1
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Mongue AJ, Baird RB. Genetic drift drives faster-Z evolution in the salmon louse Lepeophtheirus salmonis. Evolution 2024; 78:1594-1605. [PMID: 38863398 DOI: 10.1093/evolut/qpae090] [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: 01/03/2024] [Revised: 05/25/2024] [Accepted: 06/11/2024] [Indexed: 06/13/2024]
Abstract
How sex chromosomes evolve compared to autosomes remains an unresolved question in population genetics. Most studies focus on only a handful of taxa, resulting in uncertainty over whether observed patterns reflect general processes or idiosyncrasies in particular clades. For example, in female heterogametic (ZW) systems, bird Z chromosomes tend to evolve quickly but not adaptively, while in Lepidopterans they evolve adaptively, but not always quickly. To understand how these observations fit into broader evolutionary patterns, we explore Z chromosome evolution outside of these two well-studied clades. We utilize a publicly available genome, gene expression, population, and outgroup data in the salmon louse Lepeophtheirus salmonis, an important agricultural pest copepod. We find that the Z chromosome is faster evolving than autosomes, but that this effect is driven by increased drift rather than adaptive evolution. Due to high rates of female reproductive failure, the Z chromosome exhibits a slightly lower effective population size than the autosomes which is nonetheless to decrease efficiency of hemizygous selection acting on the Z. These results highlight the usefulness of organismal life history in calibrating population genetic expectations and demonstrate the value of the ever-expanding wealth of publicly available data to help resolve outstanding evolutionary questions.
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Affiliation(s)
- Andrew J Mongue
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, United States
| | - Robert B Baird
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
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2
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Toma GA, Sember A, Goes CAG, Kretschmer R, Porto-Foresti F, Bertollo LAC, Liehr T, Utsunomia R, de Bello Cioffi M. Satellite DNAs and the evolution of the multiple X 1X 2Y sex chromosomes in the wolf fish Hoplias malabaricus (Teleostei; Characiformes). Sci Rep 2024; 14:20402. [PMID: 39223262 PMCID: PMC11369246 DOI: 10.1038/s41598-024-70920-7] [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: 02/05/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
Multiple sex chromosomes usually arise from chromosomal rearrangements which involve ancestral sex chromosomes. There is a fundamental condition to be met for their long-term fixation: the meiosis must function, leading to the stability of the emerged system, mainly concerning the segregation of the sex multivalent. Here, we sought to analyze the degree of differentiation and meiotic pairing properties in the selected fish multiple sex chromosome system present in the wolf-fish Hoplias malabaricus (HMA). This species complex encompasses seven known karyotype forms (karyomorphs) where the karyomorph C (HMA-C) exhibits a nascent XY sex chromosomes from which the multiple X1X2Y system evolved in karyomorph HMA-D via a Y-autosome fusion. We combined genomic and cytogenetic approaches to analyze the satellite DNA (satDNA) content in the genome of HMA-D karyomorph and to investigate its potential contribution to X1X2Y sex chromosome differentiation. We revealed 56 satDNA monomers of which the majority was AT-rich and with repeat units longer than 100 bp. Seven out of 18 satDNA families chosen for chromosomal mapping by fluorescence in situ hybridization (FISH) formed detectable accumulation in at least one of the three sex chromosomes (X1, X2 and neo-Y). Nine satDNA monomers showed only two hybridization signals limited to HMA-D autosomes, and the two remaining ones provided no visible FISH signals. Out of seven satDNAs located on the HMA-D sex chromosomes, five mapped also to XY chromosomes of HMA-C. We showed that after the autosome-Y fusion event, the neo-Y chromosome has not substantially accumulated or eliminated satDNA sequences except for minor changes in the centromere-proximal region. Finally, based on the obtained FISHpatterns, we speculate on the possible contribution of satDNA to sex trivalent pairing and segregation.
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Affiliation(s)
- Gustavo Akira Toma
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 277 21, Liběchov, Czech Republic
| | | | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas, RS, 96010-610, Brazil
| | | | | | - Thomas Liehr
- Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, 07747, Jena, Germany.
| | | | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
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3
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Wang J, Tao W, Kocher TD, Wang D. Sex chromosome turnover and biodiversity in fishes. J Genet Genomics 2024:S1673-8527(24)00222-4. [PMID: 39233051 DOI: 10.1016/j.jgg.2024.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 08/22/2024] [Accepted: 08/26/2024] [Indexed: 09/06/2024]
Abstract
The impact of sex chromosomes and their turnover in speciation remains a subject of ongoing debate in the field of evolutionary biology. Fishes are the largest group of vertebrates, and they exhibit unparalleled sexual plasticity, as well as diverse sex-determining (SD) genes, sex chromosomes, and sex determination mechanisms. This diversity is hypothesized to be associated with the frequent turnover of sex chromosomes in fishes. Although it is evident that amh and amhr2 are repeatedly and independently recruited as SD genes, their relationship with the rapid turnover of sex chromosomes and the biodiversity of fishes remains unknown. We summarize the canonical models of sex chromosome turnover and highlight the vital roles of gene mutation and hybridization with empirical evidence. We revisit Haldane's rule and the large X-effect and propose the hypothesis that sex chromosomes accelerate speciation by multiplying genotypes via hybridization. By integrating recent findings on the turnover of SD genes, sex chromosomes, and sex determination systems in fish species, this review provides insights into the relationship between sex chromosome evolution and biodiversity in fishes.
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Affiliation(s)
- Jingrong Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Wenjing Tao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
| | - Deshou Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
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4
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Deon GA, Dos Santos RZ, Sassi FDMC, Moreira-Filho O, Vicari MR, Porto-Foresti F, Utsunomia R, Cioffi MDB. The role of satellite DNAs in the chromosomal rearrangements and the evolution of the rare XY1Y2 sex system in Harttia (Siluriformes: Loricariidae). J Hered 2024; 115:541-551. [PMID: 38757192 DOI: 10.1093/jhered/esae028] [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: 01/25/2024] [Accepted: 05/15/2024] [Indexed: 05/18/2024] Open
Abstract
The underlying processes behind the formation, evolution, and long-term maintenance of multiple sex chromosomes have been largely neglected. Among vertebrates, fishes represent the group with the highest diversity of multiple sex chromosome systems and, with six instances, the Neotropical fish genus Harttia stands out by presenting the most remarkable diversity. However, although the origin mechanism of their sex chromosome systems is well discussed, little is known about the importance of some repetitive DNA classes in the differentiation of multiple systems. In this work, by employing a combination of cytogenetic and genomic procedures, we evaluated the satellite DNA composition of H. carvalhoi with a focus on their role in the evolution, structure, and differentiation process of the rare XY1Y2 multiple-sex chromosome system. The genome of H. carvalhoi contains a total of 28 satellite DNA families, with the A + T content ranging between 38.1% and 68.1% and the predominant presence of long satellites. The in situ hybridization experiments detected 15 satellite DNAs with positive hybridization signals mainly on centromeric and pericentromeric regions of almost all chromosomes or clustered on a few pairs. Five of them presented clusters on X, Y1, and/or Y2 sex chromosomes which were therefore selected for comparative hybridization in the other three congeneric species. We found several conserved satellites accumulated on sex chromosomes and also in regions that were involved in chromosomal rearrangements. Our results provide a new contribution of satellitome studies in multiple sex chromosome systems in fishes and represent the first satellitome study for a Siluriformes species.
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Affiliation(s)
- Geize Aparecida Deon
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Rodrigo Zeni Dos Santos
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, Bauru, São Paulo, Brazil
| | | | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Marcelo Ricardo Vicari
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Fábio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, Bauru, São Paulo, Brazil
| | - Ricardo Utsunomia
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, Bauru, São Paulo, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
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5
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Cecalev D, Viçoso B, Galupa R. Compensation of gene dosage on the mammalian X. Development 2024; 151:dev202891. [PMID: 39140247 PMCID: PMC11361640 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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6
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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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7
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Olito C, Ponnikas S, Hansson B, Abbott JK. Consequences of partially recessive deleterious genetic variation for the evolution of inversions suppressing recombination between sex chromosomes1. Evolution 2024; 78:1499-1510. [PMID: 38853722 DOI: 10.1093/evolut/qpae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 03/26/2024] [Accepted: 04/25/2024] [Indexed: 06/11/2024]
Abstract
The evolution of suppressed recombination between sex chromosomes is widely hypothesized to be driven by sexually antagonistic selection (SA), where tighter linkage between the sex-determining gene(s) and nearby SA loci is favored when it couples male-beneficial alleles to the proto-Y chromosome, and female-beneficial alleles to the proto-X. Although difficult to test empirically, the SA selection hypothesis overshadows several alternatives, including an incomplete but often-repeated "sheltering" hypothesis which suggests that expansion of the sex-linked region (SLR) reduces the homozygous expression of deleterious mutations at selected loci. Here, we use population genetic models to evaluate the consequences of partially recessive deleterious mutational variation for the evolution of otherwise neutral chromosomal inversions expanding the SLR on proto-Y chromosomes. Both autosomal and SLR-expanding inversions face a race against time: lightly-loaded inversions are initially beneficial, but eventually become deleterious as they accumulate new mutations, after which their chances of fixing become negligible. In contrast, initially unloaded inversions eventually become neutral as their deleterious load reaches the same equilibrium as non-inverted haplotypes. Despite the differences in inheritance and indirect selection, SLR-expanding inversions exhibit similar evolutionary dynamics to autosomal inversions over many biologically plausible parameter conditions. Differences emerge when the population average mutation load is quite high; in this case large autosomal inversions that are lucky enough to be mutation-free can rise to intermediate to high frequencies where selection in homozygotes becomes important (Y-linked inversions never appear as homozygous karyotypes); conditions requiring either high mutation rates, highly recessive deleterious mutations, weak selection, or a combination thereof.
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Affiliation(s)
- Colin Olito
- Department of Biology, Lund University, Lund, Sweden
| | - Suvi Ponnikas
- Department of Biology, Lund University, Lund, Sweden
| | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
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8
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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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9
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Dornela AF, Soares FAF, Silva JC, Sattler MC, Clarindo WR. Carica papaya L. sex chromosome review and physical mapping of the serk 2, svp-like and mdar 4 sequences. Sci Rep 2024; 14:14830. [PMID: 38937542 PMCID: PMC11211501 DOI: 10.1038/s41598-024-65880-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/25/2024] [Indexed: 06/29/2024] Open
Abstract
Physical mapping evidences the chromosome organization and structure. Despite the data about plant cytogenomics, physical mapping has been conducted from single-copy and/or low-copy genes for few species. Carica papaya cytogenomics has been accomplished from BAC-FISH and repeatome sequences. We aimed to map the serk 2, svp-like and mdar 4 sequences in C. papaya. The sequences were amplified and the amplicons sequenced, showing similarity in relation to serk 2, svp-like and mdar 4 genes. Carica papaya diploidy was confirmed and the mitotic chromosomes characterized. The chromosome 1 exhibited the secondary constriction pericentromeric to the centromere of the long arm. So, we concluded that it is the sex chromosomes. serk 2 was mapped in the long arm interstitial portion of the sex chromosomes, and the interphase nuclei showed two fluorescence signals. Considering these results and the sequencing data from the C. papaya sex chromosomes, svp-like and mdar 4 genes were mapped in the interstitial region of the sex chromosome long arm. Both sequences showed only one fluorescence signal in the interphase nuclei. The procedure adopted here can be reproduced for other single-copy and/or low-copy genes, allowing the construction of cytogenetic maps. In addition, we revisited the cytogenomics data about C. papaya sex chromosomes, presenting a revised point of view about the structure and evolution to these chromosomes.
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Affiliation(s)
- Adeilson Frias Dornela
- Pós-Graduação em Genética e Melhoramento, Centro de Ciências Agrárias e Engenharias, Universidade Federal do Espírito Santo, Alegre, ES, 29.500-000, Brazil
| | - Fernanda Aparecida Ferrari Soares
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Viçosa, MG, 36.570-900, Brazil
| | - Jéssica Coutinho Silva
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Viçosa, MG, 36.570-900, Brazil
| | - Mariana Cansian Sattler
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Viçosa, MG, 36.570-900, Brazil
| | - Wellington Ronildo Clarindo
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Viçosa, MG, 36.570-900, Brazil.
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10
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Wang Y, Gong GN, Wang Y, Zhang RG, Hörandl E, Zhang ZX, Charlesworth D, He L. Gap-free X and Y chromosome assemblies of Salix arbutifolia reveal an evolutionary change from male to female heterogamety in willows, without a change in the position of the sex-determining locus. THE NEW PHYTOLOGIST 2024; 242:2872-2887. [PMID: 38581199 DOI: 10.1111/nph.19744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/21/2024] [Indexed: 04/08/2024]
Abstract
In the Vetrix clade of Salix, a genus of woody flowering plants, sex determination involves chromosome 15, but an XY system has changed to a ZW system. We studied the detailed genetic changes involved. We used genome sequencing, with chromosome conformation capture (Hi-C) and PacBio HiFi reads to assemble chromosome level gap-free X and Y of Salix arbutifolia, and distinguished the haplotypes in the 15X- and 15Y-linked regions, to study the evolutionary history of the sex-linked regions (SLRs). Our sequencing revealed heteromorphism of the X and Y haplotypes of the SLR, with the X-linked region being considerably larger than the corresponding Y region, mainly due to accumulated repetitive sequences and gene duplications. The phylogenies of single-copy orthogroups within the SLRs indicate that S. arbutifolia and Salix purpurea share an ancestral SLR within a repeat-rich region near the chromosome 15 centromere. During the change in heterogamety, the X-linked region changed to a W-linked one, while the Z was derived from the Y.
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Affiliation(s)
- 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, 100091, China
| | - Guang-Nan Gong
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yuan Wang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, 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
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, 37073, Göttingen, Germany
| | - Zhi-Xiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100091, China
| | - Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Li He
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
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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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12
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Setti PG, Deon GA, Zeni Dos Santos R, Goes CAG, Garnero ADV, Gunski RJ, de Oliveira EHC, Porto-Foresti F, de Freitas TRO, Silva FAO, Liehr T, Utsunomia R, Kretschmer R, de Bello Cioffi M. Evolution of bird sex chromosomes: a cytogenomic approach in Palaeognathae species. BMC Ecol Evol 2024; 24:51. [PMID: 38654159 PMCID: PMC11036779 DOI: 10.1186/s12862-024-02230-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Different patterns of sex chromosome differentiation are seen in Palaeognathae birds, a lineage that includes the ratites (Struthioniformes, Rheiformes, Apterygiformes, Casuariiformes, and the sister group Tinamiformes). While some Tinamiform species have well-differentiated W chromosomes, both Z and W of all the flightless ratites are still morphologically undifferentiated. Here, we conducted a comprehensive analysis of the ZW differentiation in birds using a combination of cytogenetic, genomic, and bioinformatic approaches. The whole set of satDNAs from the emu (Dromaius novaehollandiae) was described and characterized. Furthermore, we examined the in situ locations of these satDNAs alongside several microsatellite repeats and carried out Comparative Genomic Hybridizations in two related species: the greater rhea (Rhea americana) and the tataupa tinamou (Crypturellus tataupa). RESULTS From the 24 satDNA families identified (which represent the greatest diversity of satDNAs ever uncovered in any bird species), only three of them were found to accumulate on the emu's sex chromosomes, with no discernible accumulation observed on the W chromosome. The W chromosomes of both the greater rhea and the emu did not exhibit a significant buildup of either C-positive heterochromatin or repetitive DNAs, indicating their large undifferentiation both at morphological and molecular levels. In contrast, the tataupa tinamou has a highly differentiated W chromosome that accumulates several DNA repeats. CONCLUSION The findings provide new information on the architecture of the avian genome and an inside look at the starting points of sex chromosome differentiation in birds.
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Affiliation(s)
- Príncia Grejo Setti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, 13565-905, São Carlos, SP, Brazil
| | - Geize Aparecida Deon
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, 13565-905, São Carlos, SP, Brazil
| | | | | | - Analía Del Valle Garnero
- Campus São Gabriel, Universidade Federal do Pampa, 97307-020, São Gabriel, Rio Grande do Sul, Brazil
| | - Ricardo José Gunski
- Campus São Gabriel, Universidade Federal do Pampa, 97307-020, São Gabriel, Rio Grande do Sul, Brazil
| | - Edivaldo Herculano Corrêa de Oliveira
- Laboratório de Citogenômica e Mutagênese Ambiental, Seção de Meio Ambiente, Instituto Evandro Chagas, 67030-000, Ananindeua, PA, Brazil
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, 66075-110, Belém, PA, Brazil
| | - Fábio Porto-Foresti
- Faculdade de Ciências, Universidade Estadual Paulista, 17033-360, Bauru, São Paulo, Brazil
| | | | - Fábio Augusto Oliveira Silva
- Laboratório de Citogenômica e Mutagênese Ambiental, Seção de Meio Ambiente, Instituto Evandro Chagas, 67030-000, Ananindeua, PA, Brazil
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, 07747, Jena, Germany.
| | - Ricardo Utsunomia
- Faculdade de Ciências, Universidade Estadual Paulista, 17033-360, Bauru, São Paulo, Brazil
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, 96.010-610, Pelotas, RS, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, 13565-905, São Carlos, SP, Brazil
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13
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Sacchi B, Humphries Z, Kružlicová J, Bodláková M, Pyne C, Choudhury BI, Gong Y, Bačovský V, Hobza R, Barrett SCH, Wright SI. Phased Assembly of Neo-Sex Chromosomes Reveals Extensive Y Degeneration and Rapid Genome Evolution in Rumex hastatulus. Mol Biol Evol 2024; 41:msae074. [PMID: 38606901 PMCID: PMC11057207 DOI: 10.1093/molbev/msae074] [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: 10/06/2023] [Revised: 01/31/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024] Open
Abstract
Y chromosomes are thought to undergo progressive degeneration due to stepwise loss of recombination and subsequent reduction in selection efficiency. However, the timescales and evolutionary forces driving degeneration remain unclear. To investigate the evolution of sex chromosomes on multiple timescales, we generated a high-quality phased genome assembly of the massive older (<10 MYA) and neo (<200,000 yr) sex chromosomes in the XYY cytotype of the dioecious plant Rumex hastatulus and a hermaphroditic outgroup Rumex salicifolius. Our assemblies, supported by fluorescence in situ hybridization, confirmed that the neo-sex chromosomes were formed by two key events: an X-autosome fusion and a reciprocal translocation between the homologous autosome and the Y chromosome. The enormous sex-linked regions of the X (296 Mb) and two Y chromosomes (503 Mb) both evolved from large repeat-rich genomic regions with low recombination; however, the complete loss of recombination on the Y still led to over 30% gene loss and major rearrangements. In the older sex-linked region, there has been a significant increase in transposable element abundance, even into and near genes. In the neo-sex-linked regions, we observed evidence of extensive rearrangements without gene degeneration and loss. Overall, we inferred significant degeneration during the first 10 million years of Y chromosome evolution but not on very short timescales. Our results indicate that even when sex chromosomes emerge from repetitive regions of already-low recombination, the complete loss of recombination on the Y chromosome still leads to a substantial increase in repetitive element content and gene degeneration.
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Affiliation(s)
- Bianca Sacchi
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Zoë Humphries
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Jana Kružlicová
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Markéta Bodláková
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Cassandre Pyne
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Baharul I Choudhury
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
- Department of Biology, Queen’s University, Kingston, Canada
| | - Yunchen Gong
- Centre for Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
| | - Václav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
- Centre for Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
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14
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Mezzasalma M, Macirella R, Odierna G, Brunelli E. Karyotype Diversification and Chromosome Rearrangements in Squamate Reptiles. Genes (Basel) 2024; 15:371. [PMID: 38540430 PMCID: PMC10970613 DOI: 10.3390/genes15030371] [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: 02/26/2024] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 06/14/2024] Open
Abstract
Karyotype diversification represents an important, yet poorly understood, driver of evolution. Squamate reptiles are characterized by a high taxonomic diversity which is reflected at the karyotype level in terms of general structure, chromosome number and morphology, and insurgence of differentiated simple or multiple-sex-chromosome systems with either male or female heterogamety. The potential of squamate reptiles as unique model organisms in evolutionary cytogenetics has been recognised in recent years in several studies, which have provided novel insights into the chromosome evolutionary dynamics of different taxonomic groups. Here, we review and summarize the resulting complex, but promising, general picture from a systematic perspective, mapping some of the main squamate karyological characteristics onto their phylogenetic relationships. We highlight how all the major categories of balanced chromosome rearrangements contributed to the karyotype evolution in different taxonomic groups. We show that distinct karyotype evolutionary trends may occur, and coexist, with different frequencies in different clades. Finally, in light of the known squamate chromosome diversity and recent research advances, we discuss traditional and novel hypotheses on karyotype evolution and propose a scenario of circular karyotype evolution.
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Affiliation(s)
- Marcello Mezzasalma
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy; (R.M.); (E.B.)
| | - Rachele Macirella
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy; (R.M.); (E.B.)
| | - Gaetano Odierna
- Independent Researcher, Via Michelangelo 123, 81031 Aversa, Italy;
| | - Elvira Brunelli
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy; (R.M.); (E.B.)
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15
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Coffing GC, Tittes S, Small ST, Songco-Casey JO, Piscopo DM, Pungor JR, Miller AC, Niell CM, Kern AD. Cephalopod Sex Determination and its Ancient Evolutionary Origin Revealed by Chromosome-level Assembly of the California Two-Spot Octopus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.21.581452. [PMID: 38463997 PMCID: PMC10925132 DOI: 10.1101/2024.02.21.581452] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Sex chromosomes are critical elements of sexual reproduction in many animal and plant taxa, however they show incredible diversity and rapid turnover even within clades. Here, using a chromosome-level assembly generated with long read sequencing, we report the first evidence for genetic sex determination in cephalopods. We have uncovered a sex chromosome in California two-spot octopus (Octopus bimaculoides) in which males/females show ZZ/ZO karyotypes respectively. We show that the octopus Z chromosome is an evolutionary outlier with respect to divergence and repetitive element content as compared to other chromosomes and that it is present in all coleoid cephalopods that we have examined. Our results suggest that the cephalopod Z chromosome originated between 455 and 248 million years ago and has been conserved to the present, making it the among the oldest conserved animal sex chromosomes known.
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Affiliation(s)
- Gabrielle C. Coffing
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Silas Tittes
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Scott T. Small
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Jeremea O. Songco-Casey
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Denise M. Piscopo
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Judit R. Pungor
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Adam C. Miller
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Cristopher M. Niell
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
| | - Andrew D. Kern
- Department of Biology, University of Oregon, 77 Klamath Hall, 1210 University of Oregon, Eugene, OR, 97403, USA
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16
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Behrens KA, Zimmermann H, Blažek R, Reichard M, Koblmüller S, Kocher TD. Turnover of sex chromosomes in the Lake Tanganyika cichlid tribe Tropheini (Teleostei: Cichlidae). Sci Rep 2024; 14:2471. [PMID: 38291228 PMCID: PMC10828463 DOI: 10.1038/s41598-024-53021-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 01/25/2024] [Indexed: 02/01/2024] Open
Abstract
Sex chromosome replacement is frequent in many vertebrate clades, including fish, frogs, and lizards. In order to understand the mechanisms responsible for sex chromosome turnover and the early stages of sex chromosome divergence, it is necessary to study lineages with recently evolved sex chromosomes. Here we examine sex chromosome evolution in a group of African cichlid fishes (tribe Tropheini) which began to diverge from one another less than 4 MYA. We have evidence for a previously unknown sex chromosome system, and preliminary indications of several additional systems not previously reported in this group. We find a high frequency of sex chromosome turnover and estimate a minimum of 14 turnovers in this tribe. We date the origin of the most common sex determining system in this tribe (XY-LG5/19) near the base of one of two major sub-clades of this tribe, about 3.4 MY ago. Finally, we observe variation in the size of one sex-determining region that suggests independent evolution of evolutionary strata in species with a shared sex-determination system. Our results illuminate the rapid rate of sex chromosome turnover in the tribe Tropheini and set the stage for further studies of the dynamics of sex chromosome evolution in this group.
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Affiliation(s)
- Kristen A Behrens
- Department of Biology, University of Maryland, College Park, MD, 20742, USA.
| | - Holger Zimmermann
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 00, Brno, Czech Republic
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Radim Blažek
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 00, Brno, Czech Republic
| | - Martin Reichard
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 00, Brno, Czech Republic
- Department of Ecology and Vertebrate Zoology, University of Łódź, Łódź, Poland
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD, 20742, USA
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17
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Kubickova S, Kopecna O, Cernohorska H, Rubes J, Vozdova M. X Chromosome-Specific Repeats in Non-Domestic Bovidae. Genes (Basel) 2024; 15:159. [PMID: 38397149 PMCID: PMC10887555 DOI: 10.3390/genes15020159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Repetitive sequences form a substantial and still enigmatic part of the mammalian genome. We isolated repetitive DNA blocks of the X chromosomes of three species of the family Bovidae: Kobus defassa (KDEXr sequence), Bos taurus (BTAXr sequence) and Antilope cervicapra (ACEXr sequence). The copy numbers of the isolated sequences were assessed using qPCR, and their chromosomal localisations were analysed using FISH in ten bovid tribes and in outgroup species. Besides their localisation on the X chromosome, their presence was also revealed on the Y chromosome and autosomes in several species. The KDEXr sequence abundant in most Bovidae species also occurs in distant taxa (Perissodactyla and Carnivora) and seems to be evolutionarily older than BTAXr and ACEXr. The ACEXr sequence, visible only in several Antilopini species using FISH, is probably the youngest, and arised in an ancestor common to Bovidae and Cervidae. All three repetitive sequences analysed in this study are interspersed among gene-rich regions on the X chromosomes, apparently preventing the crossing-over in their close vicinity. This study demonstrates that repetitive sequences on the X chromosomes have undergone a fast evolution, and their variation among related species can be beneficial for evolutionary studies.
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Affiliation(s)
| | | | | | | | - Miluse Vozdova
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology-Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (J.R.)
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18
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Biedler JK, Aryan A, Qi Y, Wang A, Martinson EO, Hartman DA, Yang F, Sharma A, Morton KS, Potters M, Chen C, Dobson SL, Ebel GD, Kading RC, Paulson S, Xue RD, Strand MR, Tu Z. On the Origin and Evolution of the Mosquito Male-determining Factor Nix. Mol Biol Evol 2024; 41:msad276. [PMID: 38128148 PMCID: PMC10798136 DOI: 10.1093/molbev/msad276] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 12/02/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
The mosquito family Culicidae is divided into 2 subfamilies named the Culicinae and Anophelinae. Nix, the dominant male-determining factor, has only been found in the culicines Aedes aegypti and Aedes albopictus, 2 important arboviral vectors that belong to the subgenus Stegomyia. Here we performed sex-specific whole-genome sequencing and RNAseq of divergent mosquito species and explored additional male-inclusive datasets to investigate the distribution of Nix. Except for the Culex genus, Nix homologs were found in all species surveyed from the Culicinae subfamily, including 12 additional species from 3 highly divergent tribes comprising 4 genera, suggesting Nix originated at least 133 to 165 million years ago (MYA). Heterologous expression of 1 of 3 divergent Nix open reading frames (ORFs) in Ae. aegypti resulted in partial masculinization of genetic females as evidenced by morphology and doublesex splicing. Phylogenetic analysis suggests Nix is related to femaleless (fle), a recently described intermediate sex-determining factor found exclusively in anopheline mosquitoes. Nix from all species has a conserved structure, including 3 RNA-recognition motifs (RRMs), as does fle. However, Nix has evolved at a much faster rate than fle. The RRM3 of both Nix and fle are distantly related to the single RRM of a widely distributed and conserved splicing factor transformer-2 (tra2). The RRM3-based phylogenetic analysis suggests this domain in Nix and fle may have evolved from tra2 or a tra2-related gene in a common ancestor of mosquitoes. Our results provide insights into the evolution of sex determination in mosquitoes and will inform broad applications of mosquito-control strategies based on manipulating sex ratios toward nonbiting males.
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Affiliation(s)
- James K Biedler
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Azadeh Aryan
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Yumin Qi
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Aihua Wang
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Ellen O Martinson
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
| | - Daniel A Hartman
- Center for Vector-borne Infectious Diseases, Department of Microbiology Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Fan Yang
- Department of Entomology, Virginia Tech, Blacksburg, VA 24061, USA
| | - Atashi Sharma
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Katherine S Morton
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Mark Potters
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Chujia Chen
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
- Genetics Bioinformatics and Computational Biology PhD program, Virginia Tech, Blacksburg, VA 24061, USA
| | - Stephen L Dobson
- Department of Entomology, University of Kentucky, Lexington, KY 40503, USA
- MosquitoMate, Inc., Lexington, KY 40502, USA
| | - Gregory D Ebel
- Center for Vector-borne Infectious Diseases, Department of Microbiology Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Rebekah C Kading
- Center for Vector-borne Infectious Diseases, Department of Microbiology Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Sally Paulson
- Department of Entomology, Virginia Tech, Blacksburg, VA 24061, USA
| | - Rui-De Xue
- Anastasia Mosquito Control District, St. Augustine, FL 32092, USA
| | - Michael R Strand
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
| | - Zhijian Tu
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
- Genetics Bioinformatics and Computational Biology PhD program, Virginia Tech, Blacksburg, VA 24061, USA
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19
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Cochetel N, Minio A, Guarracino A, Garcia JF, Figueroa-Balderas R, Massonnet M, Kasuga T, Londo JP, Garrison E, Gaut BS, Cantu D. A super-pangenome of the North American wild grape species. Genome Biol 2023; 24:290. [PMID: 38111050 PMCID: PMC10729490 DOI: 10.1186/s13059-023-03133-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/30/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be captured in super-pangenomes, which provide a framework for interpreting genomic variations. RESULTS Here we report the sequencing, assembly, and annotation of nine wild North American grape genomes, which are phased and scaffolded at chromosome scale. We generate a reference-unbiased super-pangenome using pairwise whole-genome alignment methods, revealing the extent of the genomic diversity among wild grape species from sequence to gene level. The pangenome graph captures genomic variation between haplotypes within a species and across the different species, and it accurately assesses the similarity of hybrids to their parents. The species selected to build the pangenome are a great representation of the genus, as illustrated by capturing known allelic variants in the sex-determining region and for Pierce's disease resistance loci. Using pangenome-wide association analysis, we demonstrate the utility of the super-pangenome by effectively mapping short reads from genus-wide samples and identifying loci associated with salt tolerance in natural populations of grapes. CONCLUSIONS This study highlights how a reference-unbiased super-pangenome can reveal the genetic basis of adaptive traits from wild relatives and accelerate crop breeding research.
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Affiliation(s)
- Noé Cochetel
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
| | - Andrea Minio
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
| | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Human Technopole, Milan, Italy
| | - Jadran F Garcia
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
| | | | - Mélanie Massonnet
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
| | - Takao Kasuga
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Davis, CA, USA
| | - Jason P Londo
- Horticulture Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, USA
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA.
- Genome Center, University of California Davis, Davis, CA, USA.
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20
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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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21
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Scarparo G, Palanchon M, Brelsford A, Purcell J. Social antagonism facilitates supergene expansion in ants. Curr Biol 2023; 33:5085-5095.e4. [PMID: 37979579 DOI: 10.1016/j.cub.2023.10.049] [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: 04/26/2023] [Revised: 08/07/2023] [Accepted: 10/25/2023] [Indexed: 11/20/2023]
Abstract
Antagonistic selection has long been considered a major driver of the formation and expansion of sex chromosomes. For example, sexually antagonistic variation on an autosome can select for suppressed recombination between that autosome and the sex chromosome, leading to a neo-sex chromosome. Autosomal supergenes, chromosomal regions containing tightly linked variants affecting the same complex trait, share similarities with sex chromosomes, raising the possibility that sex chromosome evolution models can explain the evolution of genome structure and recombination in other contexts. We tested this premise in a Formica ant species, wherein we identified four supergene haplotypes on chromosome 3 underlying colony social organization and sex ratio. We discovered a novel rearranged supergene variant (9r) on chromosome 9 underlying queen miniaturization. The 9r is in strong linkage disequilibrium with one chromosome 3 haplotype (P2) found in multi-queen (polygyne) colonies. We suggest that queen miniaturization is strongly disfavored in the single-queen (monogyne) background and is thus socially antagonistic. As such, divergent selection experienced by ants living in alternative social "environments" (monogyne and polygyne) may have contributed to the emergence of a genetic polymorphism on chromosome 9 and associated queen-size dimorphism. Consequently, an ancestral polygyne-associated haplotype may have expanded to include the polymorphism on chromosome 9, resulting in a larger region of suppressed recombination spanning two chromosomes. This process is analogous to the formation of neo-sex chromosomes and consistent with models of expanding regions of suppressed recombination. We propose that miniaturized queens, 16%-20% smaller than queens without 9r, could be incipient intraspecific social parasites.
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Affiliation(s)
- Giulia Scarparo
- Department of Entomology, University of California, Riverside, 165 Entomology Bldg. Citrus Drive, Riverside, CA 92521, USA.
| | - Marie Palanchon
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, 2710 Life Science Bldg., Riverside, CA 92521, USA
| | - Alan Brelsford
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, 2710 Life Science Bldg., Riverside, CA 92521, USA
| | - Jessica Purcell
- Department of Entomology, University of California, Riverside, 165 Entomology Bldg. Citrus Drive, Riverside, CA 92521, USA.
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22
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Gu H, Wen J, Zhao X, Zhang X, Ren X, Cheng H, Qu L. Evolution, Inheritance, and Strata Formation of the W Chromosome in Duck (Anas platyrhynchos). Genome Biol Evol 2023; 15:evad183. [PMID: 37931036 PMCID: PMC10630070 DOI: 10.1093/gbe/evad183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 11/08/2023] Open
Abstract
The nonrecombining female-limited W chromosome is predicted to experience unique evolutionary processes. Difficulties in assembling W chromosome sequences have hindered the identification of duck W-linked sequences and their evolutionary footprint. To address this, we conducted three initial contig-level genome assemblies and developed a rigorous pipeline by which to successfully expand the W-linked data set, including 11 known genes and 24 newly identified genes. Our results indicate that the W chromosome expression may not be subject to female-specific selection; a significant convergent pattern of upregulation associated with increased female-specific selection was not detected. The genetic stability of the W chromosome is also reflected in the strong evolutionary correlation between it and the mitochondria; the complete consistency of the cladogram topology constructed from their gene sequences proves the shared maternal coevolution. By detecting the evolutionary trajectories of W-linked sequences, we have found that recombination suppression started in four distinct strata, of which three were conserved across Neognathae. Taken together, our results have revealed a unique evolutionary pattern and an independent stratum evolutionary pattern for sex chromosomes.
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Affiliation(s)
- Hongchang Gu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Junhui Wen
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiurong Zhao
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xinye Zhang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xufang Ren
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huan Cheng
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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23
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Ogawa M, Tsuneizumi K, Abe T, Nozawa M. Testing immediate dosage compensation in Drosophila miranda via irradiation with heavy-ion beams. Genes Genet Syst 2023; 98:201-206. [PMID: 37779054 DOI: 10.1266/ggs.23-00100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023] Open
Abstract
Many organisms with heteromorphic sex chromosomes possess a mechanism of dosage compensation (DC) in which X-linked genes are upregulated in males to mitigate the dosage imbalance between sexes and between chromosomes. However, how quickly the DC is established during evolution remains unknown. In this study, by irradiating Drosophila miranda male flies, which carry young sex chromosomes (the so-called neo-sex chromosomes), with heavy-ion beams, we induced deletions in the neo-Y chromosome to mimic the condition of Y-chromosome degeneration, in which functional neo-Y-linked genes are nonfunctionalized; furthermore, we tested whether their neo-X-linked gametologs were immediately upregulated. Because the males that received 2-Gy iron-ion beam irradiation exhibited lower fertility, we sequenced the genomes and transcriptomes of six F1 males derived from these males. Our pipeline identified 82 neo-Y-linked genes in which deletions were predicted in the F1 males. Only three of them showed a one-to-one gametologous relationship with the neo-X-linked genes. The candidate deletions in these three genes occurred in UTRs and did not seriously affect their expression levels. These observations indirectly suggest that DC was unlikely to have operated on the neo-X-linked genes immediately after the pseudogenization of their neo-Y-linked gametologs in D. miranda. Therefore, the dosage imbalance caused by deletions in the neo-Y-linked genes without paralogs may not have effectively been compensated, and individuals with such deletions could have exhibited lethality. Future studies on sex chromosomes at different ages will further reveal the relationship between the age of sex chromosomes and the stringency of DC.
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Affiliation(s)
- Masafumi Ogawa
- Department of Biological Sciences, Tokyo Metropolitan University
| | | | - Tomoko Abe
- Ion Beam Breeding Team, RIKEN Nishina Center for Accelerator-Based Science
| | - Masafumi Nozawa
- Department of Biological Sciences, Tokyo Metropolitan University
- Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University
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24
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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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25
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Zheng S, Tao W, Tao H, Yang H, Wu L, Shao F, Wang Z, Jin L, Peng Z, Wang D, Zhang Y. Characterization of the male-specific region containing the candidate sex-determining gene in Amur catfish (Silurus asotus) using third-generation- and pool-sequencing data. Int J Biol Macromol 2023; 248:125908. [PMID: 37482150 DOI: 10.1016/j.ijbiomac.2023.125908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
Amur catfish (Silurus asotus) is an ecologically and economically important fish species in Asia. Here, we assembled the female and male Amur catfish genomes, with genome sizes of 757.15 and 755.44 Mb, respectively, at the chromosome level using nanopore and Hi-C technologies. Consistent with the known diploid chromosome count, both genomes contained 29 chromosome-size scaffolds covering 98.80 and 98.73 % of the complete haplotypic assembly with scaffold N50 of 28.87 and 27.29 Mb, respectively. The female (n = 40) and male (n = 40) pools were re-sequenced. Comparative analysis of sequencing and re-sequencing data from both sexes confirmed the presence of an XX/XY sex determination system in Amur catfish and revealed Chr5 as the sex chromosome containing an approximately 400 kb Y-specific region (MSY). Gene annotation revealed a male-specific duplicate of amhr2, namely amhr2y, in MSY, which is male-specific in different wild populations and expressed only in the testes. Amur catfish shared partially syntenic MSY and amhr2y genes with the southern catfish (S. meridionalis, Chr24), which were located on different chromosomes. High sequence divergence between amhr2y and amhr2 and high sequence similarity with amhr2y were observed in both species. These results indicate the common origin of the sex-determining (SD) gene and transition of amhr2y in the two Silurus species. Accumulation of repetitive elements in the MSY of both species may be the main driver of the transition of amhr2y. Overall, our study provides valuable catfish genomic resources. Moreover, determination of amhr2y as the candidate SD gene in Amur catfish provides another example of amhr2 as the SD gene in fish.
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Affiliation(s)
- Shuqing Zheng
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Wenjing Tao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Hongyan Tao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Haowen Yang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Limin Wu
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, College of Fisheries, Henan Normal University, Xinxiang 453007, China
| | - Feng Shao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Zhijian Wang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Li Jin
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Zuogang Peng
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Deshou Wang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Yaoguang Zhang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
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26
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Nirchio Tursellino M, de Bello Cioffi M, de Menezes Cavalcante Sassi F, Deon GA, Oliveira C, Kuranaka M, Valdiviezo-Rivera J, Gonzalez VH, Rossi AR. Integrating Genomic and Chromosomal Data: A Cytogenetic Study of Transancistrus santarosensis (Loricariidae: Hypostominae) with Characterization of a ZZ/ZW Sex Chromosome System. Genes (Basel) 2023; 14:1662. [PMID: 37761802 PMCID: PMC10531053 DOI: 10.3390/genes14091662] [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: 07/11/2023] [Revised: 08/14/2023] [Accepted: 08/19/2023] [Indexed: 09/29/2023] Open
Abstract
The plecos (Loricariidae) fish represent a great model for cytogenetic investigations due to their variety of karyotypes, including diploid and polyploid genomes, and different types of sex chromosomes. In this study we investigate Transancistrus santarosensis a rare loricariid endemic to Ecuador, integrating cytogenetic methods with specimens' molecular identification by mtDNA, to describe the the species karyotype. We aim to verify whether sex chromosomes are cytologically identifiable and if they are associated with the accumulation of repetitive sequences present in other species of the family. The analysis of the karyotype (2n = 54 chromosomes) excludes recent centric fusion and pericentromeric inversion and suggests the presence of a ZZ/ZW sex chromosome system at an early stage of differentiation: the W chromosome is degenerated but is not characterized by the presence of differential sex-specific repetitive DNAs. Data indicate that although T. santarosensis has retained the ancestral diploid number of Loricariidae, it accumulated heterochromatin and shows non-syntenic ribosomal genes localization, chromosomal traits considered apomorphic in the family.
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Affiliation(s)
- Mauro Nirchio Tursellino
- Departamento de Acuicultura, Universidad Técnica de Machala, Av. Panamericana km 5.5, Vía Pasaje, Machala 070150, El Oro, Ecuador;
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-090, SP, Brazil; (M.d.B.C.); (F.d.M.C.S.); (G.A.D.)
| | | | - Geize Aparecida Deon
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-090, SP, Brazil; (M.d.B.C.); (F.d.M.C.S.); (G.A.D.)
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências Universidade Estadual Paulista-UNESP, Botucatu 18618-689, SP, Brazil; (C.O.); (M.K.)
| | - Mariana Kuranaka
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências Universidade Estadual Paulista-UNESP, Botucatu 18618-689, SP, Brazil; (C.O.); (M.K.)
| | - Jonathan Valdiviezo-Rivera
- Instituto Nacional de Biodiversidad, Rumipamba No. 341 y Av. Shyris, Parque La Carolina, Quito 170135, Pichincha, Ecuador;
| | - Víctor Hugo Gonzalez
- Departamento de Acuicultura, Universidad Técnica de Machala, Av. Panamericana km 5.5, Vía Pasaje, Machala 070150, El Oro, Ecuador;
| | - Anna Rita Rossi
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza—Università di Roma, Via Alfonso Borelli 50, 00161 Rome, Italy;
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27
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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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King AC, Zenker AK. Sex blind: bridging the gap between drug exposure and sex-related gene expression in Danio rerio using next-generation sequencing (NGS) data and a literature review to find the missing links in pharmaceutical and environmental toxicology studies. FRONTIERS IN TOXICOLOGY 2023; 5:1187302. [PMID: 37398910 PMCID: PMC10312089 DOI: 10.3389/ftox.2023.1187302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/01/2023] [Indexed: 07/04/2023] Open
Abstract
The sex of both humans and Danio rerio has previously been shown to affect the way individuals respond to drug exposure. Genes which allow identification of sex in juvenile zebrafish show potential to reveal these confounding variables between sex in toxicological and preclinical trials but the link between these is so far missing. These sex-specific, early expressed genes where expression is not altered by drug exposure must be carefully selected for this purpose. We aimed to discover genes which can be used in pharmaceutical trials and environmental toxicology studies to uncover sex-related variations in gene expression with drug application using the model organism Danio rerio. Previously published early sex determining genes from King et al. were evaluated as well as additional genes selected from our zebrafish Next-generation sequencing (NGS) data which are known from previously published works not to be susceptible to changes in expression with drug exposure. NGS revealed a further ten female-specific genes (vtg1, cyp17a1, cyp19a1a, igf3, ftz-f1, gdf9, foxl2a, Nr0b1, ipo4, lhcgr) and five male related candidate genes (FKBP5, apobb1, hbaa1, dmrt1, spata6) which are also expressed in juvenile zebrafish, 28 days post fertilisation (dpf). Following this, a literature review was performed to classify which of these early-expressed sex specific genes are already known to be affected by drug exposure in order to determine candidate genes to be used in pharmaceutical trials or environmental toxicology testing studies. Discovery of these early sex-determining genes in Danio rerio will allow identification of sex-related responses to drug testing to improve sex-specific healthcare and the medical treatment of human patients.
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Affiliation(s)
| | - Armin K. Zenker
- University of Applied Sciences and Arts North-Western Switzerland (FHNW), Muttenz, Switzerland
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29
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Hyden B, Zou J, Wilkerson DG, Carlson CH, Robles AR, DiFazio SP, Smart LB. Structural variation of a sex-linked region confers monoecy and implicates GATA15 as a master regulator of sex in Salix purpurea. THE NEW PHYTOLOGIST 2023; 238:2512-2523. [PMID: 36866707 DOI: 10.1111/nph.18853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/21/2023] [Indexed: 05/19/2023]
Abstract
The Salicaceae, including Populus and Salix, are dioecious perennials that utilize different sex determination systems. This family provides a useful system to better understand the evolution of dioecy and sex chromosomes. Here, a rare monoecious genotype of Salix purpurea, 94003, was self- and cross-pollinated and progeny sex ratios were used to test hypotheses on possible mechanisms of sex determination. To delimit genomic regions associated with monoecious expression, the 94003 genome sequence was assembled and DNA- and RNA-Seq of progeny inflorescences was performed. Based on alignments of progeny shotgun DNA sequences to the haplotype-resolved monoecious 94003 genome assembly and reference male and female genomes, a 1.15 Mb sex-linked region on Chr15W was confirmed to be absent in monecious plants. Inheritance of this structural variation is responsible for the loss of a male-suppressing function in what would otherwise be genetic females (ZW), resulting in monoecy (ZWH or WWH ), or lethality, if homozygous (WH WH ). We present a refined, two-gene sex determination model for Salix purpurea, mediated by ARR17 and GATA15 that is different from the single-gene ARR17-mediated system in the related genus Populus.
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Affiliation(s)
- Brennan Hyden
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
| | - Junzhu Zou
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
- Research Institute of Forestry, Chinese Academy of Forestry, Dongxiaofu No. 1, Haidian District, Beijing, 100091, China
| | - Dustin G Wilkerson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
| | - Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, ND, 58102, USA
| | - Ayiana Rivera Robles
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
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30
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Vidal JAD, Sassi FDMC, de Moraes RLR, Artoni RF, Liehr T, Cioffi MB, de Almeida MC. Giant Sex Chromosomes in Omophoita Species (Coleoptera, Chrysomelidae): Structural and Evolutionary Relationships Revealed by Zoo-FISH and Comparative Genomic Hybridization (CGH). INSECTS 2023; 14:insects14050440. [PMID: 37233068 DOI: 10.3390/insects14050440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 04/29/2023] [Accepted: 05/02/2023] [Indexed: 05/27/2023]
Abstract
The beetles of the subtribe Oedionychina (Chrysomelidae, Alticinae) are the only ones that have the atypical giant and achiasmatic sex chromosomes, which are substantially larger than the autosomes. Previous cytogenetic analyses suggest a large accumulation of repetitive DNA in the sex chromosomes. In this study, we examined the similarity of X and Y chromosomes in four Omophoita species and compared genomic differentiation to better understand the evolutionary process and the giant sex chromosomes origin. Intraspecific genomic comparation using male and female genomes of O. octoguttata and interespecific analyses using genomic DNA of O. octoguttata, O. sexnotata, O. magniguttis, and O. personata were performed. In addition, whole chromosome painting (WCP) experiments were performed with X and Y chromosome probes of O. octogutatta. CGH analysis revealed great genomic similarity between the sexes and a sex-specific region on the Y chromosome, and interspecific analysis revealed a genomic divergence between species. In contrast, WCP results revealed that the sex chromosomes of O. octoguttata have high intra- and interspecific similarity with the studied species. Our data support a common origin under the canonical evolution of the sex chromosomes in this group, as they have high genomic similarity between them.
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Affiliation(s)
- Jhon A D Vidal
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, Brazil
- Laboratório de Genética e Evolução, Departamento de Biologia Estrutural Molecular e Genética, Universidade Estadual de Ponta Grossa (UEPG), Av. Carlos Cavalcanti, 4748, Ponta Grossa 84030-900, Brazil
| | - Francisco de M C Sassi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, Brazil
| | - Renata L R de Moraes
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, Brazil
| | - Roberto F Artoni
- Laboratório de Genética e Evolução, Departamento de Biologia Estrutural Molecular e Genética, Universidade Estadual de Ponta Grossa (UEPG), Av. Carlos Cavalcanti, 4748, Ponta Grossa 84030-900, Brazil
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany
| | - Marcelo B Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, Brazil
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany
| | - Mara C de Almeida
- Laboratório de Genética e Evolução, Departamento de Biologia Estrutural Molecular e Genética, Universidade Estadual de Ponta Grossa (UEPG), Av. Carlos Cavalcanti, 4748, Ponta Grossa 84030-900, Brazil
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31
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Valero-Regalón FJ, Solé M, López-Jiménez P, Valerio-de Arana M, Martín-Ruiz M, de la Fuente R, Marín-Gual L, Renfree MB, Shaw G, Berríos S, Fernández-Donoso R, Waters PD, Ruiz-Herrera A, Gómez R, Page J. Divergent patterns of meiotic double strand breaks and synapsis initiation dynamics suggest an evolutionary shift in the meiosis program between American and Australian marsupials. Front Cell Dev Biol 2023; 11:1147610. [PMID: 37181752 PMCID: PMC10166821 DOI: 10.3389/fcell.2023.1147610] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/06/2023] [Indexed: 05/16/2023] Open
Abstract
In eutherian mammals, hundreds of programmed DNA double-strand breaks (DSBs) are generated at the onset of meiosis. The DNA damage response is then triggered. Although the dynamics of this response is well studied in eutherian mammals, recent findings have revealed different patterns of DNA damage signaling and repair in marsupial mammals. To better characterize these differences, here we analyzed synapsis and the chromosomal distribution of meiotic DSBs markers in three different marsupial species (Thylamys elegans, Dromiciops gliorides, and Macropus eugenii) that represent South American and Australian Orders. Our results revealed inter-specific differences in the chromosomal distribution of DNA damage and repair proteins, which were associated with differing synapsis patterns. In the American species T. elegans and D. gliroides, chromosomal ends were conspicuously polarized in a bouquet configuration and synapsis progressed exclusively from the telomeres towards interstitial regions. This was accompanied by sparse H2AX phosphorylation, mainly accumulating at chromosomal ends. Accordingly, RAD51 and RPA were mainly localized at chromosomal ends throughout prophase I in both American marsupials, likely resulting in reduced recombination rates at interstitial positions. In sharp contrast, synapsis initiated at both interstitial and distal chromosomal regions in the Australian representative M. eugenii, the bouquet polarization was incomplete and ephemeral, γH2AX had a broad nuclear distribution, and RAD51 and RPA foci displayed an even chromosomal distribution. Given the basal evolutionary position of T. elegans, it is likely that the meiotic features reported in this species represent an ancestral pattern in marsupials and that a shift in the meiotic program occurred after the split of D. gliroides and the Australian marsupial clade. Our results open intriguing questions about the regulation and homeostasis of meiotic DSBs in marsupials. The low recombination rates observed at the interstitial chromosomal regions in American marsupials can result in the formation of large linkage groups, thus having an impact in the evolution of their genomes.
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Affiliation(s)
| | - Mireia Solé
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
- Genetics of Male Fertility Group, Unitat de Biologia Cel·lular, Universitat Autònoma de Barcelona, Spain
| | - Pablo López-Jiménez
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - María Valerio-de Arana
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marta Martín-Ruiz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Roberto de la Fuente
- Department of Experimental Embryology, Institute of Genetics and Animal Biotechnology of The Polish Academy of Sciences, Jastrzębiec, Poland
| | - Laia Marín-Gual
- Departament de Biologia Cel·lular, Universitat Autònoma de Barcelona, Barcelona, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Barcelona, Spain
| | - Marilyn B. Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Geoff Shaw
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Soledad Berríos
- Programa de Genética Humana, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Raúl Fernández-Donoso
- Programa de Genética Humana, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Paul D. Waters
- School of Biotechnology and Biomolecular Science, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Universitat Autònoma de Barcelona, Barcelona, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Barcelona, Spain
| | - Rocío Gómez
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Jesús Page
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
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32
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Akagi T, Varkonyi-Gasic E, Shirasawa K, Catanach A, Henry IM, Mertten D, Datson P, Masuda K, Fujita N, Kuwada E, Ushijima K, Beppu K, Allan AC, Charlesworth D, Kataoka I. Recurrent neo-sex chromosome evolution in kiwifruit. NATURE PLANTS 2023; 9:393-402. [PMID: 36879018 DOI: 10.1038/s41477-023-01361-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/31/2023] [Indexed: 05/18/2023]
Abstract
Sex chromosome evolution is thought to be tightly associated with the acquisition and maintenance of sexual dimorphisms. Plant sex chromosomes have evolved independently in many lineages1,2 and can provide a powerful comparative framework to study this. We assembled and annotated genome sequences of three kiwifruit species (genus Actinidia) and uncovered recurrent sex chromosome turnovers in multiple lineages. Specifically, we observed structural evolution of the neo-Y chromosomes, which was driven via rapid bursts of transposable element insertions. Surprisingly, sexual dimorphisms were conserved in the different species studied, despite the fact that the partially sex-linked genes differ between them. Using gene editing in kiwifruit, we demonstrated that one of the two Y-chromosome-encoded sex-determining genes, Shy Girl, shows pleiotropic effects that can explain the conserved sexual dimorphisms. These plant sex chromosomes therefore maintain sexual dimorphisms through the conservation of a single gene, without a process involving interactions between separate sex-determining genes and genes for sexually dimorphic traits.
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Affiliation(s)
- Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
- Japan Science and Technology Agency (JST), PRESTO, Kawaguchi-shi, Japan.
| | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kazusa-Kamatari, Kisarazu, Japan
| | - Andrew Catanach
- The New Zealand Institute for Plant and Food Research Limited (PFR), Christchurch, New Zealand
| | - Isabelle M Henry
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA, USA
| | - Daniel Mertten
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand
| | - Paul Datson
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand
- The Kiwifruit Breeding Centre, Auckland, New Zealand
| | - Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Naoko Fujita
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Eriko Kuwada
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Koichiro Ushijima
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Kenji Beppu
- Faculty of Agriculture, Kagawa University, Miki, Kagawa, Japan
| | - Andrew C Allan
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Ikuo Kataoka
- Faculty of Agriculture, Kagawa University, Miki, Kagawa, Japan
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33
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Occurrence of Sex Chromosomes in Fish of the Genus Ancistrus with a New Description of Multiple Sex Chromosomes in the Ecuadorian Endemic Ancistrus clementinae (Loricariidae). Genes (Basel) 2023; 14:genes14020306. [PMID: 36833233 PMCID: PMC9956960 DOI: 10.3390/genes14020306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
Ancistrus Kner, 1854, is the most diverse genus among the Ancistrini (Loricariidae) with 70 valid species showing a wide geographic distribution and great taxonomic and systematic complexity. To date, about 40 Ancistrus taxa have been karyotyped, all from Brazil and Argentina, but the statistic is uncertain because 30 of these reports deal with samples that have not yet been identified at the species level. This study provides the first cytogenetic description of the bristlenose catfish, Ancistrus clementinae Rendahl, 1937, a species endemic to Ecuador, aiming to verify whether a sex chromosome system is identifiable in the species and, if so, which, and if its differentiation is associated with the presence of repetitive sequences reported for other species of the family. We associated the karyotype analysis with the COI molecular identification of the specimens. Karyotype analysis suggested the presence of a ♂ZZ/♀ZW1W2 sex chromosome system, never detected before in Ancistrus, with both W1W2 chromosomes enriched with heterochromatic blocks and 18S rDNA, in addition to GC-rich repeats (W2). No differences were observed between males and females in the distribution of 5S rDNA or telomeric repeats. Cytogenetic data here obtained confirm the huge karyotype diversity of Ancistrus, both in chromosome number and sex-determination systems.
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34
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Abeyratne CR, Macaya-Sanz D, Zhou R, Barry KW, Daum C, Haiby K, Lipzen A, Stanton B, Yoshinaga Y, Zane M, Tuskan GA, DiFazio SP. High-resolution mapping reveals hotspots and sex-biased recombination in Populus trichocarpa. G3 (BETHESDA, MD.) 2023; 13:jkac269. [PMID: 36250890 PMCID: PMC9836356 DOI: 10.1093/g3journal/jkac269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/28/2022] [Indexed: 12/14/2022]
Abstract
Fine-scale meiotic recombination is fundamental to the outcome of natural and artificial selection. Here, dense genetic mapping and haplotype reconstruction were used to estimate recombination for a full factorial Populus trichocarpa cross of 7 males and 7 females. Genomes of the resulting 49 full-sib families (N = 829 offspring) were resequenced, and high-fidelity biallelic SNP/INDELs and pedigree information were used to ascertain allelic phase and impute progeny genotypes to recover gametic haplotypes. The 14 parental genetic maps contained 1,820 SNP/INDELs on average that covered 376.7 Mb of physical length across 19 chromosomes. Comparison of parental and progeny haplotypes allowed fine-scale demarcation of cross-over regions, where 38,846 cross-over events in 1,658 gametes were observed. Cross-over events were positively associated with gene density and negatively associated with GC content and long-terminal repeats. One of the most striking findings was higher rates of cross-overs in males in 8 out of 19 chromosomes. Regions with elevated male cross-over rates had lower gene density and GC content than windows showing no sex bias. High-resolution analysis identified 67 candidate cross-over hotspots spread throughout the genome. DNA sequence motifs enriched in these regions showed striking similarity to those of maize, Arabidopsis, and wheat. These findings, and recombination estimates, will be useful for ongoing efforts to accelerate domestication of this and other biomass feedstocks, as well as future studies investigating broader questions related to evolutionary history, perennial development, phenology, wood formation, vegetative propagation, and dioecy that cannot be studied using annual plant model systems.
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Affiliation(s)
| | - David Macaya-Sanz
- Department of Forest Ecology & Genetics, CIFOR-INIA, CSIC, Madrid 28040, Spain
| | - Ran Zhou
- Warnell School of Forestry and Natural Resources, Department of Genetics, and Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Kerrie W Barry
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Christopher Daum
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | | | - Anna Lipzen
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | | | - Yuko Yoshinaga
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Matthew Zane
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Gerald A Tuskan
- Biosciences Division, Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV 26506, USA
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35
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Singh P, Taborsky M, Peichel CL, Sturmbauer C. Genomic basis of Y-linked dwarfism in cichlids pursuing alternative reproductive tactics. Mol Ecol 2023; 32:1592-1607. [PMID: 36588349 DOI: 10.1111/mec.16839] [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: 05/21/2021] [Revised: 12/08/2022] [Accepted: 12/19/2022] [Indexed: 01/03/2023]
Abstract
Sexually antagonistic selection, which favours different optima in males and females, is predicted to play an important role in the evolution of sex chromosomes. Body size is a sexually antagonistic trait in the shell-brooding cichlid fish Lamprologous callipterus, as "bourgeois" males must be large enough to carry empty snail shells to build nests whereas females must be small enough to fit into shells for breeding. In this species, there is also a second male morph: smaller "dwarf" males employ an alternative reproductive strategy by wriggling past spawning females into shells to fertilize eggs. L. callipterus male morphology is passed strictly from father to son, suggesting Y-linkage. However, sex chromosomes had not been previously identified in this species, and the genomic basis of size dimorphism was unknown. Here we used whole-genome sequencing to identify a 2.4-Mb sex-linked region on scaffold_23 with reduced coverage and single nucleotide polymorphism density in both male morphs compared to females. Within this sex region, distinct Y-haplotypes delineate the two male morphs, and candidate genes for body size (GHRHR, a known dwarfism gene) and sex determination (ADCYAP1R1) are in high linkage disequilibrium. Because differences in body size between females and males are under strong selection in L. callipterus, we hypothesize that sexual antagonism over body size initiated early events in sex chromosome evolution, followed by Y divergence to give rise to bourgeois and dwarf male reproductive strategies. Our results are consistent with the hypothesis that sexually antagonistic traits should be linked to young sex chromosomes.
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Affiliation(s)
- Pooja Singh
- Institute of Biology, University of Graz, Graz, Austria.,Aquatic Ecology Division, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
| | - Michael Taborsky
- Behavioural Ecology Division, Institute of Ecology and Evolution, University of Bern, Switzerland.,Max Planck Institute of Animal Behavior, Constance, Germany.,Institute for Advanced Study (Wissenschaftskolleg) Berlin, Berlin, Germany
| | - Catherine L Peichel
- Evolutionary Ecology Division, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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36
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Sex chromosome differentiation via changes in the Y chromosome repeat landscape in African annual killifishes Nothobranchius furzeri and N. kadleci. Chromosome Res 2022; 30:309-333. [PMID: 36208359 DOI: 10.1007/s10577-022-09707-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 01/25/2023]
Abstract
Homomorphic sex chromosomes and their turnover are common in teleosts. We investigated the evolution of nascent sex chromosomes in several populations of two sister species of African annual killifishes, Nothobranchius furzeri and N. kadleci, focusing on their under-studied repetitive landscape. We combined bioinformatic analyses of the repeatome with molecular cytogenetic techniques, including comparative genomic hybridization, fluorescence in situ hybridization with satellite sequences, ribosomal RNA genes (rDNA) and bacterial artificial chromosomes (BACs), and immunostaining of SYCP3 and MLH1 proteins to mark lateral elements of synaptonemal complexes and recombination sites, respectively. Both species share the same heteromorphic XY sex chromosome system, which thus evolved prior to their divergence. This was corroborated by sequence analysis of a putative master sex determining (MSD) gene gdf6Y in both species. Based on their divergence, differentiation of the XY sex chromosome pair started approximately 2 million years ago. In all populations, the gdf6Y gene mapped within a region rich in satellite DNA on the Y chromosome long arms. Despite their heteromorphism, X and Y chromosomes mostly pair regularly in meiosis, implying synaptic adjustment. In N. kadleci, Y-linked paracentric inversions like those previously reported in N. furzeri were detected. An inversion involving the MSD gene may suppress occasional recombination in the region, which we otherwise evidenced in the N. furzeri population MZCS-121 of the Limpopo clade lacking this inversion. Y chromosome centromeric repeats were reduced compared with the X chromosome and autosomes, which points to a role of relaxed meiotic drive in shaping the Y chromosome repeat landscape. We speculate that the recombination rate between sex chromosomes was reduced due to heterochiasmy. The observed differences between the repeat accumulations on the X and Y chromosomes probably result from high repeat turnover and may not relate closely to the divergence inferred from earlier SNP analyses.
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37
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Han W, Liu L, Wang J, Wei H, Li Y, Zhang L, Guo Z, Li Y, Liu T, Zeng Q, Xing Q, Shu Y, Wang T, Yang Y, Zhang M, Li R, Yu J, Pu Z, Lv J, Lian S, Hu J, Hu X, Bao Z, Bao L, Zhang L, Wang S. Ancient homomorphy of molluscan sex chromosomes sustained by reversible sex-biased genes and sex determiner translocation. Nat Ecol Evol 2022; 6:1891-1906. [PMID: 36280781 DOI: 10.1038/s41559-022-01898-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 09/05/2022] [Indexed: 12/15/2022]
Abstract
Contrary to classic theory prediction, sex-chromosome homomorphy is prevalent in the animal kingdom but it is unclear how ancient homomorphic sex chromosomes avoid chromosome-scale degeneration. Molluscs constitute the second largest, Precambrian-originated animal phylum and have ancient, uncharacterized homomorphic sex chromosomes. Here, we profile eight genomes of the bivalve mollusc family of Pectinidae in a phylogenetic context and show 350 million years sex-chromosome homomorphy, which is the oldest known sex-chromosome homomorphy in the animal kingdom, far exceeding the ages of well-known heteromorphic sex chromosomes such as 130-200 million years in mammals, birds and flies. The long-term undifferentiation of molluscan sex chromosomes is potentially sustained by the unexpected intertwined regulation of reversible sex-biased genes, together with the lack of sexual dimorphism and occasional sex chromosome turnover. The pleiotropic constraint of regulation of reversible sex-biased genes is widely present in ancient homomorphic sex chromosomes and might be resolved in heteromorphic sex chromosomes through gene duplication followed by subfunctionalization. The evolutionary dynamics of sex chromosomes suggest a mechanism for 'inheritance' turnover of sex-determining genes that is mediated by translocation of a sex-determining enhancer. On the basis of these findings, we propose an evolutionary model for the long-term preservation of homomorphic sex chromosomes.
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Affiliation(s)
- Wentao Han
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Liangjie Liu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jing Wang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Huilan Wei
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuli Li
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lijing Zhang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhenyi Guo
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yajuan Li
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Tian Liu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qifan Zeng
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Qiang Xing
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ya Shu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Tong Wang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yaxin Yang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Meiwei Zhang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Ruojiao Li
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jiachen Yu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhongqi Pu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jia Lv
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Shanshan Lian
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jingjie Hu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Xiaoli Hu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenmin Bao
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Lisui Bao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China.
| | - Lingling Zhang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Shi Wang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China.
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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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Sex chromosomes in the tribe Cyprichromini (Teleostei: Cichlidae) of Lake Tanganyika. Sci Rep 2022; 12:17998. [PMID: 36289404 PMCID: PMC9606112 DOI: 10.1038/s41598-022-23017-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/21/2022] [Indexed: 01/24/2023] Open
Abstract
Sex determining loci have been described on at least 12 of 22 chromosomes in East African cichlid fishes, indicating a high rate of sex chromosome turnover. To better understand the rates and patterns of sex chromosome replacement, we used new methods to characterize the sex chromosomes of the cichlid tribe Cyprichromini from Lake Tanganyika. Our k-mer based methods successfully identified sex-linked polymorphisms without the need for a reference genome. We confirm the three previously reported sex chromosomes in this group. We determined the polarity of the sex chromosome turnover on LG05 in Cyprichromis as ZW to XY. We identified a new ZW locus on LG04 in Paracyprichromis brieni. The LG15 XY locus in Paracyprichromis nigripinnis was not found in other Paracyprichromis species, and the sample of Paracyprichromis sp. "tembwe" is likely to be of hybrid origin. Although highly divergent sex chromosomes are thought to develop in a stepwise manner, we show two cases (LG05-ZW and LG05-XY) in which the region of differentiation encompasses most of the chromosome, but appears to have arisen in a single step. This study expands our understanding of sex chromosome evolution in the Cyprichromini, and indicates an even higher level of sex chromosome turnover than previously thought.
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40
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Bergman J, Schierup MH. Evolutionary dynamics of pseudoautosomal region 1 in humans and great apes. Genome Biol 2022; 23:215. [PMID: 36253794 PMCID: PMC9575207 DOI: 10.1186/s13059-022-02784-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 09/30/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The pseudoautosomal region 1 (PAR1) is a 2.7 Mb telomeric region of human sex chromosomes. PAR1 has a crucial role in ensuring proper segregation of sex chromosomes during male meiosis, exposing it to extreme recombination and mutation processes. We investigate PAR1 evolution using population genomic datasets of extant humans, eight populations of great apes, and two archaic human genome sequences. RESULTS We find that PAR1 is fast evolving and closer to evolutionary nucleotide equilibrium than autosomal telomeres. We detect a difference between substitution patterns and extant diversity in PAR1, mainly driven by the conflict between strong mutation and recombination-associated fixation bias at CpG sites. We detect excess C-to-G mutations in PAR1 of all great apes, specific to the mutagenic effect of male recombination. Despite recent evidence for Y chromosome introgression from humans into Neanderthals, we find that the Neanderthal PAR1 retained similarity to the Denisovan sequence. We find differences between substitution spectra of these archaics suggesting rapid evolution of PAR1 in recent hominin history. Frequency analysis of alleles segregating in females and males provided no evidence for recent sexual antagonism in this region. We study repeat content and double-strand break hotspot regions in PAR1 and find that they may play roles in ensuring the obligate X-Y recombination event during male meiosis. CONCLUSIONS Our study provides an unprecedented quantification of population genetic forces governing PAR1 biology across extant and extinct hominids. PAR1 evolutionary dynamics are predominantly governed by recombination processes with a strong impact on mutation patterns across all species.
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Affiliation(s)
- Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
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41
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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:iyac123. [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] [MESH Headings] [Grants] [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 Artemia 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 Artemia sp. Kazakhstan and several asexual lineages of Artemia 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, Vienna 1030, Austria
| | - Melissa A Toups
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria
- Faculty of Science and Technology, Department of Life and Environmental Sciences, Bournemouth University, Poole 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, 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 Gutenberg Universität Mainz, Mainz 55122, Germany
| | - Francisco Hontoria
- Instituto de Acuicultura de Torre de la Sal (IATS-CSIC), 12595 Ribera de Cabanes (Castellón), Spain
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria
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42
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Wang D, Li Y, Li M, Yang W, Ma X, Zhang L, Wang Y, Feng Y, Zhang Y, Zhou R, Sanderson BJ, Keefover-Ring K, Yin T, Smart LB, DiFazio SP, Liu J, Olson M, Ma T. Repeated turnovers keep sex chromosomes young in willows. Genome Biol 2022; 23:200. [PMID: 36151581 PMCID: PMC9502649 DOI: 10.1186/s13059-022-02769-w] [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: 02/21/2022] [Accepted: 09/08/2022] [Indexed: 01/10/2023] Open
Abstract
Background Salicaceae species have diverse sex determination systems and frequent sex chromosome turnovers. However, compared with poplars, the diversity of sex determination in willows is poorly understood, and little is known about the evolutionary forces driving their turnover. Here, we characterized the sex determination in two Salix species, S. chaenomeloides and S. arbutifolia, which have an XY system on chromosome 7 and 15, respectively. Results Based on the assemblies of their sex determination regions, we found that the sex determination mechanism of willows may have underlying similarities with poplars, both involving intact and/or partial homologs of a type A cytokinin response regulator (RR) gene. Comparative analyses suggested that at least two sex turnover events have occurred in Salix, one preserving the ancestral pattern of male heterogamety, and the other changing heterogametic sex from XY to ZW, which could be partly explained by the “deleterious mutation load” and “sexually antagonistic selection” theoretical models. We hypothesize that these repeated turnovers keep sex chromosomes of willow species in a perpetually young state, leading to limited degeneration. Conclusions Our findings further improve the evolutionary trajectory of sex chromosomes in Salicaceae species, explore the evolutionary forces driving the repeated turnovers of their sex chromosomes, and provide a valuable reference for the study of sex chromosomes in other species. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02769-w.
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Affiliation(s)
- Deyan Wang
- 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
| | - Yiling Li
- 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
| | - Mengmeng Li
- 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
| | - Wenlu Yang
- 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
| | - Xinzhi 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
| | - Lei Zhang
- 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
| | - Yubo Wang
- 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
| | - Yanlin Feng
- 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
| | - Yuanyuan Zhang
- 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
| | - Ran Zhou
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Brian J Sanderson
- Department of Biology, West Virginia University, Morgantown, WV, USA.,Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Ken Keefover-Ring
- Departments of Botany and Geography, University of Wisconsin-Madison, Madison, WI, USA
| | - Tongming Yin
- The Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, Nanjing, China
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Jianquan Liu
- 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.
| | - Matthew Olson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.
| | - 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.
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43
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Heterogeneous Evolution of Sex Chromosomes in the Torrent Frog Genus Amolops. Int J Mol Sci 2022; 23:ijms231911146. [PMID: 36232446 PMCID: PMC9570394 DOI: 10.3390/ijms231911146] [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: 08/23/2022] [Revised: 09/16/2022] [Accepted: 09/16/2022] [Indexed: 11/30/2022] Open
Abstract
In sharp contrast to birds and mammals, in numerous cold-blooded vertebrates, sex chromosomes have been described as homomorphic. This sex chromosome homomorphy has been suggested to result from the high turnovers often observed across deeply diverged clades. However, little is known about the tempo and mode of sex chromosome evolution among the most closely related species. Here, we examined the evolution of sex chromosome among nine species of the torrent frog genus Amolops. We analyzed male and female GBS and RAD-seq from 182 individuals and performed PCR verification for 176 individuals. We identified signatures of sex chromosomes involving two pairs of chromosomes. We found that sex-chromosome homomorphy results from both turnover and X–Y recombination in the Amolops species, which simultaneously exhibits heterogeneous evolution on homologous and non-homologous sex chromosomes. A low turnover rate of non-homologous sex chromosomes exists in these torrent frogs. The ongoing X–Y recombination in homologous sex chromosomes will act as an indispensable force in preventing sex chromosomes from differentiating.
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44
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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:evac116. [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] [MESH Headings] [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, Colorado, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - Daren C Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA
| | - Giulia I M Pasquesi
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Aundrea K Westfall
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
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45
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Abstract
Understanding sex differences in physiology and disease requires the identification of the molecular agents that cause phenotypic sex differences. Two groups of such agents are genes located on the sex chromosomes, and gonadal hormones. The former have coherent linkage to chromosomes that form differently in the two sexes under the influence of genomic forces that are not related to reproductive function, whereas the latter have a direct or indirect relationship to reproduction. Evidence published in the past 5 years supports the identification of several agents of sexual differentiation encoded by the X chromosome in mice, including Kdm5c, Kdm6a, Ogt and Xist. These X chromosome agents have wide pleiotropic effects, potentially influencing sex differences in many different tissues, a characteristic shared with the gonadal hormones. The identification of X chromosome agents of sexual differentiation will facilitate understanding of complex intersecting gene pathways underlying sex differences in disease.
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Affiliation(s)
- Arthur P Arnold
- Department of Integrative Biology & Physiology, University of California, Los Angeles, Los Angeles, CA, USA.
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46
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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: 7] [Impact Index Per Article: 3.5] [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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47
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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: 3] [Impact Index Per Article: 1.5] [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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Kim KW, De-Kayne R, Gordon IJ, Omufwoko KS, Martins DJ, Ffrench-Constant R, Martin SH. Stepwise evolution of a butterfly supergene via duplication and inversion. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210207. [PMID: 35694743 PMCID: PMC9189502 DOI: 10.1098/rstb.2021.0207] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Supergenes maintain adaptive clusters of alleles in the face of genetic mixing. Although usually attributed to inversions, supergenes can be complex, and reconstructing the precise processes that led to recombination suppression and their timing is challenging. We investigated the origin of the BC supergene, which controls variation in warning coloration in the African monarch butterfly, Danaus chrysippus. By generating chromosome-scale assemblies for all three alleles, we identified multiple structural differences. Most strikingly, we find that a region of more than 1 million bp underwent several segmental duplications at least 7.5 Ma. The resulting duplicated fragments appear to have triggered four inversions in surrounding parts of the chromosome, resulting in stepwise growth of the region of suppressed recombination. Phylogenies for the inversions are incongruent with the species tree and suggest that structural polymorphisms have persisted for at least 4.1 Myr. In addition to the role of duplications in triggering inversions, our results suggest a previously undescribed mechanism of recombination suppression through independent losses of divergent duplicated tracts. Overall, our findings add support for a stepwise model of supergene evolution involving a variety of structural changes. This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’.
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Affiliation(s)
- Kang-Wook Kim
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Rishi De-Kayne
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Ian J Gordon
- Centre of Excellence in Biodiversity and Natural Resource Management, University of Rwanda, Huye Campus, Huye, Rwanda
| | | | - Dino J Martins
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, USA.,Mpala Research Centre, Nanyuki, Kenya
| | | | - Simon H Martin
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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She H, Xu Z, Zhang H, Wu J, Wang X, Liu Z, Qian W. Remarkable Divergence of the Sex-Linked Region between Two Wild Spinach Progenitors, Spinacia turkestanica and Spinacia tetrandra. BIOLOGY 2022; 11:1138. [PMID: 36009765 PMCID: PMC9404990 DOI: 10.3390/biology11081138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
The sex-linked region (SLR) plays an important role in determining the sex of a plant. The SLR of the Y chromosome, composed of a 14.1-Mb inversion and a 10-Mb Y-duplication region (YDR), was deciphered in Spinacia oleracea previously. However, our understanding of the SLR in its wild relatives, S. turkestanica and S. tetrandra, remains limited. In this study, we used 63 resequencing data from the three Spinacia species to infer the evolution of the SLR among the Spinacia species. In the SLR, all the cultivated spinach and S. turkestanica accessions were clustered into two distinct categories with both sexes, while the S. tetrandra accessions of both sexes were grouped. This suggests that S. oleracea shared a similar SLR with S. turkestanica, but not with S. tetrandra, which was further confirmed based on the population structure and principal component analysis. Furthermore, we identified 3910 fully sex-linked SNPs in S. oleracea and 92.82% of them were available in S. turkestanica, while none of the SNPs were adopted in S. tetrandra. Genome coverage in males and females supported the hypothesis that the YDR increasingly expanded during its evolution. Otherwise, we identified 13 sex-linked transposable element insertion polymorphisms within the inversion in both S. oleracea and S. turkestanica, demonstrating that the transposable element insertions might have occurred before the recombination suppression event of the inversion. The SLR was conserved compared with the pseudoautosomal region given that the genetic hitchhiking process occurred in the SLR during its evolution. Our findings will significantly advance our understanding of the characteristics and evolution of the SLR in Spinacia species.
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Affiliation(s)
| | | | | | | | | | - Zhiyuan Liu
- Correspondence: (Z.L.); (W.Q.); Tel.: +86-010-62194559 (W.Q.)
| | - Wei Qian
- Correspondence: (Z.L.); (W.Q.); Tel.: +86-010-62194559 (W.Q.)
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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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