general.
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Affiliation(s)
- Paul Jay
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-sur-Yvette, France
- * E-mail:
| | - Emilie Tezenas
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-sur-Yvette, France
- Univ. Lille, CNRS, UMR 8198 –Evo-Eco-Paleo, F-59000 Lille, France
- Université Paris Cité, CNRS, MAP 5, F-75006 Paris, France
| | - Amandine Véber
- Université Paris Cité, CNRS, MAP 5, F-75006 Paris, France
| | - Tatiana Giraud
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-sur-Yvette, France
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43
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A chromosome predisposed for sex. Nature 2022; 606:257-258. [PMID: 35650395 DOI: 10.1038/d41586-022-01129-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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44
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Moore EC, Thomas GWC, Mortimer S, Kopania EEK, Hunnicutt KE, Clare-Salzler ZJ, Larson EL, Good JM. The evolution of widespread recombination suppression on the dwarf hamster (Phodopus) X chromosome. Genome Biol Evol 2022; 14:6596369. [PMID: 35642315 PMCID: PMC9185382 DOI: 10.1093/gbe/evac080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 11/24/2022] Open
Abstract
The X chromosome of therian mammals shows strong conservation among distantly related species, limiting insights into the distinct selective processes that have shaped sex chromosome evolution. We constructed a chromosome-scale de novo genome assembly for the Siberian dwarf hamster (Phodopus sungorus), a species reported to show extensive recombination suppression across an entire arm of the X chromosome. Combining a physical genome assembly based on shotgun and long-range proximity ligation sequencing with a dense genetic map, we detected widespread suppression of female recombination across ∼65% of the Phodopus X chromosome. This region of suppressed recombination likely corresponds to the Xp arm, which has previously been shown to be highly heterochromatic. Using additional sequencing data from two closely related species (P. campbelli and P. roborovskii), we show that recombination suppression on Xp appears to be independent of major structural rearrangements. The suppressed Xp arm was enriched for several transposable element families and de-enriched for genes primarily expressed in placenta, but otherwise showed similar gene densities, expression patterns, and rates of molecular evolution when compared to the recombinant Xq arm. Phodopus Xp gene content and order was also broadly conserved relative to the more distantly related rat X chromosome. These data suggest that widespread suppression of recombination has likely evolved through the transient induction of facultative heterochromatin on the Phodopus Xp arm without major changes in chromosome structure or genetic content. Thus, substantial changes in the recombination landscape have so far had relatively subtle influences on patterns of X-linked molecular evolution in these species.
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Affiliation(s)
- Emily C Moore
- Division of Biological Sciences, The University of Montana, Missoula, Montana, 59812, USA
| | - Gregg W C Thomas
- Division of Biological Sciences, The University of Montana, Missoula, Montana, 59812, USA
| | - Sebastian Mortimer
- Division of Biological Sciences, The University of Montana, Missoula, Montana, 59812, USA
| | - Emily E K Kopania
- Division of Biological Sciences, The University of Montana, Missoula, Montana, 59812, USA
| | - Kelsie E Hunnicutt
- Department of Biological Sciences, The University of Denver, Denver, Colorado, 80208, USA
| | | | - Erica L Larson
- Department of Biological Sciences, The University of Denver, Denver, Colorado, 80208, USA
| | - Jeffrey M Good
- Division of Biological Sciences, The University of Montana, Missoula, Montana, 59812, USA
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45
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Mank JE. Are plant and animal sex chromosomes really all that different? Philos Trans R Soc Lond B Biol Sci 2022; 377:20210218. [PMID: 35306885 PMCID: PMC8935310 DOI: 10.1098/rstb.2021.0218] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Sex chromosomes in plants have often been contrasted with those in animals with the goal of identifying key differences that can be used to elucidate fundamental evolutionary properties. For example, the often homomorphic sex chromosomes in plants have been compared to the highly divergent systems in some animal model systems, such as birds, Drosophila and therian mammals, with many hypotheses offered to explain the apparent dissimilarities, including the younger age of plant sex chromosomes, the lesser prevalence of sexual dimorphism, or the greater extent of haploid selection. Furthermore, many plant sex chromosomes lack complete sex chromosome dosage compensation observed in some animals, including therian mammals, Drosophila, some poeciliids, and Anolis, and plant dosage compensation, where it exists, appears to be incomplete. Even the canonical theoretical models of sex chromosome formation differ somewhat between plants and animals. However, the highly divergent sex chromosomes observed in some animal groups are actually the exception, not the norm, and many animal clades are far more similar to plants in their sex chromosome patterns. This begs the question of how different are plant and animal sex chromosomes, and which of the many unique properties of plants would be expected to affect sex chromosome evolution differently than animals? In fact, plant and animal sex chromosomes exhibit more similarities than differences, and it is not at all clear that they differ in terms of sexual conflict, dosage compensation, or even degree of divergence. Overall, the largest difference between these two groups is the greater potential for haploid selection in plants compared to animals. This may act to accelerate the expansion of the non-recombining region at the same time that it maintains gene function within it. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.
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Affiliation(s)
- Judith E Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada.,Centre for Ecology and Conservation, University of Exeter, Penryn, UK
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46
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The evolution of gene regulation on sex chromosomes. Trends Genet 2022; 38:844-855. [DOI: 10.1016/j.tig.2022.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 11/20/2022]
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47
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Pinto BJ, Keating SE, Nielsen SV, Scantlebury DP, Daza JD, Gamble T. Chromosome-Level Genome Assembly Reveals Dynamic Sex Chromosomes in Neotropical Leaf-Litter Geckos (Sphaerodactylidae: Sphaerodactylus). J Hered 2022; 113:272-287. [PMID: 35363859 PMCID: PMC9270867 DOI: 10.1093/jhered/esac016] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 03/24/2022] [Indexed: 02/07/2023] Open
Abstract
Sex determination is a critical element of successful vertebrate development, suggesting that sex chromosome systems might be evolutionarily stable across lineages. For example, mammals and birds have maintained conserved sex chromosome systems over long evolutionary time periods. Other vertebrates, in contrast, have undergone frequent sex chromosome transitions, which is even more amazing considering we still know comparatively little across large swaths of their respective phylogenies. One reptile group in particular, the gecko lizards (infraorder Gekkota), shows an exceptional lability with regard to sex chromosome transitions and may possess the majority of transitions within squamates (lizards and snakes). However, detailed genomic and cytogenetic information about sex chromosomes is lacking for most gecko species, leaving large gaps in our understanding of the evolutionary processes at play. To address this, we assembled a chromosome-level genome for a gecko (Sphaerodactylidae: Sphaerodactylus) and used this assembly to search for sex chromosomes among six closely related species using a variety of genomic data, including whole-genome re-sequencing, RADseq, and RNAseq. Previous work has identified XY systems in two species of Sphaerodactylus geckos. We expand upon that work to identify between two and four sex chromosome cis-transitions (XY to a new XY) within the genus. Interestingly, we confirmed two different linkage groups as XY sex chromosome systems that were previously unknown to act as sex chromosomes in tetrapods (syntenic with Gallus chromosome 3 and Gallus chromosomes 18/30/33), further highlighting a unique and fascinating trend that most linkage groups have the potential to act as sex chromosomes in squamates.
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Affiliation(s)
- Brendan J Pinto
- Address correspondence to B. J. Pinto at the address above, or e-mail:
| | - Shannon E Keating
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Stuart V Nielsen
- Department of Biological Sciences, Louisiana State University in Shreveport, Shreveport, LA 71115, USA,Division of Herpetology, Florida Museum of Natural History, Gainesville, FL 32611, USA
| | | | - Juan D Daza
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX 77340, USA
| | - Tony Gamble
- Milwaukee Public Museum, Milwaukee, WI 53233, USA,Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA,Bell Museum of Natural History, University of Minnesota, St Paul, MN 55455, USA
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48
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Trujillo N, Martínez-Pacheco M, Soldatini C, Ancona S, Young RC, Albores-Barajas YV, Orta AH, Rodríguez C, Székely T, Drummond H, Urrutia AO, Cortez D. Lack of age-related mosaic loss of W chromosome in long-lived birds. Biol Lett 2022; 18:20210553. [PMID: 35193370 PMCID: PMC8864339 DOI: 10.1098/rsbl.2021.0553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Females and males often exhibit different survival in nature, and it has been hypothesized that sex chromosomes may play a role in driving differential survival rates. For instance, the Y chromosome in mammals and the W chromosome in birds are often degenerated, with reduced numbers of genes, and loss of the Y chromosome in old men is associated with shorter life expectancy. However, mosaic loss of sex chromosomes has not been investigated in any non-human species. Here, we tested whether mosaic loss of the W chromosome (LOW) occurs with ageing in wild birds as a natural consequence of cellular senescence. Using loci-specific PCR and a target sequencing approach we estimated LOW in both young and adult individuals of two long-lived bird species and showed that the copy number of W chromosomes remains constant across age groups. Our results suggest that LOW is not a consequence of cellular ageing in birds. We concluded that the inheritance of the W chromosome in birds, unlike the Y chromosome in mammals, is more stable.
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Affiliation(s)
- Nancy Trujillo
- Centro de Ciencias Genómicas, UNAM, CP62210, Cuernavaca, México
| | - Mónica Martínez-Pacheco
- Laboratorio de Biología Celular y Molecular, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, CP76010, Querétaro, México
| | - Cecilia Soldatini
- Centro de Investigación Científica y Educación Superior de Ensenada - Unidad La Paz, Calle Miraflores 334, CP23050, La Paz, Baja California Sur, México
| | - Sergio Ancona
- Instituto de Ecología, UNAM, Ciudad Universitaria, CP04510, Ciudad de México, México
| | - Rebecca C Young
- Instituto de Ecología, UNAM, Ciudad Universitaria, CP04510, Ciudad de México, México
| | - Yuri V Albores-Barajas
- CONACYT. Consejo Nacional de Ciencia y Tecnología, Av. Insurgentes Sur 1582, Col. Crédito Constructor. Alcaldía Benito Juárez, CP03940, Ciudad de México, México.,Universidad Autónoma de Baja California Sur., Km. 5.5 Carr. 1. La Paz, Baja California Sur, México
| | - Alberto H Orta
- Centro de Ciencias Genómicas, UNAM, CP62210, Cuernavaca, México
| | - Cristina Rodríguez
- Instituto de Ecología, UNAM, Ciudad Universitaria, CP04510, Ciudad de México, México
| | - Tamas Székely
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK.,Department of Evolutionary Zoology and Human Biology, University of Debrecen, Debrecen H-4032, Hungary
| | - Hugh Drummond
- Instituto de Ecología, UNAM, Ciudad Universitaria, CP04510, Ciudad de México, México
| | - Araxi O Urrutia
- Instituto de Ecología, UNAM, Ciudad Universitaria, CP04510, Ciudad de México, México.,Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Diego Cortez
- Centro de Ciencias Genómicas, UNAM, CP62210, Cuernavaca, México
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49
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The Sister Chromatid Division of the Heteromorphic Sex Chromosomes in Silene Species and Their Transmissibility towards the Mitosis. Int J Mol Sci 2022; 23:ijms23052422. [PMID: 35269563 PMCID: PMC8910698 DOI: 10.3390/ijms23052422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 01/20/2023] Open
Abstract
Young sex chromosomes possess unique and ongoing dynamics that allow us to understand processes that have an impact on their evolution and divergence. The genus Silene includes species with evolutionarily young sex chromosomes, and two species of section Melandrium, namely Silene latifolia (24, XY) and Silene dioica (24, XY), are well-established models of sex chromosome evolution, Y chromosome degeneration, and sex determination. In both species, the X and Y chromosomes are strongly heteromorphic and differ in the genomic composition compared to the autosomes. It is generally accepted that for proper cell division, the longest chromosomal arm must not exceed half of the average length of the spindle axis at telophase. Yet, it is not clear what are the dynamics between males and females during mitosis and how the cell compensates for the presence of the large Y chromosome in one sex. Using hydroxyurea cell synchronization and 2D/3D microscopy, we determined the position of the sex chromosomes during the mitotic cell cycle and determined the upper limit for the expansion of sex chromosome non-recombining region. Using 3D specimen preparations, we found that the velocity of the large chromosomes is compensated by the distant positioning from the central interpolar axis, confirming previous mathematical modulations.
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50
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Ottenburghs J. Avian introgression patterns are consistent with Haldane's Rule. J Hered 2022; 113:363-370. [PMID: 35134952 PMCID: PMC9308041 DOI: 10.1093/jhered/esac005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/27/2022] [Indexed: 11/13/2022] Open
Abstract
According to Haldane’s Rule, the heterogametic sex will show the greatest fitness reduction in a hybrid cross. In birds, where sex is determined by a ZW system, female hybrids are expected to experience lower fitness compared to male hybrids. This pattern has indeed been observed in several bird groups, but it is unknown whether the generality of Haldane’s Rule also extends to the molecular level. First, given the lower fitness of female hybrids, we can expect maternally inherited loci (i.e., mitochondrial and W-linked loci) to show lower introgression rates than biparentally inherited loci (i.e., autosomal loci) in females. Second, the faster evolution of Z-linked loci compared to autosomal loci and the hemizygosity of the Z-chromosome in females might speed up the accumulation of incompatible alleles on this sex chromosome, resulting in lower introgression rates for Z-linked loci than for autosomal loci. I tested these expectations by conducting a literature review which focused on studies that directly quantified introgression rates for autosomal, sex-linked, and mitochondrial loci. Although most studies reported introgression rates in line with Haldane’s Rule, it remains important to validate these genetic patterns with estimates of hybrid fitness and supporting field observations to rule out alternative explanations. Genomic data provide exciting opportunities to obtain a more fine-grained picture of introgression rates across the genome, which can consequently be linked to ecological and behavioral observations, potentially leading to novel insights into the genetic mechanisms underpinning Haldane’s Rule.
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Affiliation(s)
- Jente Ottenburghs
- Wildlife Ecology and Conservation, Wageningen University & Research, Wageningen, The Netherlands.,Forest Ecology and Forest Management, Wageningen University & Research, Wageningen, The Netherlands
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