1
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Scott MF, Immler S. One-factor sex determination evolves without linkage between feminizing and masculinizing mutations. Proc Biol Sci 2024; 291:20240693. [PMID: 38981518 DOI: 10.1098/rspb.2024.0693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/21/2024] [Indexed: 07/11/2024] Open
Abstract
The evolution of separate sexes from cosexuality requires at least two mutations: a feminizing allele to cause female development and a masculinizing allele to cause male development. Classically, the double mutant is assumed to be sterile, which leads to two-factor sex determination where male and female sex chromosomes differ at two loci. However, several species appear to have one-factor sex determination where sexual development depends on variation at a single locus. We show that one-factor sex determination evolves when the double mutant develops as a male or a female. The feminizing allele fixes when the double mutant is male, and the masculinizing allele fixes when the double mutant is female. The other locus then gives XY or ZW sex determination based on dominance: for example, a dominant masculinizer becomes a Y chromosome. Although the resulting sex determination system differs, the conditions required for feminizers and masculinizers to spread are the same as in classical models, with the important difference that the two alleles do not need to be linked. Thus, we reveal alternative pathways for the evolution of sex determination and discuss how they can be distinguished using new data on the genetics of sex determination.
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Affiliation(s)
- Michael F Scott
- School of Biological Sciences, University of East Anglia, Norwich Research Park , Norwich NR4 7TJ, UK
| | - Simone Immler
- School of Biological Sciences, University of East Anglia, Norwich Research Park , Norwich NR4 7TJ, UK
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2
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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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3
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Crepaldi C, Cabral-de-Mello DC, Parise-Maltempi PP. Comparative analysis of transposable elements dynamics in fish with different sex chromosome systems. Genome 2024. [PMID: 38739948 DOI: 10.1139/gen-2023-0134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Transposable elements (TEs) are widespread genomic components with substantial roles in genome evolution and sex chromosome differentiation. In this study, we compared the TE composition of three closely related fish with different sex chromosome systems: Megaleporinus elongatus (Z1Z1Z2Z2/Z1W1Z2W2), Megaleporinus macrocephalus (ZZ/ZW) (both with highly differentiated W sex chromosomes), and Leporinus friderici (without heteromorphic sex chromosomes). We created custom TE libraries for each species using clustering methods and manual annotation and prediction, and we predicted TE temporal dynamics through divergence-based analysis. The TE abundance ranged from 16% to 21% in the three mobilomes, with L. friderici having the lowest overall. Despite the recent amplification of TEs in all three species, we observed differing expansion activities, particularly between the two genera. Both Megaleporinus recently experienced high retrotransposon activity, with a reduction in DNA TEs, which could have implications in sex chromosome composition. In contrast, L. friderici showed the opposite pattern. Therefore, despite having similar TE compositions, Megaleporinus and Leporinus exhibit distinct TE histories that likely evolved after their separation, highlighting a rapid TE expansion over short evolutionary periods.
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Affiliation(s)
- Carolina Crepaldi
- Universidade Estadual Paulista (UNESP) "Júlio de Mesquita Filho", Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Rio Claro, Brazil
| | - Diogo Cavalcanti Cabral-de-Mello
- Universidade Estadual Paulista (UNESP) "Júlio de Mesquita Filho", Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Rio Claro, Brazil
| | - Patricia Pasquali Parise-Maltempi
- Universidade Estadual Paulista (UNESP) "Júlio de Mesquita Filho", Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Rio Claro, Brazil
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4
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Bentz PC, Liu Z, Yang JB, Zhang L, Burrows S, Burrows J, Kanno A, Mao Z, Leebens-Mack J. Young evolutionary origins of dioecy in the genus Asparagus. AMERICAN JOURNAL OF BOTANY 2024; 111:e16276. [PMID: 38297448 DOI: 10.1002/ajb2.16276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 10/31/2023] [Accepted: 11/17/2023] [Indexed: 02/02/2024]
Abstract
PREMISE Dioecy (separate sexes) has independently evolved numerous times across the angiosperm phylogeny and is recently derived in many lineages. However, our understanding is limited regarding the evolutionary mechanisms that drive the origins of dioecy in plants. The recent and repeated evolution of dioecy across angiosperms offers an opportunity to make strong inferences about the ecological, developmental, and molecular factors influencing the evolution of dioecy, and thus sex chromosomes. The genus Asparagus (Asparagaceae) is an emerging model taxon for studying dioecy and sex chromosome evolution, yet estimates for the age and origin of dioecy in the genus are lacking. METHODS We use plastome sequences and fossil time calibrations in phylogenetic analyses to investigate the age and origin of dioecy in the genus Asparagus. We also review the diversity of sexual systems present across the genus to address contradicting reports in the literature. RESULTS We estimate that dioecy evolved once or twice approximately 2.78-3.78 million years ago in Asparagus, of which roughly 27% of the species are dioecious and the remaining are hermaphroditic with monoclinous flowers. CONCLUSIONS Our findings support previous work implicating a young age and the possibility of two origins of dioecy in Asparagus, which appear to be associated with rapid radiations and range expansion out of Africa. Lastly, we speculate that paleoclimatic oscillations throughout northern Africa may have helped set the stage for the origin(s) of dioecy in Asparagus approximately 2.78-3.78 million years ago.
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Affiliation(s)
- Philip C Bentz
- Department of Plant Biology, University of Georgia, Athens, GA, 30605, USA
| | - Zhengjie Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Le Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | | | | | - Akira Kanno
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Zichao Mao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, 30605, USA
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5
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Cīrulis A, Nordén AK, Churcher AM, Ramm SA, Zadesenets KS, Abbott JK. Sex-limited experimental evolution drives transcriptomic divergence in a hermaphrodite. Genome Biol Evol 2024; 16:evad235. [PMID: 38155579 PMCID: PMC10786194 DOI: 10.1093/gbe/evad235] [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: 02/22/2023] [Revised: 12/12/2023] [Accepted: 12/23/2023] [Indexed: 12/30/2023] Open
Abstract
The evolution of gonochorism from hermaphroditism is linked with the formation of sex chromosomes, as well as the evolution of sex-biased and sex-specific gene expression to allow both sexes to reach their fitness optimum. There is evidence that sexual selection drives the evolution of male-biased gene expression in particular. However, previous research in this area in animals comes from either theoretical models or comparative studies of already old sex chromosomes. We therefore investigated changes in gene expression under 3 different selection regimes for the simultaneous hermaphrodite Macrostomum lignano subjected to sex-limited experimental evolution (i.e. selection for fitness via eggs, sperm, or a control regime allowing both). After 21 and 22 generations of selection for male-specific or female-specific fitness, we characterized changes in whole-organism gene expression. We found that female-selected lines had changed the most in their gene expression. Although annotation for this species is limited, gene ontology term and Kyoto Encyclopedia of Genes and Genomes pathway analyses suggest that metabolic changes (e.g. biosynthesis of amino acids and carbon metabolism) are an important adaptive component. As predicted, we found that the expression of genes previously identified as testis-biased candidates tended to be downregulated in the female-selected lines. We did not find any significant expression differences for previously identified candidates of other sex-specific organs, but this may simply reflect that few transcripts have been characterized in this way. In conclusion, our experiment suggests that changes in testis-biased gene expression are important in the early evolution of sex chromosomes and gonochorism.
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Affiliation(s)
- Aivars Cīrulis
- Department of Biology, Lund University, 223 62 Lund, Sweden
- Laboratory of Microbiology and Pathology, Institute of Food Safety, Animal Health and Environment “BIOR,”Riga LV-1076, Latvia
- Faculty of Biology, University of Latvia, Riga LV-1004, Latvia
| | - Anna K Nordén
- Department of Biology, Lund University, 223 62 Lund, Sweden
| | - Allison M Churcher
- Department of Molecular Biology, National Bioinformatics Infrastructure Sweden, Umeå University, 901 87 Umeå, Sweden
| | - Steven A Ramm
- Department of Evolutionary Biology, Bielefeld University, 33615 Bielefeld, Germany
- UMR 6553 ECOBIO, Université de Rennes, 35042 Rennes, France
| | - Kira S Zadesenets
- Department of Molecular Genetics, Cell Biology and Bionformatics, The Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russian Federation
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6
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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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7
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She H, Liu Z, Li S, Xu Z, Zhang H, Cheng F, Wu J, Wang X, Deng C, Charlesworth D, Gao W, Qian W. Evolution of the spinach sex-linked region within a rarely recombining pericentromeric region. PLANT PHYSIOLOGY 2023; 193:1263-1280. [PMID: 37403642 DOI: 10.1093/plphys/kiad389] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 07/06/2023]
Abstract
Sex chromosomes have evolved independently in many different plant lineages. Here, we describe reference genomes for spinach (Spinacia oleracea) X and Y haplotypes by sequencing homozygous XX females and YY males. The long arm of 185-Mb chromosome 4 carries a 13-Mb X-linked region (XLR) and 24.1-Mb Y-linked region (YLR), of which 10 Mb is Y specific. We describe evidence that this reflects insertions of autosomal sequences creating a "Y duplication region" or "YDR" whose presence probably directly reduces genetic recombination in the immediately flanking regions, although both the X and Y sex-linked regions are within a large pericentromeric region of chromosome 4 that recombines rarely in meiosis of both sexes. Sequence divergence estimates using synonymous sites indicate that YDR genes started diverging from their likely autosomal progenitors about 3 MYA, around the time when the flanking YLR stopped recombining with the XLR. These flanking regions have a higher density of repetitive sequences in the YY than the XX assembly and include slightly more pseudogenes compared with the XLR, and the YLR has lost about 11% of the ancestral genes, suggesting some degeneration. Insertion of a male-determining factor would have caused Y linkage across the entire pericentromeric region, creating physically small, highly recombining, terminal pseudoautosomal regions. These findings provide a broader understanding of the origin of sex chromosomes in spinach.
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Affiliation(s)
- Hongbing She
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiyuan Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shufen Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Zhaosheng Xu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Helong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chuanliang Deng
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Deborah Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Wujun Gao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Wei Qian
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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de Menezes Cavalcante Sassi F, Sember A, Deon GA, Liehr T, Padutsch N, Oyakawa OT, Vicari MR, Bertollo LAC, Moreira-Filho O, de Bello Cioffi M. Homeology of sex chromosomes in Amazonian Harttia armored catfishes supports the X-fission hypothesis for the X 1X 2Y sex chromosome system origin. Sci Rep 2023; 13:15756. [PMID: 37735233 PMCID: PMC10514344 DOI: 10.1038/s41598-023-42617-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/12/2023] [Indexed: 09/23/2023] Open
Abstract
The Neotropical monophyletic catfish genus Harttia represents an excellent model to study karyotype and sex chromosome evolution in teleosts. Its species split into three phylogenetic clades distributed along the Brazilian territory and they differ widely in karyotype traits, including the presence of standard or multiple sex chromosome systems in some members. Here, we investigate the chromosomal rearrangements and associated synteny blocks involved in the origin of a multiple X1X2Y sex chromosome system present in three out of six sampled Amazonian-clade species. Using 5S and 18S ribosomal DNA fluorescence in situ hybridization and whole chromosome painting with probes corresponding to X1 and X2 chromosomes of X1X2Y system from H. punctata, we confirm previous assumptions that X1X2Y sex chromosome systems of H. punctata, H. duriventris and H. villasboas represent the same linkage groups which also form the putative XY sex chromosomes of H. rondoni. The shared homeology between X1X2Y sex chromosomes suggests they might have originated once in the common ancestor of these closely related species. A joint arrangement of mapped H. punctata X1 and X2 sex chromosomes in early diverging species of different Harttia clades suggests that the X1X2Y sex chromosome system may have formed through an X chromosome fission rather than previously proposed Y-autosome fusion.
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Affiliation(s)
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská, 89, Liběchov, Czech Republic
| | - Geize Aparecida Deon
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Thomas Liehr
- Institut für Humangenetik, Universitätsklinikum Jena, 07747, Jena, Germany.
| | - Niklas Padutsch
- Institut für Humangenetik, Universitätsklinikum Jena, 07747, Jena, Germany
| | | | - Marcelo Ricardo Vicari
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
| | - Luiz Antonio Carlos Bertollo
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Orlando Moreira-Filho
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Marcelo de Bello Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
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9
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Smith SH, Hsiung K, Böhne A. Evaluating the role of sexual antagonism in the evolution of sex chromosomes: new data from fish. Curr Opin Genet Dev 2023; 81:102078. [PMID: 37379742 DOI: 10.1016/j.gde.2023.102078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/07/2023] [Accepted: 06/07/2023] [Indexed: 06/30/2023]
Abstract
The recent increase in available molecular and genomic data for diverse taxa helps to shed new light on long-standing theories. Research into sex chromosome evolution has particularly benefited from a growing number of studies of fish, motivated by their highly diverse mechanisms of sex determination. Sexual antagonism is regularly cited as an influential force in sex chromosome emergence; however, this so far proves difficult to demonstrate. In this review, we highlight recent developments in the investigation of sexual antagonism in sex chromosome research in fish. We find strong emphasis placed on study-organism specific genomic features and patterns of recombination, rather than evidence for a comprehensive role of sexual antagonism. In this light, we discuss the alternative models of sex chromosome evolution. We conclude that fish represents a key resource for further research, provided attention is given to species-specific effects while simultaneously integrating comparative studies across taxa for a vital and comprehensive understanding of sex chromosome evolution and investigation of proposed models.
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Affiliation(s)
- Sophie Helen Smith
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 127, 53113 Bonn, Germany. https://twitter.com/@shg_smith
| | - Kevin Hsiung
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 127, 53113 Bonn, Germany. https://twitter.com/@KevinKHsiung
| | - Astrid Böhne
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 127, 53113 Bonn, Germany.
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10
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Masuda K, Akagi T. Evolution of sex in crops: recurrent scrap and rebuild. BREEDING SCIENCE 2023; 73:95-107. [PMID: 37404348 PMCID: PMC10316312 DOI: 10.1270/jsbbs.22082] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/20/2022] [Indexed: 07/06/2023]
Abstract
Sexuality is the main strategy for maintaining genetic diversity within a species. In flowering plants (angiosperms), sexuality is derived from ancestral hermaphroditism and multiple sexualities can be expressed in an individual. The mechanisms conferring chromosomal sex determination in plants (or dioecy) have been studied for over a century by both biologists and agricultural scientists, given the importance of this field for crop cultivation and breeding. Despite extensive research, the sex determining gene(s) in plants had not been identified until recently. In this review, we dissect plant sex evolution and determining systems, with a focus on crop species. We introduced classic studies with theoretical, genetic, and cytogenic approaches, as well as more recent research using advanced molecular and genomic techniques. Plants have undergone very frequent transitions into, and out of, dioecy. Although only a few sex determinants have been identified in plants, an integrative viewpoint on their evolutionary trends suggests that recurrent neofunctionalization events are potentially common, in a "scrap and (re)build" cycle. We also discuss the potential association between crop domestication and transitions in sexual systems. We focus on the contribution of duplication events, which are particularly frequent in plant taxa, as a trigger for the creation of new sexual systems.
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Affiliation(s)
- Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
- JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan
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11
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Pleiotropic effects of Shy Girl underpin kiwifruit sex chromosome evolution. NATURE PLANTS 2023; 9:381-382. [PMID: 36899135 DOI: 10.1038/s41477-023-01379-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
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12
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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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13
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Charlesworth D. Why and how do Y chromosome stop recombining? J Evol Biol 2023; 36:632-636. [PMID: 36683363 DOI: 10.1111/jeb.14137] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/21/2022] [Accepted: 11/24/2022] [Indexed: 01/24/2023]
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14
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Heterochiasmy and Sex Chromosome Evolution in Silene. Genes (Basel) 2023; 14:genes14030543. [PMID: 36980816 PMCID: PMC10048291 DOI: 10.3390/genes14030543] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 02/24/2023] Open
Abstract
The evolution of a non-recombining sex-specific region is a key step in sex chromosome evolution. Suppression of recombination between the (proto-) X- and Y-chromosomes in male meiosis creates a non-recombining Y-linked region (NRY), while the X-chromosome continues to recombine in females. Lack of recombination in the NRY defines its main properties—genetic degeneration and accumulation of repetitive DNA, making X and Y chromosomes very different from each other. How and why recombination suppression on sex chromosomes evolves remains controversial. A strong difference in recombination rates between the sexes (heterochiasmy) can facilitate or even cause recombination suppression. In the extreme case—complete lack of recombination in the heterogametic sex (achiasmy)—the entire sex-specific chromosome is automatically non-recombining. In this study, I analyse sex-specific recombination rates in a dioecious plant Silene latifolia (Caryophyllaceae), which evolved separate sexes and sex chromosomes ~11 million years ago. I reconstruct high-density RNAseq-based genetic maps including over five thousand genic markers for the two sexes separately. The comparison of the male and female maps reveals only modest heterochiasmy across the genome, with the exception of the sex chromosomes, where recombination is suppressed in males. This indicates that heterochiasmy likely played only a minor, if any, role in NRY evolution in S. latifolia, as recombination suppression is specific to NRY rather than to the entire genome in males. Other mechanisms such as structural rearrangements and/or epigenetic modifications were likely involved, and comparative genome analysis and genetic mapping in multiple Silene species will help to shed light on the mechanism(s) of recombination suppression that led to the evolution of sex chromosomes.
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15
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Long X, Charlesworth D, Qi J, Wu R, Chen M, Wang Z, Xu L, Fu H, Zhang X, Chen X, He L, Zheng L, Huang Z, Zhou Q. Independent Evolution of Sex Chromosomes and Male Pregnancy-Related Genes in Two Seahorse Species. Mol Biol Evol 2022; 40:6964685. [PMID: 36578180 PMCID: PMC9851323 DOI: 10.1093/molbev/msac279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/14/2022] [Accepted: 12/22/2022] [Indexed: 12/30/2022] Open
Abstract
Unlike birds and mammals, many teleosts have homomorphic sex chromosomes, and changes in the chromosome carrying the sex-determining locus, termed "turnovers", are common. Recent turnovers allow studies of several interesting questions. One question is whether the new sex-determining regions evolve to become completely non-recombining, and if so, how and why. Another is whether (as predicted) evolutionary changes that benefit one sex accumulate in the newly sex-linked region. To study these questions, we analyzed the genome sequences of two seahorse species of the Syngnathidae, a fish group in which many species evolved a unique structure, the male brood pouch. We find that both seahorse species have XY sex chromosome systems, but their sex chromosome pairs are not homologs, implying that at least one turnover event has occurred. The Y-linked regions occupy 63.9% and 95.1% of the entire sex chromosome of the two species and do not exhibit extensive sequence divergence with their X-linked homologs. We find evidence for occasional recombination between the extant sex chromosomes that may account for their homomorphism. We argue that these Y-linked regions did not evolve by recombination suppression after the turnover, but by the ancestral nature of the low crossover rates in these chromosome regions. With such an ancestral crossover landscape, a turnover can instantly create an extensive Y-linked region. Finally, we test for adaptive evolution of male pouch-related genes after they became Y-linked in the seahorse.
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Affiliation(s)
- Xin Long
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China,Research Center for Intelligent Computing Platforms, Zhejiang Lab, Hangzhou 311100, China
| | - Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3LF, UK
| | - Jianfei Qi
- Department of Aquaculture, Fisheries Research Institute of Fujian, Xiamen 361013, China
| | - Ruiqiong Wu
- Fujian Key Laboratory of Developmental and Neural Biology & Southern Center for Biomedical Research, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China
| | - Meiling Chen
- Fujian Key Laboratory of Developmental and Neural Biology & Southern Center for Biomedical Research, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China
| | - Zongji Wang
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Luohao Xu
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Honggao Fu
- Fujian Key Laboratory of Developmental and Neural Biology & Southern Center for Biomedical Research, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China
| | - Xueping Zhang
- Fujian Key Laboratory of Developmental and Neural Biology & Southern Center for Biomedical Research, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China
| | - Xinxin Chen
- Department of Aquaculture, Fisheries Research Institute of Fujian, Xiamen 361013, China
| | - Libin He
- Department of Aquaculture, Fisheries Research Institute of Fujian, Xiamen 361013, China
| | | | | | - Qi Zhou
- Corresponding authors: E-mails: ; ;
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16
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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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17
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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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18
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Zhang S, Wu Z, Ma D, Zhai J, Han X, Jiang Z, Liu S, Xu J, Jiao P, Li Z. Chromosome-scale assemblies of the male and female Populus euphratica genomes reveal the molecular basis of sex determination and sexual dimorphism. Commun Biol 2022; 5:1186. [PMCID: PMC9636151 DOI: 10.1038/s42003-022-04145-7] [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: 05/08/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Reference-quality genomes of both sexes are essential for studying sex determination and sex-chromosome evolution, as their gene contents and expression profiles differ. Here, we present independent chromosome-level genome assemblies for the female (XX) and male (XY) genomes of desert poplar (Populus euphratica), resolving a 22.7-Mb X and 24.8-Mb Y chromosome. We also identified a relatively complete 761-kb sex-linked region (SLR) in the peritelomeric region on chromosome 14 (Y). Within the SLR, recombination around the partial repeats for the feminizing factor ARR17 (ARABIDOPSIS RESPONSE REGULATOR 17) was potentially suppressed by flanking palindromic arms and the dense accumulation of retrotransposons. The inverted small segments S1 and S2 of ARR17 exhibited relaxed selective pressure and triggered sex determination by generating 24-nt small interfering RNAs that induce male-specific hyper-methylation at the promoter of the autosomal targeted ARR17. We also detected two male-specific fusion genes encoding proteins with NB-ARC domains at the breakpoint region of an inversion in the SLR that may be responsible for the observed sexual dimorphism in immune responses. Our results show that the SLR appears to follow proposed evolutionary dynamics for sex chromosomes and advance our understanding of sex determination and the evolution of sex chromosomes in Populus. Reference-quality genomes of both sexes of the dioecious tree species, Populus euphratica, provide further insight into the evolution of Populus sex chromosomes and highlight male-specific fusion genes that may contribute to sexual dimorphism.
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Affiliation(s)
- Shanhe Zhang
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
| | - Zhihua Wu
- grid.453534.00000 0001 2219 2654College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004 China
| | - De Ma
- grid.410753.4Novogene Bioinformatics Institute, Beijing, 100083 China
| | - Juntuan Zhai
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
| | - Xiaoli Han
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
| | - Zhenbo Jiang
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
| | - Shuo Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, 430074 China
| | - Jingdong Xu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, 430074 China
| | - Peipei Jiao
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
| | - Zhijun Li
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
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19
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Qiu S, Yong L, Wilson A, Croft DP, Graham C, Charlesworth D. Partial sex linkage and linkage disequilibrium on the guppy sex chromosome. Mol Ecol 2022; 31:5524-5537. [PMID: 36005298 PMCID: PMC9826361 DOI: 10.1111/mec.16674] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 08/01/2022] [Accepted: 08/09/2022] [Indexed: 01/11/2023]
Abstract
The guppy Y chromosome has been considered a model system for the evolution of suppressed recombination between sex chromosomes, and it has been proposed that complete sex-linkage has evolved across about 3 Mb surrounding this fish's sex-determining locus, followed by recombination suppression across a further 7 Mb of the 23 Mb XY pair, forming younger "evolutionary strata". Sequences of the guppy genome show that Y is very similar to the X chromosome. Knowing which parts of the Y are completely nonrecombining, and whether there is indeed a large completely nonrecombining region, are important for understanding its evolution. Here, we describe analyses of PoolSeq data in samples from within multiple natural populations from Trinidad, yielding new results that support previous evidence for occasional recombination between the guppy Y and X. We detected recent demographic changes, notably that downstream populations have higher synonymous site diversity than upstream ones and other expected signals of bottlenecks. We detected evidence of associations between sequence variants and the sex-determining locus, rather than divergence under a complete lack of recombination. Although recombination is infrequent, it is frequent enough that associations with SNPs can suggest the region in which the sex-determining locus must be located. Diversity is elevated across a physically large region of the sex chromosome, conforming to predictions for a genome region with infrequent recombination that carries one or more sexually antagonistic polymorphisms. However, no consistently male-specific variants were found, supporting the suggestion that any completely sex-linked region may be very small.
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Affiliation(s)
- Suo Qiu
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Lengxob Yong
- Centre for Ecology and Conservation, College of Life and Environmental SciencesUniversity of ExeterPenrynUK,Marine Resources Research InstituteSouth Carolina Department of Natural ResourcesCharlestonSouth CarolinaUSA
| | - Alastair Wilson
- Centre for Ecology and Conservation, College of Life and Environmental SciencesUniversity of ExeterPenrynUK
| | - Darren P. Croft
- Centre for Research in Animal Behaviour, College of Life and Environmental SciencesUniversity of ExeterExeterUK
| | - Chay Graham
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
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20
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Kazama Y, Kitoh M, Kobayashi T, Ishii K, Krasovec M, Yasui Y, Abe T, Kawano S, Filatov DA. A CLAVATA3-like Gene Acts as a Gynoecium Suppression Function in White Campion. Mol Biol Evol 2022; 39:msac195. [PMID: 36166820 PMCID: PMC9550985 DOI: 10.1093/molbev/msac195] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
How do separate sexes originate and evolve? Plants provide many opportunities to address this question as they have diverse mating systems and separate sexes (dioecy) that evolved many times independently. The classic "two-factor" model for evolution of separate sexes proposes that males and females can evolve from hermaphrodites via the spread of male and female sterility mutations that turn hermaphrodites into females and males, respectively. This widely accepted model was inspired by early genetic work in dioecious white campion (Silene latifolia) that revealed the presence of two sex-determining factors on the Y-chromosome, though the actual genes remained unknown. Here, we report identification and functional analysis of the putative sex-determining gene in S. latifolia, corresponding to the gynoecium suppression factor (GSF). We demonstrate that GSF likely corresponds to a Y-linked CLV3-like gene that is specifically expressed in early male flower buds and encodes the protein that suppresses gynoecium development in S. latifolia. Interestingly, GSFY has a dysfunctional X-linked homolog (GSFX) and their synonymous divergence (dS = 17.9%) is consistent with the age of sex chromosomes in this species. We propose that female development in S. latifolia is controlled via the WUSCHEL-CLAVATA feedback loop, with the X-linked WUSCHEL-like and Y-linked CLV3-like genes, respectively. Evolution of dioecy in the S. latifolia ancestor likely involved inclusion of ancestral GSFY into the nonrecombining region on the nascent Y-chromosome and GSFX loss of function, which resulted in disbalance of the WUSCHEL-CLAVATA feedback loop between the sexes and ensured gynoecium suppression in males.
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Affiliation(s)
- Yusuke Kazama
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Kenjojima, Matsuoka, Eiheiji-cho, Japan
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Moe Kitoh
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Kenjojima, Matsuoka, Eiheiji-cho, Japan
| | - Taiki Kobayashi
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Kenjojima, Matsuoka, Eiheiji-cho, Japan
| | - Kotaro Ishii
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
| | - Marc Krasovec
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Yasuo Yasui
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tomoko Abe
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shigeyuki Kawano
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, FSB-601, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- Future Center Initiative, The University of Tokyo, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan
| | - Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
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21
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Elkrewi M, Khauratovich U, Toups MA, Bett VK, Mrnjavac A, Macon A, Fraisse C, Sax L, Huylmans AK, Hontoria F, Vicoso B. ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. Genetics 2022; 222:6670797. [PMID: 35977389 PMCID: PMC9526061 DOI: 10.1093/genetics/iyac123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.
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Affiliation(s)
- Marwan Elkrewi
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria
| | - Uladzislava Khauratovich
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria.,Department of Chromosome Biology, Max Perutz Labs, University of Vienna, 1030, Austria
| | - Melissa A Toups
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria.,Department of Life and Environmental Sciences, Faculty of Science and Technology, Bournemouth University, BH12 5BB, UK
| | | | - Andrea Mrnjavac
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria
| | - Ariana Macon
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria
| | - Christelle Fraisse
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria.,CNRS, Univ. Lille, UMR 8198-Evo-Eco-Paleo, F-59000 Lille, France
| | - Luca Sax
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria.,Lewis and Clark College, Portland, OR 97219, USA
| | - Ann Kathrin Huylmans
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria.,Institute of Organismic and Molecular Evolution, Johannes Guttenberg Universität Mainz, Mainz, 55122, Germany
| | - Francisco Hontoria
- Instituto de Acuicultura de Torre de la Sal (IATS-CSIC), Ribera de Cabanes, 12595, Spain
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria
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22
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Mendel's laws of heredity on his 200th birthday: What have we learned by considering exceptions? Heredity (Edinb) 2022; 129:1-3. [PMID: 35778507 DOI: 10.1038/s41437-022-00552-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 12/20/2022] Open
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23
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Evolution of sexual systems, sex chromosomes and sex-linked gene transcription in flatworms and roundworms. Nat Commun 2022; 13:3239. [PMID: 35688815 PMCID: PMC9187692 DOI: 10.1038/s41467-022-30578-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/06/2022] [Indexed: 12/02/2022] Open
Abstract
Many species with separate male and female individuals (termed ‘gonochorism’ in animals) have sex-linked genome regions. Here, we investigate evolutionary changes when genome regions become completely sex-linked, by analyses of multiple species of flatworms (Platyhelminthes; among which schistosomes recently evolved gonochorism from ancestral hermaphroditism), and roundworms (Nematoda) which have undergone independent translocations of different autosomes. Although neither the evolution of gonochorism nor translocations fusing ancestrally autosomal regions to sex chromosomes causes inevitable loss of recombination, we document that formerly recombining regions show genomic signatures of recombination suppression in both taxa, and become strongly genetically degenerated, with a loss of most genes. Comparisons with hermaphroditic flatworm transcriptomes show masculinisation and some defeminisation in schistosome gonad gene expression. We also find evidence that evolution of sex-linkage in nematodes is accompanied by transcriptional changes and dosage compensation. Our analyses also identify sex-linked genes that could assist future research aimed at controlling some of these important parasites. Transitions between hermaphroditic and separate sexes are relatively understudied in animals compared to pants. Here, Wang et al. reconstruct the evolution of separate sexes in the flatworms and complex changes of sex chromosomes in the roundworms.
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24
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Rifkin JL, Hnatovska S, Yuan M, Sacchi BM, Choudhury BI, Gong Y, Rastas P, Barrett SCH, Wright SI. Recombination landscape dimorphism and sex chromosome evolution in the dioecious plant Rumex hastatulus. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210226. [PMID: 35306892 PMCID: PMC8935318 DOI: 10.1098/rstb.2021.0226] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
There is growing evidence from diverse taxa for sex differences in the genomic landscape of recombination, but the causes and consequences of these differences remain poorly understood. Strong recombination landscape dimorphism between the sexes could have important implications for the dynamics of sex chromosome evolution because low recombination in the heterogametic sex can favour the spread of sexually antagonistic alleles. Here, we present a sex-specific linkage map and revised genome assembly of Rumex hastatulus and provide the first evidence and characterization of sex differences in recombination landscape in a dioecious plant. We present data on significant sex differences in recombination, with regions of very low recombination in males covering over half of the genome. This pattern is evident on both sex chromosomes and autosomes, suggesting that pre-existing differences in recombination may have contributed to sex chromosome formation and divergence. Our analysis of segregation distortion suggests that haploid selection due to pollen competition occurs disproportionately in regions with low male recombination. We hypothesize that sex differences in the recombination landscape have contributed to the formation of a large heteromorphic pair of sex chromosomes in R. hastatulus, but more comparative analyses of recombination will be important to investigate this hypothesis further. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.
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Affiliation(s)
- Joanna L Rifkin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2
| | - Solomiya Hnatovska
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2
| | - Meng Yuan
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2
| | - Bianca M Sacchi
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2
| | - Baharul I Choudhury
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2.,Department of Biology, Queen's University, Kingston, ON, Canada K7L 396
| | - Yunchen Gong
- Centre for Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada M5S 3B2
| | - Pasi Rastas
- Institute of Biotechnology, 00014 University of Helsinki, Helsinki, Finland
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2.,Centre for Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada M5S 3B2
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25
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Zluvova J, Kubat Z, Hobza R, Janousek B. Adaptive changes of the autosomal part of the genome in a dioecious clade of Silene. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210228. [PMID: 35306886 PMCID: PMC8935319 DOI: 10.1098/rstb.2021.0228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The genus Silene brings many opportunities for the study of various processes involved in the evolution of dioecy and young sex chromosomes. Here we focus on a dioecious clade in Silene subgenus Silene and closely related species. This study provides improved support for monophyly of this clade (based on inclusion of further dioecious species) and a new estimate of its age (ca 2.3 million years). We observed a rise in adaptive evolution in the autosomal and pseudoautosomal parts of the genome on the branch where dioecy originated. This increase is not a result of the accumulation of sexually antagonistic genes in the pseudoautosomal region. It is also not caused by the coevolution of genes acting in mitochondria (despite the possibility that dioecy along this branch could have evolved from a nucleo-cytoplasmic male sterility-based system). After considering other possibilities, the most parsimonious explanation for the increase seen in the number of positively selected codons is the adaptive evolution of genes involved in the adaptation of the autosomal part of the genome to dioecy, as described in Charnov's sex-allocation theory. As the observed coincidence cannot prove causality, studies in other dioecious clades are necessary to allow the formation of general conclusions. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.
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Affiliation(s)
- Jitka Zluvova
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno CZ - 612 65, Czech Republic
| | - Zdenek Kubat
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno CZ - 612 65, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno CZ - 612 65, Czech Republic
| | - Bohuslav Janousek
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno CZ - 612 65, Czech Republic
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26
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Marais GAB, Lemaître JF. Sex chromosomes, sex ratios and sex gaps in longevity in plants. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210219. [PMID: 35306888 PMCID: PMC8935291 DOI: 10.1098/rstb.2021.0219] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In animals, males and females can display markedly different longevity (also called sex gaps in longevity, SGL). Sex chromosomes contribute to establishing these SGLs. X-hemizygosity and toxicity of the Y chromosomes are two mechanisms that have been suggested to reduce male longevity (Z-hemizygosity and W toxicity in females in ZW systems). In plants, SGLs are known to exist, but the role of sex chromosomes remains to be established. Here, by using adult sex ratio as a proxy for measuring SGLs, we explored the relationship between sex chromosomes and SGLs across 43 plant species. Based on the knowledge accumulated in animals, we specifically asked whether: (i) species with XY systems tend to have female-biased sex ratios (reduced male longevity) and species with ZW ones tend to have male-biased sex ratios (reduced female longevity); and (ii) this pattern was stronger in heteromorphic systems compared to homomorphic ones. Our results tend to support these predictions although we lack statistical power because of a small number of ZW systems and the absence of any heteromorphic ZW system in the dataset. We discuss the implications of these findings, which we hope will stimulate further research on sex differences in lifespan and ageing across plants. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.
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Affiliation(s)
- Gabriel A B Marais
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal.,LBBE, CNRS/Univ. Lyon 1, Campus de la Doua, Villeurbanne, France
| | - J-F Lemaître
- LBBE, CNRS/Univ. Lyon 1, Campus de la Doua, Villeurbanne, France
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27
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Charlesworth D. Some thoughts about the words we use for thinking about sex chromosome evolution. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210314. [PMID: 35306893 PMCID: PMC8935297 DOI: 10.1098/rstb.2021.0314] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Sex chromosomes are familiar to most biologists since they first learned about genetics. However, research over the past 100 years has revealed that different organisms have evolved sex-determining systems independently. The differences in the ages of systems, and in how they evolved, both affect whether sex chromosomes have evolved. However, the diversity means that the terminology used tends to emphasize either the similarities or the differences, sometimes causing misunderstandings. In this article, I discuss some concepts where special care is needed with terminology. The following four terms regularly create problems: ‘sex chromosome’, ‘master sex-determining gene’, ‘evolutionary strata’ and ‘genetic degeneration’. There is no generally correct or wrong use of these words, but efforts are necessary to make clear how they are to be understood in specific situations. I briefly outline some widely accepted ideas about sex chromosomes, and then discuss these ‘problem terms’, highlighting some examples where careful use of the words helps bring to light current uncertainties and interesting questions for future work. This article is part of the theme issue ‘Sex determination and sex chromosome evolution in land plants’.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3LF, UK
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28
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Muyle A, Marais GAB, Bačovský V, Hobza R, Lenormand T. Dosage compensation evolution in plants: theories, controversies and mechanisms. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210222. [PMID: 35306896 PMCID: PMC8935305 DOI: 10.1098/rstb.2021.0222] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In a minority of flowering plants, separate sexes are genetically determined by sex chromosomes. The Y chromosome has a non-recombining region that degenerates, causing a reduced expression of Y genes. In some species, the lower Y expression is accompanied by dosage compensation (DC), a mechanism that re-equalizes male and female expression and/or brings XY male expression back to its ancestral level. Here, we review work on DC in plants, which started as early as the late 1960s with cytological approaches. The use of transcriptomics fired a controversy as to whether DC existed in plants. Further work revealed that various plants exhibit partial DC, including a few species with young and homomorphic sex chromosomes. We are starting to understand the mechanisms responsible for DC in some plants, but in most species, we lack the data to differentiate between global and gene-by-gene DC. Also, it is unknown why some species evolve many dosage compensated genes while others do not. Finally, the forces that drive DC evolution remain mysterious, both in plants and animals. We review the multiple evolutionary theories that have been proposed to explain DC patterns in eukaryotes with XY or ZW sex chromosomes. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.
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Affiliation(s)
- Aline Muyle
- Laboratoire 'Biométrie et Biologie Evolutive', CNRS/Université Lyon 1, Lyon, France
| | - Gabriel A B Marais
- Laboratoire 'Biométrie et Biologie Evolutive', CNRS/Université Lyon 1, Lyon, France.,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Václav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno, Czech Republic
| | - Thomas Lenormand
- CEFE, University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
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29
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Gong W, Filatov DA. Evolution of the sex-determining region in Ginkgo biloba. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210229. [PMID: 35306884 PMCID: PMC8935300 DOI: 10.1098/rstb.2021.0229] [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: 12/15/2022] Open
Abstract
Sex chromosomes or sex-determining regions (SDR) have been discovered in many dioecious plant species, including the iconic ‘living fossil' Ginkgo biloba, though the location and size of the SDR in G. biloba remain contradictory. Here we resolve these controversies and analyse the evolution of the SDR in this species. Based on transcriptome sequencing data from four genetic crosses we reconstruct male- and female-specific genetic maps and locate the SDR to the middle of chromosome 2. Integration of the genetic maps with the genome sequence reveals that recombination in and around the SDR is suppressed in a region of about 50 Mb in both males and females. However, occasional recombination does occur except a small, less than 5 Mb long region that does not recombine in males. Based on synonymous divergence between homologous X- and Y-linked genes in this region, we infer that the Ginkgo SDR is fairly old—at least of Cretaceous origin. The analysis of substitution rates and gene expression reveals only slight Y-degeneration. These results are consistent with findings in other dioecious plants with homomorphic sex chromosomes, where the SDR is typically small and evolves in a region with pre-existing reduced recombination, surrounded by long actively recombining pseudoautosomal regions. This article is part of the theme issue ‘Sex determination and sex chromosome evolution in land plants’.
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Affiliation(s)
- Wei Gong
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, People's Republic of China.,Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, UK
| | - Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, UK
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30
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Bačovský V, Čegan R, Tihlaříková E, Neděla V, Hudzieczek V, Smrža L, Janíček T, Beneš V, Hobza R. Chemical genetics in Silene latifolia elucidate regulatory pathways involved in gynoecium development. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2354-2368. [PMID: 35045170 DOI: 10.1093/jxb/erab538] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Dioecious plants possess diverse sex determination systems and unique mechanisms of reproductive organ development; however, little is known about how sex-linked genes shape the expression of regulatory cascades that lead to developmental differences between sexes. In Silene latifolia, a dioecious plant with stable dimorphism in floral traits, early experiments suggested that female-regulator genes act on the factors that determine the boundaries of the flower whorls. To identify these regulators, we sequenced the transcriptome of male flowers with fully developed gynoecia, induced by rapid demethylation in the parental generation. Eight candidates were found to have a positive role in gynoecium promotion, floral organ size, and whorl boundary, and affect the expression of class B MADS-box flower genes. To complement our transcriptome analysis, we closely examined the floral organs in their native state using field emission environmental scanning electron microscopy, and examined the differences between females and androhermaphrodites in their placenta and ovule organization. Our results reveal the regulatory pathways potentially involved in sex-specific flower development in the classical model of dioecy, S. latifolia. These pathways include previously hypothesized and unknown female-regulator genes that act on the factors that determine the flower boundaries, and a negative regulator of anther development, SUPERMAN-like (SlSUP).
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Affiliation(s)
- Václav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Radim Čegan
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Eva Tihlaříková
- Environmental Electron Microscopy Group, Institute of Scientific Instruments of the Czech Academy of Sciences, Kralovopolska 147, 612 64 Brno, Czech Republic
| | - Vilém Neděla
- Environmental Electron Microscopy Group, Institute of Scientific Instruments of the Czech Academy of Sciences, Kralovopolska 147, 612 64 Brno, Czech Republic
| | - Vojtěch Hudzieczek
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Lubomír Smrža
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Tomáš Janíček
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Vladimír Beneš
- EMBL Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, D-69117 Heidelberg, Germany
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
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31
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The Sister Chromatid Division of the Heteromorphic Sex Chromosomes in Silene Species and Their Transmissibility towards the Mitosis. Int J Mol Sci 2022; 23:ijms23052422. [PMID: 35269563 PMCID: PMC8910698 DOI: 10.3390/ijms23052422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 01/20/2023] Open
Abstract
Young sex chromosomes possess unique and ongoing dynamics that allow us to understand processes that have an impact on their evolution and divergence. The genus Silene includes species with evolutionarily young sex chromosomes, and two species of section Melandrium, namely Silene latifolia (24, XY) and Silene dioica (24, XY), are well-established models of sex chromosome evolution, Y chromosome degeneration, and sex determination. In both species, the X and Y chromosomes are strongly heteromorphic and differ in the genomic composition compared to the autosomes. It is generally accepted that for proper cell division, the longest chromosomal arm must not exceed half of the average length of the spindle axis at telophase. Yet, it is not clear what are the dynamics between males and females during mitosis and how the cell compensates for the presence of the large Y chromosome in one sex. Using hydroxyurea cell synchronization and 2D/3D microscopy, we determined the position of the sex chromosomes during the mitotic cell cycle and determined the upper limit for the expansion of sex chromosome non-recombining region. Using 3D specimen preparations, we found that the velocity of the large chromosomes is compensated by the distant positioning from the central interpolar axis, confirming previous mathematical modulations.
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32
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Villamil N, Li X, Seddon E, Pannell JR. Simulated herbivory enhances leaky sex expression in the dioecious herb Mercurialis annua. ANNALS OF BOTANY 2022; 129:79-86. [PMID: 34668537 PMCID: PMC8829902 DOI: 10.1093/aob/mcab129] [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: 09/09/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND AIMS Plant reproductive traits are widely understood to be responsive to the selective pressures exerted by pollinators, but there is also increasing evidence for an important role for antagonists such as herbivores in shaping these traits. Many dioecious species show leaky sex expression, with males and females occasionally producing flowers of the opposite sex. Here, we asked to what extent leakiness in sex expression in Mercurialis annua (Euphorbiaceae) might also be plastically responsive to simulated herbivory. This is important because enhanced leakiness in dioecious populations could lead to a shift in both the mating system and in the conditions for transitions between combined and separate sexes. METHODS We examined the effect of simulated herbivory on the sexual expression of males and females of M. annua in two experiments in which different levels of simulated herbivory led to enhanced leakiness in both sexes. KEY RESULTS We showed that leaky sex expression in both males and females of the wind-pollinated dioecious herb M. annua is enhanced in response to simulated herbivory, increasing the probability for and the degree of leakiness in both sexes. We also found that leakiness was greater in larger females but not in larger males. CONCLUSIONS We discuss hypotheses for a possible functional link between herbivory and leaky sex expression, and consider what simulated herbivory-induced leakiness might imply for the evolutionary ecology of plant reproductive systems, especially the breakdown of dioecy and the evolution of hermaphroditism.
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Affiliation(s)
- Nora Villamil
- Department of Ecology and Evolution, Université de Lausanne, Switzerland
| | - Xinji Li
- Department of Ecology and Evolution, Université de Lausanne, Switzerland
| | - Emily Seddon
- Department of Ecology and Evolution, Université de Lausanne, Switzerland
- Vegetation Ecologist, NatureServe, Boulder, CO 80301, USA
| | - John R Pannell
- Department of Ecology and Evolution, Université de Lausanne, Switzerland
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33
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Nürnberger B, Baird SJE, Čížková D, Bryjová A, Mudd AB, Blaxter ML, Szymura JM. A dense linkage map for a large repetitive genome: discovery of the sex-determining region in hybridizing fire-bellied toads (Bombina bombina and Bombina variegata). G3 (BETHESDA, MD.) 2021; 11:6353606. [PMID: 34849761 PMCID: PMC8664441 DOI: 10.1093/g3journal/jkab286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/16/2021] [Indexed: 12/20/2022]
Abstract
Genomic analysis of hybrid zones offers unique insights into emerging reproductive isolation and the dynamics of introgression. Because hybrid genomes consist of blocks inherited from one or the other parental taxon, linkage information is essential. In most cases, the spectrum of local ancestry tracts can be efficiently uncovered from dense linkage maps. Here, we report the development of such a map for the hybridizing toads, Bombina bombina and Bombina variegata (Anura: Bombinatoridae). Faced with the challenge of a large (7–10 Gb), repetitive genome, we set out to identify a large number of Mendelian markers in the nonrepetitive portion of the genome that report B. bombina vs B. variegata ancestry with appropriately quantified statistical support. Bait sequences for targeted enrichment were selected from a draft genome assembly, after filtering highly repetitive sequences. We developed a novel approach to infer the most likely diplotype per sample and locus from the raw read mapping data, which is robust to over-merging and obviates arbitrary filtering thresholds. Validation of the resulting map with 4755 markers underscored the large-scale synteny between Bombina and Xenopus tropicalis. By assessing the sex of late-stage F2 tadpoles from histological sections, we identified the sex-determining region in the Bombina genome to 7 cM on LG5, which is homologous to X. tropicalis chromosome 5, and inferred male heterogamety. Interestingly, chromosome 5 has been repeatedly recruited as a sex chromosome in anurans with XY sex determination.
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Affiliation(s)
- Beate Nürnberger
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, 603 65 Brno, Czech Republic
| | - Stuart J E Baird
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, 603 65 Brno, Czech Republic
| | - Dagmar Čížková
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, 603 65 Brno, Czech Republic
| | - Anna Bryjová
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, 603 65 Brno, Czech Republic
| | - Austin B Mudd
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, 94720 CA, USA
| | - Mark L Blaxter
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Jacek M Szymura
- Department of Comparative Anatomy, Jagiellonian University, 30-387 Kraków, Poland
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34
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Crepaldi C, Martí E, Gonçalves ÉM, Martí DA, Parise-Maltempi PP. Genomic Differences Between the Sexes in a Fish Species Seen Through Satellite DNAs. Front Genet 2021; 12:728670. [PMID: 34659353 PMCID: PMC8514694 DOI: 10.3389/fgene.2021.728670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/13/2021] [Indexed: 11/14/2022] Open
Abstract
Neotropical fishes have highly diversified karyotypic and genomic characteristics and present many diverse sex chromosome systems, with various degrees of sex chromosome differentiation. Knowledge on their sex-specific composition and evolution, however, is still limited. Satellite DNAs (satDNAs) are tandemly repeated sequences with pervasive genomic distribution and distinctive evolutionary pathways, and investigating satDNA content might shed light into how genome architecture is organized in fishes and in their sex chromosomes. The present study investigated the satellitome of Megaleporinus elongatus, a freshwater fish with a proposed Z1Z1Z2Z2/Z1W1Z2W2 multiple sex chromosome system that encompasses a highly heterochromatic and differentiated W1 chromosome. The species satellitome comprises of 140 different satDNA families, including previously isolated sequences and new families found in this study. This diversity is remarkable considering the relatively low proportion that satDNAs generally account for the M. elongatus genome (around only 5%). Differences between the sexes in regards of satDNA content were also evidenced, as these sequences are 14% more abundant in the female genome. The occurrence of sex-biased signatures of satDNA evolution in the species is tightly linked to satellite enrichment associated with W1 in females. Although both sexes share practically all satDNAs, the overall massive amplification of only a few of them accompanied the W1 differentiation. We also investigated the expansion and diversification of the two most abundant satDNAs of M. elongatus, MelSat01-36 and MelSat02-26, both highly amplified sequences in W1 and, in MelSat02-26’s case, also harbored by Z2 and W2 chromosomes. We compared their occurrences in M. elongatus and the sister species M. macrocephalus (with a standard ZW sex chromosome system) and concluded that both satDNAs have led to the formation of highly amplified arrays in both species; however, they formed species-specific organization on female-restricted sex chromosomes. Our results show how satDNA composition is highly diversified in M. elongatus, in which their accumulation is significantly contributing to W1 differentiation and not satDNA diversity per se. Also, the evolutionary behavior of these repeats may be associated with genome plasticity and satDNA variability between the sexes and between closely related species, influencing how seemingly homeologous heteromorphic sex chromosomes undergo independent satDNA evolution.
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Affiliation(s)
- Carolina Crepaldi
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências (IB), Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Emiliano Martí
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências (IB), Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Évelin Mariani Gonçalves
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências (IB), Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Dardo Andrea Martí
- Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical (IBS), Universidad Nacional de Misiones (UNaM), CONICET, Posadas, Argentina
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35
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Fraser BA, Whiting JR, Paris JR, Weadick CJ, Parsons PJ, Charlesworth D, Bergero R, Bemm F, Hoffmann M, Kottler VA, Liu C, Dreyer C, Weigel D. Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata). Genome Biol Evol 2021; 12:1789-1805. [PMID: 32853348 PMCID: PMC7643365 DOI: 10.1093/gbe/evaa187] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 02/06/2023] Open
Abstract
Theory predicts that the sexes can achieve greater fitness if loci with sexually antagonistic polymorphisms become linked to the sex determining loci, and this can favor the spread of reduced recombination around sex determining regions. Given that sex-linked regions are frequently repetitive and highly heterozygous, few complete Y chromosome assemblies are available to test these ideas. The guppy system (Poecilia reticulata) has long been invoked as an example of sex chromosome formation resulting from sexual conflict. Early genetics studies revealed that male color patterning genes are mostly but not entirely Y-linked, and that X-linkage may be most common in low-predation populations. More recent population genomic studies of guppies have reached varying conclusions about the size and placement of the Y-linked region. However, this previous work used a reference genome assembled from short-read sequences from a female guppy. Here, we present a new guppy reference genome assembly from a male, using long-read PacBio single-molecule real-time sequencing and chromosome contact information. Our new assembly sequences across repeat- and GC-rich regions and thus closes gaps and corrects mis-assemblies found in the short-read female-derived guppy genome. Using this improved reference genome, we then employed broad population sampling to detect sex differences across the genome. We identified two small regions that showed consistent male-specific signals. Moreover, our results help reconcile the contradictory conclusions put forth by past population genomic studies of the guppy sex chromosome. Our results are consistent with a small Y-specific region and rare recombination in male guppies.
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Affiliation(s)
| | | | | | | | | | - Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, United Kingdom
| | - Roberta Bergero
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, United Kingdom
| | - Felix Bemm
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Margarete Hoffmann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Verena A Kottler
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Chang Liu
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Christine Dreyer
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
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36
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Xue L, Gao Y, Wu M, Tian T, Fan H, Huang Y, Huang Z, Li D, Xu L. Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair. Genome Biol 2021; 22:203. [PMID: 34253240 PMCID: PMC8273981 DOI: 10.1186/s13059-021-02430-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/01/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The origin of sex chromosomes requires the establishment of recombination suppression between the proto-sex chromosomes. In many fish species, the sex chromosome pair is homomorphic with a recent origin, providing species for studying how and why recombination suppression evolved in the initial stages of sex chromosome differentiation, but this requires accurate sequence assembly of the X and Y (or Z and W) chromosomes, which may be difficult if they are recently diverged. RESULTS Here we produce a haplotype-resolved genome assembly of zig-zag eel (Mastacembelus armatus), an aquaculture fish, at the chromosomal scale. The diploid assembly is nearly gap-free, and in most chromosomes, we resolve the centromeric and subtelomeric heterochromatic sequences. In particular, the Y chromosome, including its highly repetitive short arm, has zero gaps. Using resequencing data, we identify a ~7 Mb fully sex-linked region (SLR), spanning the sex chromosome centromere and almost entirely embedded in the pericentromeric heterochromatin. The SLRs on the X and Y chromosomes are almost identical in sequence and gene content, but both are repetitive and heterochromatic, consistent with zero or low recombination. We further identify an HMG-domain containing gene HMGN6 in the SLR as a candidate sex-determining gene that is expressed at the onset of testis development. CONCLUSIONS Our study supports the idea that preexisting regions of low recombination, such as pericentromeric regions, can give rise to SLR in the absence of structural variations between the proto-sex chromosomes.
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Affiliation(s)
- Lingzhan Xue
- College of Fisheries, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Huazhong Agricultural University, Wuhan, 430070, China.,Aquaculture and Genetic Breeding Laboratory, Freshwater Fisheries Research Institute of Fujian, Fuzhou, 350002, China
| | - Yu Gao
- College of Animal Science and Technology, Key Laboratory for Plateau Fishery Resources Conservation and Sustainable Utilization of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
| | - Meiying Wu
- Aquaculture and Genetic Breeding Laboratory, Freshwater Fisheries Research Institute of Fujian, Fuzhou, 350002, China
| | - Tian Tian
- Aquaculture and Genetic Breeding Laboratory, Freshwater Fisheries Research Institute of Fujian, Fuzhou, 350002, China
| | - Haiping Fan
- Freshwater Fisheries Research Institute of Fujian, Fuzhou, 350002, China
| | - Yongji Huang
- Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Zhen Huang
- Fujian Key Laboratory of Developmental and Neural Biology & Southern Center for Biomedical Research, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China. .,Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization, Fuzhou, 350117, Fujian, China.
| | - Dapeng Li
- College of Fisheries, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Huazhong Agricultural University, Wuhan, 430070, China. .,Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China.
| | - Luohao Xu
- Department of Neurosciences and Developmental Biology, University of Vienna, 1090, Vienna, Austria.
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Martínez P, Robledo D, Taboada X, Blanco A, Moser M, Maroso F, Hermida M, Gómez-Tato A, Álvarez-Blázquez B, Cabaleiro S, Piferrer F, Bouza C, Lien S, Viñas AM. A genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiatiated ZZ/ZW sex determination of turbot (Scophthalmus maximus). Genomics 2021; 113:1705-1718. [PMID: 33838278 DOI: 10.1016/j.ygeno.2021.04.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/20/2021] [Accepted: 04/05/2021] [Indexed: 01/10/2023]
Abstract
BACKGROUND Understanding sex determination (SD) across taxa is a major challenge for evolutionary biology. The new genomic tools are paving the way to identify genomic features underlying SD in fish, a group frequently showing limited sex chromosome differentiation and high SD evolutionary turnover. Turbot (Scophthalmus maximus) is a commercially important flatfish with an undifferentiated ZW/ZZ SD system and remarkable sexual dimorphism. Here we describe a new long-read turbot genome assembly used to disentangle the genetic architecture of turbot SD by combining genomics and classical genetics approaches. RESULTS The new turbot genome assembly consists of 145 contigs (N50 = 22.9 Mb), 27 of them representing >95% of its estimated genome size. A genome wide association study (GWAS) identified a ~ 6.8 Mb region on chromosome 12 associated with sex in 69.4% of the 36 families analyzed. The highest associated markers flanked sox2, the only gene in the region showing differential expression between sexes before gonad differentiation. A single SNP showed consistent differences between Z and W chromosomes. The analysis of a broad sample of families suggested the presence of additional genetic and/or environmental factors on turbot SD. CONCLUSIONS The new chromosome-level turbot genome assembly, one of the most contiguous fish assemblies to date, facilitated the identification of sox2 as a consistent candidate gene putatively driving SD in this species. This chromosome SD system barely showed any signs of differentiation, and other factors beyond the main QTL seem to control SD in a certain proportion of families.
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Affiliation(s)
- Paulino Martínez
- Departament of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain.
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK.
| | - Xoana Taboada
- Departament of Zoology, Genetics and Physical Anthropology, Faculty of Biology, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Andrés Blanco
- Departament of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain.
| | - Michel Moser
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Francesco Maroso
- Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Miguel Hermida
- Departament of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain.
| | - Antonio Gómez-Tato
- Departament of Mathematics, Faculty of Mathematics, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Blanca Álvarez-Blázquez
- Instituto Español de Oceanografía (IEO), Centro Oceanográfico de Vigo, Cabo Estay-Canido, 36280 Vigo, Spain.
| | - Santiago Cabaleiro
- Cluster de Acuicultura de Galicia (Punta do Couso), Aguiño-Ribeira, 15695 A Coruña, Spain.
| | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), 08003 Barcelona, Spain.
| | - Carmen Bouza
- Departament of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus de Lugo, 27002 Lugo, Spain.
| | - Sigbjørn Lien
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Ana M Viñas
- Departament of Zoology, Genetics and Physical Anthropology, Faculty of Biology, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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38
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Renner SS, Müller NA. Plant sex chromosomes defy evolutionary models of expanding recombination suppression and genetic degeneration. NATURE PLANTS 2021; 7:392-402. [PMID: 33782581 DOI: 10.1038/s41477-021-00884-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/18/2021] [Indexed: 05/17/2023]
Abstract
Hundreds of land plant lineages have independently evolved separate sexes in either gametophytes (dioicy) or sporophytes (dioecy), but 43% of all dioecious angiosperms are found in just 34 entirely dioecious clades, suggesting that their mode of sex determination evolved a long time ago. Here, we review recent insights on the molecular mechanisms that underlie the evolutionary change from individuals that each produce male and female gametes to individuals specializing in the production of just one type of gamete. The canonical model of sex chromosome evolution in plants predicts that two sex-determining genes will become linked in a sex-determining region (SDR), followed by expanding recombination suppression, chromosome differentiation and, ultimately, degeneration. Experimental work, however, is showing that single genes function as master regulators in model systems, such as the liverwort Marchantia and the angiosperms Diospyros and Populus. In Populus, this type of regulatory function has been demonstrated by genome editing. In other systems, including Actinidia, Asparagus and Vitis, two coinherited factors appear to independently regulate female and male function, yet sex chromosome differentiation has remained low. We discuss the best-understood systems and evolutionary pathways to dioecy, and present a meta-analysis of the sizes and ages of SDRs. We propose that limited sexual conflict explains why most SDRs are small and sex chromosomes remain homomorphic. It appears that models of increasing recombination suppression with age do not apply because selection favours mechanisms in which sex determination depends on minimal differences, keeping it surgically precise.
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Affiliation(s)
- Susanne S Renner
- Systematic Botany and Mycology, University of Munich (LMU), Munich, Germany.
| | - Niels A Müller
- Thünen Institute of Forest Genetics, Grosshansdorf, Germany.
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Gutiérrez-Valencia J, Hughes PW, Berdan EL, Slotte T. The Genomic Architecture and Evolutionary Fates of Supergenes. Genome Biol Evol 2021; 13:6178796. [PMID: 33739390 PMCID: PMC8160319 DOI: 10.1093/gbe/evab057] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2021] [Indexed: 12/25/2022] Open
Abstract
Supergenes are genomic regions containing sets of tightly linked loci that control multi-trait phenotypic polymorphisms under balancing selection. Recent advances in genomics have uncovered significant variation in both the genomic architecture as well as the mode of origin of supergenes across diverse organismal systems. Although the role of genomic architecture for the origin of supergenes has been much discussed, differences in the genomic architecture also subsequently affect the evolutionary trajectory of supergenes and the rate of degeneration of supergene haplotypes. In this review, we synthesize recent genomic work and historical models of supergene evolution, highlighting how the genomic architecture of supergenes affects their evolutionary fate. We discuss how recent findings on classic supergenes involved in governing ant colony social form, mimicry in butterflies, and heterostyly in flowering plants relate to theoretical expectations. Furthermore, we use forward simulations to demonstrate that differences in genomic architecture affect the degeneration of supergenes. Finally, we discuss implications of the evolution of supergene haplotypes for the long-term fate of balanced polymorphisms governed by supergenes.
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Affiliation(s)
- Juanita Gutiérrez-Valencia
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Sweden
| | - P William Hughes
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Sweden
| | - Emma L Berdan
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Sweden
| | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Sweden
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40
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Charlesworth D. When and how do sex-linked regions become sex chromosomes? Evolution 2021; 75:569-581. [PMID: 33592115 DOI: 10.1111/evo.14196] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 12/22/2022]
Abstract
The attention given to heteromorphism and genetic degeneration of "classical sex chromosomes" (Y chromosomes in XY systems, and the W in ZW systems that were studied first and are best described) has perhaps created the impression that the absence of recombination between sex chromosomes is inevitable. I here argue that continued recombination is often to be expected, that absence of recombination is surprising and demands further study, and that the involvement of selection in reduced recombination is not yet well understood. Despite a long history of investigations of sex chromosome pairs, there is a need for more quantitative approaches to studying sex-linked regions. I describe a scheme to help understand the relationships between different properties of sex-linked regions. Specifically, I focus on their sizes (differentiating between small regions and extensive fully sex-linked ones), the times when they evolved, and their differentiation, and review studies using DNA sequencing in nonmodel organisms that are providing information about the processes causing these properties.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
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41
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Wright SI. Deborah Charlesworth, winner of the society for the study of evolution's inaugural lifetime achievement award: Evolutionary biology for the genomics era. Evolution 2021; 75:566-568. [PMID: 33592116 DOI: 10.1111/evo.14195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 11/29/2022]
Affiliation(s)
- Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
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42
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Rifkin JL, Beaudry FEG, Humphries Z, Choudhury BI, Barrett SCH, Wright SI. Widespread Recombination Suppression Facilitates Plant Sex Chromosome Evolution. Mol Biol Evol 2021; 38:1018-1030. [PMID: 33095227 PMCID: PMC7947811 DOI: 10.1093/molbev/msaa271] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Classical models suggest that recombination rates on sex chromosomes evolve in a stepwise manner to localize sexually antagonistic variants in the sex in which they are beneficial, thereby lowering rates of recombination between X and Y chromosomes. However, it is also possible that sex chromosome formation occurs in regions with preexisting recombination suppression. To evaluate these possibilities, we constructed linkage maps and a chromosome-scale genome assembly for the dioecious plant Rumex hastatulus. This species has a polymorphic karyotype with a young neo-sex chromosome, resulting from a Robertsonian fusion between the X chromosome and an autosome, in part of its geographic range. We identified the shared and neo-sex chromosomes using comparative genetic maps of the two cytotypes. We found that sex-linked regions of both the ancestral and the neo-sex chromosomes are embedded in large regions of low recombination. Furthermore, our comparison of the recombination landscape of the neo-sex chromosome to its autosomal homolog indicates that low recombination rates mainly preceded sex linkage. These patterns are not unique to the sex chromosomes; all chromosomes were characterized by massive regions of suppressed recombination spanning most of each chromosome. This represents an extreme case of the periphery-biased recombination seen in other systems with large chromosomes. Across all chromosomes, gene and repetitive sequence density correlated with recombination rate, with patterns of variation differing by repetitive element type. Our findings suggest that ancestrally low rates of recombination may facilitate the formation and subsequent evolution of heteromorphic sex chromosomes.
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Affiliation(s)
- Joanna L Rifkin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Felix E G Beaudry
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Zoë Humphries
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Baharul I Choudhury
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
- Centre for Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
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Montgomery JS, Giacomini DA, Weigel D, Tranel PJ. Male-specific Y-chromosomal regions in waterhemp (Amaranthus tuberculatus) and Palmer amaranth (Amaranthus palmeri). THE NEW PHYTOLOGIST 2021; 229:3522-3533. [PMID: 33301599 DOI: 10.1111/nph.17108] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/13/2020] [Indexed: 05/16/2023]
Abstract
Amaranthus tuberculatus and Amaranthus palmeri are agronomically important weed species, both with stable dioecious reproductive systems. An understanding of the genetic basis of sex determination may lead to new methods of managing these troublesome weeds. Previous research identified genomic sequences associated with maleness in each species. Male-specific sequences were used to identify genomic regions in both species that are believed to contain sex-determining genes, i.e. the male-specific Y (MSY) region. These regions were compared to understand if sex determination is controlled via the same physiological pathway and if dioecy evolved independently. A contiguously assembled candidate MSY region identified in Amaranthus palmeri is approximately 1.3 Mb with 121 predicted gene models. In Amaranthus tuberculatus, several contigs, with combined length of 4.6 Mb and with 147 gene models, were identified as belonging to the MSY region. Synteny was not detected between the two species' candidate MSY regions but they shared two predicted genes. With lists of candidate genes for sex determination containing fewer than 200 in each species, future research can address whether sex determination is controlled via similar physiological pathways and whether dioecy has indeed evolved independently in these species.
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Affiliation(s)
- Jacob S Montgomery
- Department of Crop Sciences, University of Illinois, Turner Hall, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
| | - Darci A Giacomini
- Department of Crop Sciences, University of Illinois, Turner Hall, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen, 72076, Germany
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Turner Hall, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
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Martínez C, Jamilena M. To be a male or a female flower, a question of ethylene in cucurbits. CURRENT OPINION IN PLANT BIOLOGY 2021; 59:101981. [PMID: 33517096 DOI: 10.1016/j.pbi.2020.101981] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/20/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Within the Cucurbitaceae family, most of its species develop unisexual female and male flowers, either on the same plant (monoecy) or on different plants (dioecy). As in other plant families, these two sex morphotypes have evolved from hermaphrodite species; however, many evolutionary events have occurred in cucurbits allowing easy conversion from dioecy to monoecy and vice versa. The variability in sex morphotypes is higher in the domesticated species of the family, which together with recent advances in genomics, make cucurbits an ideal model to study the genetic and molecular mechanisms that control sex determination in plants. Conventional studies demonstrated that ethylene was the master regulator of sex determination in cucurbits, although some cultivated species may respond differently to ethylene action. In this article, we survey the new advances in hormonal and genetic control of sex determination in cucurbit species, control which establishes the ethylene biosynthesis and signaling genes as being those that determine the floral meristem towards a male, female or hermaphrodite flower. The interactions between these genes are integrated into a model that explains the occurrence and distribution of unisexal and hermaphrodite flowers within the different sex morphotypes. We underline the significance of this scientific progress with regard to breeding programs for agronomically-important sex-associated traits.
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Affiliation(s)
- Cecilia Martínez
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, 04120 Almería, Spain
| | - Manuel Jamilena
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, 04120 Almería, Spain.
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45
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Jesionek W, Bodláková M, Kubát Z, Čegan R, Vyskot B, Vrána J, Šafář J, Puterova J, Hobza R. Fundamentally different repetitive element composition of sex chromosomes in Rumex acetosa. ANNALS OF BOTANY 2021; 127:33-47. [PMID: 32902599 PMCID: PMC7750719 DOI: 10.1093/aob/mcaa160] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIMS Dioecious species with well-established sex chromosomes are rare in the plant kingdom. Most sex chromosomes increase in size but no comprehensive analysis of the kind of sequences that drive this expansion has been presented. Here we analyse sex chromosome structure in common sorrel (Rumex acetosa), a dioecious plant with XY1Y2 sex determination, and we provide the first chromosome-specific repeatome analysis for a plant species possessing sex chromosomes. METHODS We flow-sorted and separately sequenced sex chromosomes and autosomes in R. acetosa using the two-dimensional fluorescence in situ hybridization in suspension (FISHIS) method and Illumina sequencing. We identified and quantified individual repeats using RepeatExplorer, Tandem Repeat Finder and the Tandem Repeats Analysis Program. We employed fluorescence in situ hybridization (FISH) to analyse the chromosomal localization of satellites and transposons. KEY RESULTS We identified a number of novel satellites, which have, in a fashion similar to previously known satellites, significantly expanded on the Y chromosome but not as much on the X or on autosomes. Additionally, the size increase of Y chromosomes is caused by non-long terminal repeat (LTR) and LTR retrotransposons, while only the latter contribute to the enlargement of the X chromosome. However, the X chromosome is populated by different LTR retrotransposon lineages than those on Y chromosomes. CONCLUSIONS The X and Y chromosomes have significantly diverged in terms of repeat composition. The lack of recombination probably contributed to the expansion of diverse satellites and microsatellites and faster fixation of newly inserted transposable elements (TEs) on the Y chromosomes. In addition, the X and Y chromosomes, despite similar total counts of TEs, differ significantly in the representation of individual TE lineages, which indicates that transposons proliferate preferentially in either the paternal or the maternal lineage.
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Affiliation(s)
- Wojciech Jesionek
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice, Brno, Czech Republic
- For correspondence. E-mail: or
| | - Markéta Bodláková
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
| | - Zdeněk Kubát
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
| | - Radim Čegan
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
| | - Boris Vyskot
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů, Olomouc-Holice, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů, Olomouc-Holice, Czech Republic
| | - Janka Puterova
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
- Brno University of Technology, Faculty of Information Technology, Centre of Excellence IT4Innovations, Bozetechova, Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
- For correspondence. E-mail: or
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46
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Rodríguez Lorenzo JL, Hubinský M, Vyskot B, Hobza R. Histone post-translational modifications in Silene latifolia X and Y chromosomes suggest a mammal-like dosage compensation system. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 299:110528. [PMID: 32900432 DOI: 10.1016/j.plantsci.2020.110528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/07/2020] [Accepted: 05/09/2020] [Indexed: 06/11/2023]
Abstract
Silene latifolia is a model organism to study evolutionary young heteromorphic sex chromosome evolution in plants. Previous research indicates a Y-allele gene degeneration and a dosage compensation system already operating. Here, we propose an epigenetic approach based on analysis of several histone post-translational modifications (PTMs) to find the first epigenetic hints of the X:Y sex chromosome system regulation in S. latifolia. Through chromatin immunoprecipitation we interrogated six genes from X and Y alleles. Several histone PTMS linked to DNA methylation and transcriptional repression (H3K27me3, H3K23me, H3K9me2 and H3K9me3) and to transcriptional activation (H3K4me3 and H4K5, 8, 12, 16ac) were used. DNA enrichment (Immunoprecipitated DNA/input DNA) was analyzed and showed three main results: (i) promoters of the Y allele are associated with heterochromatin marks, (ii) promoters of the X allele in males are associated with activation of transcription marks and finally, (iii) promoters of X alleles in females are associated with active and repressive marks. Our finding indicates a transcription activation of X allele and transcription repression of Y allele in males. In females we found a possible differential regulation (up X1, down X2) of each female X allele. These results agree with the mammal-like epigenetic dosage compensation regulation.
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Affiliation(s)
- José Luis Rodríguez Lorenzo
- The Czech Academy of Sciences, Institute of Biophysics v.v.i., Department of Plant Developmental Genetics, Královopolská 135, 612 65, Brno, Czech Republic.
| | - Marcel Hubinský
- The Czech Academy of Sciences, Institute of Biophysics v.v.i., Department of Plant Developmental Genetics, Královopolská 135, 612 65, Brno, Czech Republic
| | - Boris Vyskot
- The Czech Academy of Sciences, Institute of Biophysics v.v.i., Department of Plant Developmental Genetics, Královopolská 135, 612 65, Brno, Czech Republic
| | - Roman Hobza
- The Czech Academy of Sciences, Institute of Biophysics v.v.i., Department of Plant Developmental Genetics, Královopolská 135, 612 65, Brno, Czech Republic
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47
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Badouin H, Velt A, Gindraud F, Flutre T, Dumas V, Vautrin S, Marande W, Corbi J, Sallet E, Ganofsky J, Santoni S, Guyot D, Ricciardelli E, Jepsen K, Käfer J, Berges H, Duchêne E, Picard F, Hugueney P, Tavares R, Bacilieri R, Rustenholz C, Marais GAB. The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication. Genome Biol 2020; 21:223. [PMID: 32892750 PMCID: PMC7487632 DOI: 10.1186/s13059-020-02131-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 08/05/2020] [Indexed: 12/22/2022] Open
Abstract
Background A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. vinifera). It is known that V. sylvestris has an XY system and V. vinifera a modified Y haplotype (Yh) and that the sex locus is small, but it has not previously been precisely characterized. Results We generate a high-quality de novo reference genome for V. sylvestris, onto which we map whole-genome re-sequencing data of a cross to locate the sex locus. Assembly of the full X, Y, and Yh haplotypes of V. sylvestris and V. vinifera sex locus and examining their gene content and expression profiles during flower development in wild and cultivated accessions show that truncation and deletion of tapetum and pollen development genes on the X haplotype likely causes male sterility, while the upregulation of a Y allele of a cytokinin regulator (APRT3) may cause female sterility. The downregulation of this cytokinin regulator in the Yh haplotype may be sufficient to trigger reversal to hermaphroditism. Molecular dating of X and Y haplotypes is consistent with the sex locus being as old as the Vitis genus, but the mechanism by which recombination was suppressed remains undetermined. Conclusions We describe the genomic and evolutionary characterization of the sex locus of cultivated and wild grapevine, providing a coherent model of sex determination in the latter and for transition from dioecy to hermaphroditism during domestication.
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Affiliation(s)
- Hélène Badouin
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France.
| | - Amandine Velt
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - François Gindraud
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Timothée Flutre
- GQE-Le Moulon, INRAE, Univ. Paris-Sud, CNRS, AgroParisTech, Univ. Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Vincent Dumas
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - Sonia Vautrin
- INRAE, Centre National de Ressources Génomiques Végétales, F-31326, Castanet-Tolosan, France
| | - William Marande
- INRAE, Centre National de Ressources Génomiques Végétales, F-31326, Castanet-Tolosan, France
| | - Jonathan Corbi
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Erika Sallet
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Jérémy Ganofsky
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Sylvain Santoni
- INRAE, UMR AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | | | - Kristen Jepsen
- IGM Genomics Center, University of California, San Diego, La Jolla, CA, USA
| | - Jos Käfer
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Hélène Berges
- INRAE, Centre National de Ressources Génomiques Végétales, F-31326, Castanet-Tolosan, France
| | - Eric Duchêne
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - Franck Picard
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Philippe Hugueney
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - Raquel Tavares
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Roberto Bacilieri
- INRAE, UMR AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France.
| | - Camille Rustenholz
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France.
| | - Gabriel A B Marais
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France.
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48
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Baránková S, Pascual-Díaz JP, Sultana N, Alonso-Lifante MP, Balant M, Barros K, D'Ambrosio U, Malinská H, Peska V, Pérez Lorenzo I, Kovařík A, Vyskot B, Janoušek B, Garcia S. Sex-chrom, a database on plant sex chromosomes. THE NEW PHYTOLOGIST 2020; 227:1594-1604. [PMID: 32357248 DOI: 10.1111/nph.16635] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 04/25/2020] [Indexed: 05/15/2023]
Affiliation(s)
- Simona Baránková
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Joan Pere Pascual-Díaz
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
| | - Nusrat Sultana
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
- Department of Botany, Faculty of Life and Earth Sciences, Jagannath University, Dhaka, 1100, Bangladesh
| | - Maria Pilar Alonso-Lifante
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
| | - Manica Balant
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
| | - Karina Barros
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
| | - Ugo D'Ambrosio
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
| | - Hana Malinská
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
- Department of Biology, Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, 400 96, Ústí nad Labem, Czech Republic
| | - Vratislav Peska
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Iván Pérez Lorenzo
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
| | - Aleš Kovařík
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Boris Vyskot
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Bohuslav Janoušek
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Sònia Garcia
- Institut Botanic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
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49
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Ferretti ABSM, Milani D, Palacios-Gimenez OM, Ruiz-Ruano FJ, Cabral-de-Mello DC. High dynamism for neo-sex chromosomes: satellite DNAs reveal complex evolution in a grasshopper. Heredity (Edinb) 2020; 125:124-137. [PMID: 32499661 PMCID: PMC7426270 DOI: 10.1038/s41437-020-0327-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/24/2020] [Accepted: 05/25/2020] [Indexed: 12/18/2022] Open
Abstract
A common characteristic of sex chromosomes is the accumulation of repetitive DNA, which accounts for their diversification and degeneration. In grasshoppers, the X0 sex-determining system in males is considered ancestral. However, in some species, derived variants like neo-XY in males evolved several times independently by Robertsonian translocation. This is the case of Ronderosia bergii, in which further large pericentromeric inversion in the neo-Y also took place, making this species particularly interesting for investigating sex chromosome evolution. Here, we characterized the satellite DNAs (satDNAs) and transposable elements (TEs) of the species to investigate the quantitative differences in repeat composition between male and female genomes putatively associated with sex chromosomes. We found a total of 53 satDNA families and 56 families of TEs. The satDNAs were 13.5% more abundant in males than in females, while TEs were just 1.02% more abundant in females. These results imply differential amplification of satDNAs on neo-Y chromosome and a minor role of TEs in sex chromosome differentiation. We showed highly differentiated neo-XY sex chromosomes owing to major amplification of satDNAs in neo-Y. Furthermore, chromosomal mapping of satDNAs suggests high turnover of neo-sex chromosomes in R. bergii at the intrapopulation level, caused by multiple paracentric inversions, amplifications, and transpositions. Finally, the species is an example of the action of repetitive DNAs in the generation of variability for sex chromosomes after the suppression of recombination, and helps understand sex chromosome evolution at the intrapopulation level.
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Affiliation(s)
- Ana B S M Ferretti
- Departamento de Biologia Geral e Aplicada, UNESP-Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo, Brazil
| | - Diogo Milani
- Departamento de Biologia Geral e Aplicada, UNESP-Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo, Brazil
| | - Octavio M Palacios-Gimenez
- Department of Organismal Biology, Uppsala University, Evolutionary Biology Centre, Uppsala, Sweden
- Department of Ecology and Genetics, Uppsala University, Evolutionary Biology Centre, Uppsala, Sweden
| | - Francisco J Ruiz-Ruano
- Department of Organismal Biology, Uppsala University, Evolutionary Biology Centre, Uppsala, Sweden
- Department of Ecology and Genetics, Uppsala University, Evolutionary Biology Centre, Uppsala, Sweden
| | - Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, UNESP-Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo, Brazil.
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50
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Peichel CL, McCann SR, Ross JA, Naftaly AFS, Urton JR, Cech JN, Grimwood J, Schmutz J, Myers RM, Kingsley DM, White MA. Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution. Genome Biol 2020; 21:177. [PMID: 32684159 PMCID: PMC7368989 DOI: 10.1186/s13059-020-02097-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/08/2020] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Heteromorphic sex chromosomes have evolved repeatedly across diverse species. Suppression of recombination between X and Y chromosomes leads to degeneration of the Y chromosome. The progression of degeneration is not well understood, as complete sequence assemblies of heteromorphic Y chromosomes have only been generated across a handful of taxa with highly degenerate sex chromosomes. Here, we describe the assembly of the threespine stickleback (Gasterosteus aculeatus) Y chromosome, which is less than 26 million years old and at an intermediate stage of degeneration. Our previous work identified that the non-recombining region between the X and the Y spans approximately 17.5 Mb on the X chromosome. RESULTS We combine long-read sequencing with a Hi-C-based proximity guided assembly to generate a 15.87 Mb assembly of the Y chromosome. Our assembly is concordant with cytogenetic maps and Sanger sequences of over 90 Y chromosome BAC clones. We find three evolutionary strata on the Y chromosome, consistent with the three inversions identified by our previous cytogenetic analyses. The threespine stickleback Y shows convergence with more degenerate sex chromosomes in the retention of haploinsufficient genes and the accumulation of genes with testis-biased expression, many of which are recent duplicates. However, we find no evidence for large amplicons identified in other sex chromosome systems. We also report an excellent candidate for the master sex-determination gene: a translocated copy of Amh (Amhy). CONCLUSIONS Together, our work shows that the evolutionary forces shaping sex chromosomes can cause relatively rapid changes in the overall genetic architecture of Y chromosomes.
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Affiliation(s)
- Catherine L. Peichel
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Shaugnessy R. McCann
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Joseph A. Ross
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195 USA
| | | | - James R. Urton
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195 USA
| | - Jennifer N. Cech
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195 USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - David M. Kingsley
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Michael A. White
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Department of Genetics, University of Georgia, Athens, GA 30602 USA
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