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Raimondeau P, Ksouda S, Marande W, Fuchs AL, Gryta H, Theron A, Puyoou A, Dupin J, Cheptou PO, Vautrin S, Valière S, Manzi S, Baali-Cherif D, Chave J, Christin PA, Besnard G. A hemizygous supergene controls homomorphic and heteromorphic self-incompatibility systems in Oleaceae. Curr Biol 2024; 34:1977-1986.e8. [PMID: 38626764 DOI: 10.1016/j.cub.2024.03.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 02/29/2024] [Accepted: 03/18/2024] [Indexed: 04/18/2024]
Abstract
Self-incompatibility (SI) has evolved independently multiple times and prevents self-fertilization in hermaphrodite angiosperms. Several groups of Oleaceae such as jasmines exhibit distylous flowers, with two compatibility groups each associated with a specific floral morph.1 Other Oleaceae species in the olive tribe have two compatibility groups without associated morphological variation.2,3,4,5 The genetic basis of both homomorphic and dimorphic SI systems in Oleaceae is unknown. By comparing genomic sequences of three olive subspecies (Olea europaea) belonging to the two compatibility groups, we first locate the genetic determinants of SI within a 700-kb hemizygous region present only in one compatibility group. We then demonstrate that the homologous hemizygous region also controls distyly in jasmine. Phylogenetic analyses support a common origin of both systems, following a segmental genomic duplication in a common ancestor. Examination of the gene content of the hemizygous region in different jasmine and olive species suggests that the mechanisms determining compatibility groups and floral phenotypes (whether homomorphic or dimorphic) in Oleaceae rely on the presence/absence of two genes involved in gibberellin and brassinosteroid regulation.
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Affiliation(s)
- Pauline Raimondeau
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France; Yale Institute of Biospheric Studies, New Haven, CT 06520, USA
| | - Sayam Ksouda
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France
| | - William Marande
- INRAE, Centre National de Ressources Génomiques Végétales, 31326 Castanet-Tolosan, France
| | - Anne-Laure Fuchs
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France
| | - Hervé Gryta
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France
| | - Anthony Theron
- INRAE, Centre National de Ressources Génomiques Végétales, 31326 Castanet-Tolosan, France
| | - Aurore Puyoou
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France
| | - Julia Dupin
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France
| | - Pierre-Olivier Cheptou
- CEFE (Centre d'Ecologie Fonctionnelle et Evolutive), UMR 5175, CNRS, Université de Montpellier, Université Paul Valéry, EPHE, IRD, 34293 Montpellier, France
| | - Sonia Vautrin
- INRAE, Centre National de Ressources Génomiques Végétales, 31326 Castanet-Tolosan, France
| | - Sophie Valière
- INRAE, US 1426, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France
| | - Sophie Manzi
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France
| | - Djamel Baali-Cherif
- Laboratoire de Recherche sur les Zones Arides, USTHB/ENSA, 16000 Alger, Algeria
| | - Jérôme Chave
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Guillaume Besnard
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France.
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2
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Filatov DA. Evolution of a plant sex chromosome driven by expanding pericentromeric recombination suppression. Sci Rep 2024; 14:1373. [PMID: 38228625 DOI: 10.1038/s41598-024-51153-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/01/2024] [Indexed: 01/18/2024] Open
Abstract
Recombination suppression around sex-determining gene(s) is a key step in evolution of sex chromosomes, but it is not well understood how it evolves. Recently evolved sex-linked regions offer an opportunity to understand the mechanisms of recombination cessation. This paper analyses such a region on Silene latifolia (Caryophyllaceae) sex chromosomes, where recombination was suppressed in the last 120 thousand years ("stratum 3"). Locating the boundaries of the stratum 3 in S. latifolia genome sequence revealed that this region is far larger than assumed previously-it is about 14 Mb long and includes 202 annotated genes. A gradient of X:Y divergence detected in the stratum 3, with divergence increasing proximally, indicates gradual recombination cessation, possibly caused by expansion of pericentromeric recombination suppression (PRS) into the pseudoautosomal region. Expansion of PRS was also the likely cause for the formation of the older stratum 2 on S. latifolia sex chromosomes. The role of PRS in sex chromosome evolution has been underappreciated, but it may be a significant factor, especially in the species with large chromosomes where PRS is often extensive.
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Affiliation(s)
- Dmitry A Filatov
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK.
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3
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Yazdi HP, Olito C, Kawakami T, Unneberg P, Schou MF, Cloete SWP, Hansson B, Cornwallis CK. The evolutionary maintenance of ancient recombining sex chromosomes in the ostrich. PLoS Genet 2023; 19:e1010801. [PMID: 37390104 DOI: 10.1371/journal.pgen.1010801] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/28/2023] [Indexed: 07/02/2023] Open
Abstract
Sex chromosomes have evolved repeatedly across the tree of life and often exhibit extreme size dimorphism due to genetic degeneration of the sex-limited chromosome (e.g. the W chromosome of some birds and Y chromosome of mammals). However, in some lineages, ancient sex-limited chromosomes have escaped degeneration. Here, we study the evolutionary maintenance of sex chromosomes in the ostrich (Struthio camelus), where the W remains 65% the size of the Z chromosome, despite being more than 100 million years old. Using genome-wide resequencing data, we show that the population scaled recombination rate of the pseudoautosomal region (PAR) is higher than similar sized autosomes and is correlated with pedigree-based recombination rate in the heterogametic females, but not homogametic males. Genetic variation within the sex-linked region (SLR) (π = 0.001) was significantly lower than in the PAR, consistent with recombination cessation. Conversely, genetic variation across the PAR (π = 0.0016) was similar to that of autosomes and dependent on local recombination rates, GC content and to a lesser extent, gene density. In particular, the region close to the SLR was as genetically diverse as autosomes, likely due to high recombination rates around the PAR boundary restricting genetic linkage with the SLR to only ~50Kb. The potential for alleles with antagonistic fitness effects in males and females to drive chromosome degeneration is therefore limited. While some regions of the PAR had divergent male-female allele frequencies, suggestive of sexually antagonistic alleles, coalescent simulations showed this was broadly consistent with neutral genetic processes. Our results indicate that the degeneration of the large and ancient sex chromosomes of the ostrich may have been slowed by high recombination in the female PAR, reducing the scope for the accumulation of sexually antagonistic variation to generate selection for recombination cessation.
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Affiliation(s)
| | - Colin Olito
- Department of Biology, Lund University, Lund, Sweden
| | - Takeshi Kawakami
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- Embark Veterinary, Inc., Boston, Massachusetts, United States of America
| | - Per Unneberg
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mads F Schou
- Department of Biology, Lund University, Lund, Sweden
| | - Schalk W P Cloete
- Directorate Animal Sciences, Western Cape Department of Agriculture, Elsenburg, South Africa
- Department of Animal Sciences, Stellenbosch University, Matieland, South Africa
| | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
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4
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Yue J, Krasovec M, Kazama Y, Zhang X, Xie W, Zhang S, Xu X, Kan B, Ming R, Filatov DA. The origin and evolution of sex chromosomes, revealed by sequencing of the Silene latifolia female genome. Curr Biol 2023:S0960-9822(23)00678-4. [PMID: 37290443 DOI: 10.1016/j.cub.2023.05.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/07/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
White campion (Silene latifolia, Caryophyllaceae) was the first vascular plant where sex chromosomes were discovered. This species is a classic model for studies on plant sex chromosomes due to presence of large, clearly distinguishable X and Y chromosomes that originated de novo about 11 million years ago (mya), but lack of genomic resources for this relatively large genome (∼2.8 Gb) remains a significant hurdle. Here we report S. latifolia female genome assembly integrated with sex-specific genetic maps of this species, focusing on sex chromosomes and their evolution. The analysis reveals a highly heterogeneous recombination landscape with strong reduction in recombination rate in the central parts of all chromosomes. Recombination on the X chromosome in female meiosis primarily occurs at the very ends, and over 85% of the X chromosome length is located in a massive (∼330 Mb) gene-poor, rarely recombining pericentromeric region (Xpr). The results indicate that the non-recombining region on the Y chromosome (NRY) initially evolved in a relatively small (∼15 Mb), actively recombining region at the end of the q-arm, possibly as a result of inversion on the nascent X chromosome. The NRY expanded about 6 mya via linkage between the Xpr and the sex-determining region, which may have been caused by expanding pericentromeric recombination suppression on the X chromosome. These findings shed light on the origin of sex chromosomes in S. latifolia and yield genomic resources to assist ongoing and future investigations into sex chromosome evolution.
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Affiliation(s)
- Jingjing Yue
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Marc Krasovec
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK; Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Yusuke Kazama
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Kenjojima, Matsuoka, Eiheiji-cho, Fukui 910-1195, Japan
| | - Xingtan Zhang
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518100, China
| | - Wangyang Xie
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shencheng Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518100, China
| | - Xiuming Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361100, China
| | - Baolin Kan
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ray Ming
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Dmitry A Filatov
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK.
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5
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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: 9] [Impact Index Per Article: 4.5] [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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6
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Dagilis AJ, Sardell JM, Josephson MP, Su Y, Kirkpatrick M, Peichel CL. Searching for signatures of sexually antagonistic selection on stickleback sex chromosomes. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210205. [PMID: 35694749 PMCID: PMC9189504 DOI: 10.1098/rstb.2021.0205] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Intralocus sexually antagonistic selection occurs when an allele is beneficial to one sex but detrimental to the other. This form of selection is thought to be key to the evolution of sex chromosomes but is hard to detect. Here we perform an analysis of phased young sex chromosomes to look for signals of sexually antagonistic selection in the Japan Sea stickleback (Gasterosteus nipponicus). Phasing allows us to date the suppression of recombination on the sex chromosome and provides unprecedented resolution to identify sexually antagonistic selection in the recombining region of the chromosome. We identify four windows with elevated divergence between the X and Y in the recombining region, all in or very near genes associated with phenotypes potentially under sexually antagonistic selection in humans. We are unable, however, to rule out the alternative hypothesis that the peaks of divergence result from demographic effects. Thus, although sexually antagonistic selection is a key hypothesis for the formation of supergenes on sex chromosomes, it remains challenging to detect. This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’.
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Affiliation(s)
- Andrius J Dagilis
- Department of Integrative Biology, University of Texas, Austin TX 78712, USA.,Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jason M Sardell
- Department of Integrative Biology, University of Texas, Austin TX 78712, USA
| | - Matthew P Josephson
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Yiheng Su
- Department of Computer Science, University of Texas, Austin TX 78712, USA
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin TX 78712, USA
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
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7
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Filatov DA. Recent expansion of the non-recombining sex-linked region on Silene latifolia sex chromosomes. J Evol Biol 2022; 35:1696-1708. [PMID: 35834179 PMCID: PMC10083954 DOI: 10.1111/jeb.14063] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/19/2022] [Accepted: 06/21/2022] [Indexed: 11/27/2022]
Abstract
Evolution of a non-recombining sex-specific region on the Y (or W) chromosome (NRY) is a key step in sex chromosome evolution, but how recombination suppression evolves is not well understood. Studies in many different organisms indicated that NRY evolution often involves several expansion steps. Why such NRY expansions occur remains unclear, although it is though that they are likely driven by sexually antagonistic selection. This paper describes a recent NRY expansion due to shift of the pseudoautosomal boundary on the sex chromosomes of a dioecious plant Silene latifolia. The shift resulted in inclusion of at least 16 pseudoautosomal genes into the NRY. This region is pseudoautosomal in closely related Silene dioica and Silene diclinis, indicating that the NRY expansion occurred in S. latifolia after it speciated from the other species ~120 thousand years ago. As S. latifolia and S. dioica actively hybridise across Europe, interspecific gene flow could blur the PAR boundary in these species. The pseudoautosomal genes have significantly elevated genetic diversity (π ~ 3% at synonymous sites), which is consistent with balancing selection maintaining diversity in this region. The recent shift of the PAR boundary in S. latifolia offers an opportunity to study the process of on-going NRY expansion.
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8
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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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9
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Molecular Sex Identification in the Hardy Rubber Tree ( Eucommia ulmoides Oliver) via ddRAD Markers. Int J Genomics 2020; 2020:2420976. [PMID: 32509842 PMCID: PMC7246395 DOI: 10.1155/2020/2420976] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/03/2020] [Indexed: 11/18/2022] Open
Abstract
Eucommia ulmoides, also known as the industrially and medicinally important hardy rubber tree, is the sole species of Eucommiaceae. Nevertheless, its dioecious property hinders sex recognition by traditional morphological observation at very early developmental stages, thus inhibiting breeding and economic cropping. In this study, double-digest restriction site-associated DNA sequencing (ddRAD-seq) was applied to screen sex-linked molecular markers for sex identification and investigation of the sex determination system in 20 male and female E. ulmoides individual plants, respectively. In consequence, five candidate male-specific loci but no female-specific loci were predicated among the 183,752 male and 147,122 female catalogue loci by bioinformatics analysis. Subsequent PCR (polymerase chain reaction) amplification and Sanger sequencing examinations were performed on another 24 individuals, 12 for each sex, from a separate population. One ideal sex-linked locus, MSL4, was identified among the five putative male-specific loci that were found using ddRAD data. MSL4 is 479 bp in length and highly conserved in all the male individuals, suggesting its feature of being stable and repeatable. Our results also indicated that the sex of E. ulmoides is likely determined genetically. In short, this study provides a consistent and reproducible ddRAD marker (MSL4) that is able to discriminate male from female seedlings in E. ulmoides, which will be valuable for rapid breeding practice and better commercial production of this economically important tree.
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10
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The Location of the Pseudoautosomal Boundary in Silene latifolia. Genes (Basel) 2020; 11:genes11060610. [PMID: 32486434 PMCID: PMC7348893 DOI: 10.3390/genes11060610] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/25/2020] [Accepted: 05/28/2020] [Indexed: 12/19/2022] Open
Abstract
Y-chromosomes contain a non-recombining region (NRY), and in many organisms it was shown that the NRY expanded over time. How and why the NRY expands remains unclear. Young sex chromosomes, where NRY expansion occurred recently or is on-going, offer an opportunity to study the causes of this process. Here, we used the plant Silene latifolia, where sex chromosomes evolved ~11 million years ago, to study the location of the boundary between the NRY and the recombining pseudoautosomal region (PAR). The previous work devoted to the NRY/PAR boundary in S. latifolia was based on a handful of genes with locations approximately known from the genetic map. Here, we report the analysis of 86 pseudoautosomal and sex-linked genes adjacent to the S. latifolia NRY/PAR boundary to establish the location of the boundary more precisely. We take advantage of the dense genetic map and polymorphism data from wild populations to identify 20 partially sex-linked genes located in the “fuzzy boundary”, that rarely recombines in male meiosis. Genes proximal to this fuzzy boundary show no evidence of recombination in males, while the genes distal to this partially-sex-linked region are actively recombining in males. Our results provide a more accurate location for the PAR boundary in S. latifolia, which will help to elucidate the causes of PAR boundary shifts leading to NRY expansion over time.
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11
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Otto SP. Evolutionary potential for genomic islands of sexual divergence on recombining sex chromosomes. THE NEW PHYTOLOGIST 2019; 224:1241-1251. [PMID: 31361905 DOI: 10.1111/nph.16083] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/22/2019] [Indexed: 06/10/2023]
Abstract
Differentiated sex chromosomes are thought to develop through the accumulation of polymorphisms at loci subject to opposing selection between males and females, and/or between haploids and diploids. As sex chromosomes differentiate, reduced recombination becomes favored between selected loci and the sex-determining region, strengthening genetic associations between alleles favored in a sex and the corresponding sex chromosome. Here a model is analyzed to explore whether polymorphism at one sexually or ploidally antagonistic locus facilitates the spread of rare alleles at other loci experiencing antagonistic selection, promoting further differentiation of the sex chromosomes. It is found that antagonistic polymorphisms can spread and capture other such loci, building 'genomic islands' of differentiation on sex chromosomes, but the conditions are very restrictive, requiring the loci to be strongly selected, tightly linked and distant from the sex-determining region. Epistatic interactions can facilitate the promotion of polymorphism among selected loci, but only if preferentially favoring heterozygotes. Although these results apply to any taxa, plants provide a fertile ground for testing these and related theories given the recurrent evolutionary transitions to dioecy, which provide multiple opportunities to track the early evolution of sex chromosomes.
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Affiliation(s)
- Sarah P Otto
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
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12
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Martin H, Carpentier F, Gallina S, Godé C, Schmitt E, Muyle A, Marais GAB, Touzet P. Evolution of Young Sex Chromosomes in Two Dioecious Sister Plant Species with Distinct Sex Determination Systems. Genome Biol Evol 2019; 11:350-361. [PMID: 30649306 PMCID: PMC6364797 DOI: 10.1093/gbe/evz001] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2019] [Indexed: 12/14/2022] Open
Abstract
In the last decade, progress has been made in methods to identify the sex determination system in plants. This gives the opportunity to study sex chromosomes that arose independently at different phylogenetic scales, and thus allows the discovery and the understanding of early stages of sex chromosome evolution. In the genus Silene, sex chromosomes have evolved independently in at least two clades from a nondioecious ancestor, the Melandrium and Otites sections. In the latter, sex chromosomes could be younger than in the section Melandrium, based on phylogenetic studies and as no heteromorphic sex chromosomes have been detected. This section might also exhibit lability in sex determination, because male heterogamy and female heterogamy have been suggested to occur. In this study, we investigated the sex determination system of two dioecious species in the section Otites (Silene otites and its close relative Silene pseudotites). Applying the new probabilistic method SEX-DETector on RNA-seq data from cross-controlled progenies, we inferred their most likely sex determination system and a list of putative autosomal and sex-linked contigs. We showed that the two phylogenetically close species differed in their sex determination system (XY versus ZW) with sex chromosomes that derived from two different pairs of autosomes. We built a genetic map of the sex chromosomes and showed that both pairs exhibited a large region with lack of recombination. However, the sex-limited chromosomes exhibited no strong degeneration. Finally, using the “ancestral” autosomal expression of sex-linked orthologs of nondioecious S. nutans, we found a slight signature of dosage compensation in the heterogametic females of S. otites.
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Affiliation(s)
- Hélène Martin
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, France.,Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Fantin Carpentier
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, France.,Ecologie Systématique Evolution, Université Paris Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | | | - Cécile Godé
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, France
| | - Eric Schmitt
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, France
| | - Aline Muyle
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France.,Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine
| | - Gabriel A B Marais
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
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13
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Charlesworth D. Evolution of recombination rates between sex chromosomes. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0456. [PMID: 29109220 DOI: 10.1098/rstb.2016.0456] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2017] [Indexed: 11/12/2022] Open
Abstract
In species with genetic sex-determination, the chromosomes carrying the sex-determining genes have often evolved non-recombining regions and subsequently evolved the full set of characteristics denoted by the term 'sex chromosomes'. These include size differences, creating chromosomal heteromorphism, and loss of gene functions from one member of the chromosome pair. Such characteristics and changes have been widely reviewed, and underlie molecular genetic approaches that can detect sex chromosome regions. This review deals mainly with the evolution of new non-recombining regions, focusing on how certain evolutionary situations select for suppressed recombination (rather than the proximate mechanisms causing suppressed recombination between sex chromosomes). Particularly important is the likely involvement of sexually antagonistic polymorphisms in genome regions closely linked to sex-determining loci. These may be responsible for the evolutionary strata of sex chromosomes that have repeatedly formed by recombination suppression evolving across large genome regions. More studies of recently evolved non-recombining sex-determining regions should help to test this hypothesis empirically, and may provide evidence about whether other situations can sometimes lead to sex-linked regions evolving. Similarities with other non-recombining genome regions are discussed briefly, to illustrate common features of the different cases, though no general properties apply to all of them.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratory, University of Edinburgh, King's Buildings, Edinburgh EH9 3FL, UK
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14
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Veltsos P, Cossard G, Beaudoing E, Beydon G, Savova Bianchi D, Roux C, C González-Martínez S, R Pannell J. Size and Content of the Sex-Determining Region of the Y Chromosome in Dioecious Mercurialis annua, a Plant with Homomorphic Sex Chromosomes. Genes (Basel) 2018; 9:E277. [PMID: 29844299 PMCID: PMC6027223 DOI: 10.3390/genes9060277] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/16/2018] [Accepted: 05/23/2018] [Indexed: 01/01/2023] Open
Abstract
Dioecious plants vary in whether their sex chromosomes are heteromorphic or homomorphic, but even homomorphic sex chromosomes may show divergence between homologues in the non-recombining, sex-determining region (SDR). Very little is known about the SDR of these species, which might represent particularly early stages of sex-chromosome evolution. Here, we assess the size and content of the SDR of the diploid dioecious herb Mercurialis annua, a species with homomorphic sex chromosomes and mild Y-chromosome degeneration. We used RNA sequencing (RNAseq) to identify new Y-linked markers for M. annua. Twelve of 24 transcripts showing male-specific expression in a previous experiment could be amplified by polymerase chain reaction (PCR) only from males, and are thus likely to be Y-linked. Analysis of genome-capture data from multiple populations of M. annua pointed to an additional six male-limited (and thus Y-linked) sequences. We used these markers to identify and sequence 17 sex-linked bacterial artificial chromosomes (BACs), which form 11 groups of non-overlapping sequences, covering a total sequence length of about 1.5 Mb. Content analysis of this region suggests that it is enriched for repeats, has low gene density, and contains few candidate sex-determining genes. The BACs map to a subset of the sex-linked region of the genetic map, which we estimate to be at least 14.5 Mb. This is substantially larger than estimates for other dioecious plants with homomorphic sex chromosomes, both in absolute terms and relative to their genome sizes. Our data provide a rare, high-resolution view of the homomorphic Y chromosome of a dioecious plant.
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Affiliation(s)
- Paris Veltsos
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
- Department of Biology, Jordan Hall, 1001 East Third Street, Indiana University, Bloomington, IN 47405, USA.
| | - Guillaume Cossard
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Emmanuel Beaudoing
- Faculty of Biology and Medicine, University of Lausanne, Bâtiment Génopode, 1014 Lausanne, Switzerland.
| | - Genséric Beydon
- National Centre for Genomic Resources (CNRGV), 24 Chemin de Borde Rouge-Auzeville-CS52627, 31326 Castanet Tolosan Cedex, France.
| | | | - Camille Roux
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
- CNRS, University of Lille, UMR 8198-Evo-Eco-Paleo, F-59000 Lille, France.
| | - Santiago C González-Martínez
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
- BIOGECO, INRA, University of Bordeaux, 33610 Cestas, France.
| | - John R Pannell
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
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15
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A Comparison of Selective Pressures in Plant X-Linked and Autosomal Genes. Genes (Basel) 2018; 9:genes9050234. [PMID: 29751495 PMCID: PMC5977174 DOI: 10.3390/genes9050234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 04/23/2018] [Accepted: 04/26/2018] [Indexed: 01/30/2023] Open
Abstract
Selection is expected to work differently in autosomal and X-linked genes because of their ploidy difference and the exposure of recessive X-linked mutations to haploid selection in males. However, it is not clear whether these expectations apply to recently evolved sex chromosomes, where many genes retain functional X- and Y-linked gametologs. We took advantage of the recently evolved sex chromosomes in the plant Silene latifolia and its closely related species to compare the selective pressures between hemizygous and non-hemizygous X-linked genes as well as between X-linked genes and autosomal genes. Our analysis, based on over 1000 genes, demonstrated that, similar to animals, X-linked genes in Silene evolve significantly faster than autosomal genes—the so-called faster-X effect. Contrary to expectations, faster-X divergence was detectable only for non-hemizygous X-linked genes. Our phylogeny-based analyses of selection revealed no evidence for faster adaptation in X-linked genes compared to autosomal genes. On the other hand, partial relaxation of purifying selection was apparent on the X-chromosome compared to the autosomes, consistent with a smaller genetic diversity in S. latifolia X-linked genes (πx = 0.016; πaut = 0.023). Thus, the faster-X divergence in S. latifolia appears to be a consequence of the smaller effective population size rather than of a faster adaptive evolution on the X-chromosome. We argue that this may be a general feature of “young” sex chromosomes, where the majority of X-linked genes are not hemizygous, preventing haploid selection in heterogametic sex.
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16
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Puterova J, Kubat Z, Kejnovsky E, Jesionek W, Cizkova J, Vyskot B, Hobza R. The slowdown of Y chromosome expansion in dioecious Silene latifolia due to DNA loss and male-specific silencing of retrotransposons. BMC Genomics 2018; 19:153. [PMID: 29458354 PMCID: PMC5819184 DOI: 10.1186/s12864-018-4547-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/13/2018] [Indexed: 11/10/2022] Open
Abstract
Background The rise and fall of the Y chromosome was demonstrated in animals but plants often possess the large evolutionarily young Y chromosome that is thought has expanded recently. Break-even points dividing expansion and shrinkage phase of plant Y chromosome evolution are still to be determined. To assess the size dynamics of the Y chromosome, we studied intraspecific genome size variation and genome composition of male and female individuals in a dioecious plant Silene latifolia, a well-established model for sex-chromosomes evolution. Results Our genome size data are the first to demonstrate that regardless of intraspecific genome size variation, Y chromosome has retained its size in S. latifolia. Bioinformatics study of genome composition showed that constancy of Y chromosome size was caused by Y chromosome DNA loss and the female-specific proliferation of recently active dominant retrotransposons. We show that several families of retrotransposons have contributed to genome size variation but not to Y chromosome size change. Conclusions Our results suggest that the large Y chromosome of S. latifolia has slowed down or stopped its expansion. Female-specific proliferation of retrotransposons, enlarging the genome with exception of the Y chromosome, was probably caused by silencing of highly active retrotransposons in males and represents an adaptive mechanism to suppress degenerative processes in the haploid stage. Sex specific silencing of transposons might be widespread in plants but hidden in traditional hermaphroditic model plants. Electronic supplementary material The online version of this article (10.1186/s12864-018-4547-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Janka Puterova
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 612 00, Brno, Czech Republic.,Department of Information Systems, Faculty of Information Technology, Brno University of Technology, 61200, Brno, Czech Republic
| | - Zdenek Kubat
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 612 00, Brno, Czech Republic.
| | - Eduard Kejnovsky
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 612 00, Brno, Czech Republic
| | - Wojciech Jesionek
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 612 00, Brno, Czech Republic
| | - Jana Cizkova
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Czech Academy of Sciences, 783 71, Olomouc - Holice, Czech Republic
| | - Boris Vyskot
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 612 00, Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 612 00, Brno, Czech Republic. .,Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Czech Academy of Sciences, 783 71, Olomouc - Holice, Czech Republic.
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17
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Wang W, Zhang X. Identification of the Sex-Biased Gene Expression and Putative Sex-Associated Genes in Eucommia ulmoides Oliver Using Comparative Transcriptome Analyses. Molecules 2017; 22:E2255. [PMID: 29258253 PMCID: PMC6149867 DOI: 10.3390/molecules22122255] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 11/29/2017] [Accepted: 12/14/2017] [Indexed: 12/04/2022] Open
Abstract
Eucommia ulmoides is a model representative of the dioecious plants with sex differentiation at initiation. Nevertheless, the genetic mechanisms of sexual dimorphism and sex determination in E. ulmoides remain poorly understood. In this study de novo transcriptome sequencing on Illumina platform generated >45 billion high-quality bases from fresh leaves of six male and female individuals of E. ulmoides. A total of 148,595 unigenes with an average length of 801 base-pairs (bp) were assembled. Through comparative transcriptome analyses, 116 differentially expressed genes (DEGs) between the males and the females were detected, including 73 male-biased genes and 43 female-biased genes. Of these DEGs, three female-biased genes were annotated to be related with the sexually dimorphic gutta content in E. ulmoides. One male-biased DEG was identified as putative MADS box gene APETALA3, a B class floral organ identity gene in the flowering plants. SNPs calling analyses further confirmed that the APETALA3-like gene was probably involved in the sex determination in E. ulmoides. Four other male-biased DEGs were potential sex-associated genes as well with segregated SNPs in accord with sex type. In addition, the SNPs density was 1.02 per kilobase (kb) in the expressed genes of E. ulmoides, implying a relatively high genetic diversity.
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Affiliation(s)
- Wencai Wang
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510000, China.
| | - Xianzhi Zhang
- Department of Forestry Protection, College of Forestry, Northwest A&F University, Yangling 712100, China.
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18
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Pratlong M, Haguenauer A, Chenesseau S, Brener K, Mitta G, Toulza E, Bonabaud M, Rialle S, Aurelle D, Pontarotti P. Evidence for a genetic sex determination in Cnidaria, the Mediterranean red coral ( Corallium rubrum). ROYAL SOCIETY OPEN SCIENCE 2017. [PMID: 28405374 DOI: 10.5061/dryad.rs7bm] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Sexual reproduction is widespread among eukaryotes, and the sex-determining processes vary greatly among species. While genetic sex determination (GSD) has been intensively described in bilaterian species, no example has yet been recorded among non-bilaterians. However, the quasi-ubiquitous repartition of GSD among multicellular species suggests that similar evolutionary forces can promote this system, and that these forces could occur also in non-bilaterians. Studying sex determination across the range of Metazoan diversity is indeed important to understand better the evolution of this mechanism and its lability. We tested the existence of sex-linked genes in the gonochoric red coral (Corallium rubrum, Cnidaria) using restriction site-associated DNA sequencing. We analysed 27 461 single nucleotide polymorphisms (SNPs) in 354 individuals from 12 populations including 53 that were morphologically sexed. We found a strong association between the allele frequencies of 472 SNPs and the sex of individuals, suggesting an XX/XY sex-determination system. This result was confirmed by the identification of 435 male-specific loci. An independent test confirmed that the amplification of these loci enabled us to identify males with absolute certainty. This is the first demonstration of a GSD system among non-bilaterian species and a new example of its convergence in multicellular eukaryotes.
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Affiliation(s)
- M Pratlong
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France; Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
| | - A Haguenauer
- Aix Marseille Univ, Avignon Université , CNRS, IRD, IMBE , Marseille , France
| | - S Chenesseau
- Aix Marseille Univ, Avignon Université , CNRS, IRD, IMBE , Marseille , France
| | - K Brener
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER , Montpellier Université , Perpignan , France
| | - G Mitta
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER , Montpellier Université , Perpignan , France
| | - E Toulza
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER , Montpellier Université , Perpignan , France
| | - M Bonabaud
- UMS BioCampus- MGX Montpellier GenomiX , Institut de Génomique Fonctionelle , 141 rue de la Cardonnille, 34094 Montpellier Cedex 05 , France
| | - S Rialle
- UMS BioCampus- MGX Montpellier GenomiX , Institut de Génomique Fonctionelle , 141 rue de la Cardonnille, 34094 Montpellier Cedex 05 , France
| | - D Aurelle
- Aix Marseille Univ, Avignon Université , CNRS, IRD, IMBE , Marseille , France
| | - P Pontarotti
- Aix Marseille Univ , CNRS, Centrale Marseille, I2M , Marseille , France
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19
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Pratlong M, Haguenauer A, Chenesseau S, Brener K, Mitta G, Toulza E, Bonabaud M, Rialle S, Aurelle D, Pontarotti P. Evidence for a genetic sex determination in Cnidaria, the Mediterranean red coral ( Corallium rubrum). ROYAL SOCIETY OPEN SCIENCE 2017; 4:160880. [PMID: 28405374 PMCID: PMC5383831 DOI: 10.1098/rsos.160880] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/01/2017] [Indexed: 05/29/2023]
Abstract
Sexual reproduction is widespread among eukaryotes, and the sex-determining processes vary greatly among species. While genetic sex determination (GSD) has been intensively described in bilaterian species, no example has yet been recorded among non-bilaterians. However, the quasi-ubiquitous repartition of GSD among multicellular species suggests that similar evolutionary forces can promote this system, and that these forces could occur also in non-bilaterians. Studying sex determination across the range of Metazoan diversity is indeed important to understand better the evolution of this mechanism and its lability. We tested the existence of sex-linked genes in the gonochoric red coral (Corallium rubrum, Cnidaria) using restriction site-associated DNA sequencing. We analysed 27 461 single nucleotide polymorphisms (SNPs) in 354 individuals from 12 populations including 53 that were morphologically sexed. We found a strong association between the allele frequencies of 472 SNPs and the sex of individuals, suggesting an XX/XY sex-determination system. This result was confirmed by the identification of 435 male-specific loci. An independent test confirmed that the amplification of these loci enabled us to identify males with absolute certainty. This is the first demonstration of a GSD system among non-bilaterian species and a new example of its convergence in multicellular eukaryotes.
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Affiliation(s)
- M. Pratlong
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
- Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
| | - A. Haguenauer
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
| | - S. Chenesseau
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
| | - K. Brener
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER, Montpellier Université, Perpignan, France
| | - G. Mitta
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER, Montpellier Université, Perpignan, France
| | - E. Toulza
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER, Montpellier Université, Perpignan, France
| | - M. Bonabaud
- UMS BioCampus- MGX Montpellier GenomiX, Institut de Génomique Fonctionelle, 141 rue de la Cardonnille, 34094 Montpellier Cedex 05, France
| | - S. Rialle
- UMS BioCampus- MGX Montpellier GenomiX, Institut de Génomique Fonctionelle, 141 rue de la Cardonnille, 34094 Montpellier Cedex 05, France
| | - D. Aurelle
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
| | - P. Pontarotti
- Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
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20
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Guirao-Rico S, Sánchez-Gracia A, Charlesworth D. Sequence diversity patterns suggesting balancing selection in partially sex-linked genes of the plant Silene latifolia are not generated by demographic history or gene flow. Mol Ecol 2017; 26:1357-1370. [PMID: 28035715 DOI: 10.1111/mec.13969] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 12/02/2016] [Accepted: 12/12/2016] [Indexed: 01/16/2023]
Abstract
DNA sequence diversity in genes in the partially sex-linked pseudoautosomal region (PAR) of the sex chromosomes of the plant Silene latifolia is higher than expected from within-species diversity of other genes. This could be the footprint of sexually antagonistic (SA) alleles that are maintained by balancing selection in a PAR gene (or genes) and affect polymorphism in linked genome regions. SA selection is predicted to occur during sex chromosome evolution, but it is important to test whether the unexpectedly high sequence polymorphism could be explained without it, purely by the combined effects of partial linkage with the sex-determining region and the population's demographic history, including possible introgression from Silene dioica. To test this, we applied approximate Bayesian computation-based model choice to autosomal sequence diversity data, to find the most plausible scenario for the recent history of S. latifolia and then to estimate the posterior density of the most relevant parameters. We then used these densities to simulate variation to be expected at PAR genes. We conclude that an excess of variants at high frequencies at PAR genes should arise in S. latifolia populations only for genes with strong associations with fully sex-linked genes, which requires closer linkage with the fully sex-linked region than that estimated for the PAR genes where apparent deviations from neutrality were observed. These results support the need to invoke selection to explain the S. latifolia PAR gene diversity, and encourage further work to test the possibility of balancing selection due to sexual antagonism.
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Affiliation(s)
- Sara Guirao-Rico
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JN, UK
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
| | - Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JN, UK
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21
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Campos JL, Qiu S, Guirao-Rico S, Bergero R, Charlesworth D. Recombination changes at the boundaries of fully and partially sex-linked regions between closely related Silene species pairs. Heredity (Edinb) 2016; 118:395-403. [PMID: 27827389 DOI: 10.1038/hdy.2016.113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/05/2016] [Accepted: 10/05/2016] [Indexed: 11/09/2022] Open
Abstract
The establishment of a region of suppressed recombination is a critical change during sex chromosome evolution, leading to such properties as Y (and W) chromosome genetic degeneration, accumulation of repetitive sequences and heteromorphism. Although chromosome inversions can cause large regions to have suppressed recombination, and inversions are sometimes involved in sex chromosome evolution, gradual expansion of the non-recombining region could potentially sometimes occur. We here test whether closer linkage has recently evolved between the sex-determining region and several genes that are partially sex-linked in Silene latifolia, using Silene dioica, a closely related dioecious plants whose XY sex chromosome system is inherited from a common ancestor. The S. latifolia pseudoautosomal region (PAR) includes several genes extremely closely linked to the fully Y-linked region. These genes were added to an ancestral PAR of the sex chromosome pair in two distinct events probably involving translocations of autosomal genome regions causing multiple genes to become partially sex-linked. Close linkage with the PAR boundary must have evolved since these additions, because some genes added in both events now show almost complete sex linkage in S. latifolia. We compared diversity patterns of five such S. latifolia PAR boundary genes with their orthologues in S. dioica, including all three regions of the PAR (one gene that was in the ancestral PAR and two from each of the added regions). The results suggest recent recombination suppression in S. latifolia, since its split from S. dioica.
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Affiliation(s)
- J L Campos
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - S Qiu
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - S Guirao-Rico
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - R Bergero
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - D Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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22
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Tennessen JA, Govindarajulu R, Liston A, Ashman T. Homomorphic ZW chromosomes in a wild strawberry show distinctive recombination heterogeneity but a small sex-determining region. THE NEW PHYTOLOGIST 2016; 211:1412-23. [PMID: 27102236 PMCID: PMC5074332 DOI: 10.1111/nph.13983] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 03/21/2016] [Indexed: 05/10/2023]
Abstract
Recombination in ancient, heteromorphic sex chromosomes is typically suppressed at the sex-determining region (SDR) and proportionally elevated in the pseudoautosomal region (PAR). However, little is known about recombination dynamics of young, homomorphic plant sex chromosomes. We examine male and female function in crosses and unrelated samples of the dioecious octoploid strawberry Fragaria chiloensis in order to map the small and recently evolved SDR controlling both traits and to examine recombination patterns on the incipient ZW chromosome. The SDR of this ZW system is located within a 280 kb window, in which the maternal recombination rate is lower than the paternal one. In contrast to the SDR, the maternal PAR recombination rate is much higher than the rates of the paternal PAR or autosomes, culminating in an elevated chromosome-wide rate. W-specific divergence is elevated within the SDR and a single polymorphism is observed in high species-wide linkage disequilibrium with sex. Selection for recombination suppression within the small SDR may be weak, but fluctuating sex ratios could favor elevated recombination in the PAR to remove deleterious mutations on the W. The recombination dynamics of this nascent sex chromosome with a modestly diverged SDR may be typical of other dioecious plants.
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Affiliation(s)
- Jacob A. Tennessen
- Department of Integrative BiologyOregon State UniversityCorvallisOR97331USA
| | | | - Aaron Liston
- Department of Botany and Plant PathologyOregon State UniversityCorvallisOR97331USA
| | - Tia‐Lynn Ashman
- Department of Biological SciencesUniversity of PittsburghPittsburghPA15260‐3929USA
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23
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Takahata S, Yago T, Iwabuchi K, Hirakawa H, Suzuki Y, Onodera Y. Comparison of Spinach Sex Chromosomes with Sugar Beet Autosomes Reveals Extensive Synteny and Low Recombination at the Male-Determining Locus. J Hered 2016; 107:679-685. [PMID: 27563071 DOI: 10.1093/jhered/esw055] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Accepted: 08/22/2016] [Indexed: 01/06/2023] Open
Abstract
Spinach (Spinacia oleracea, 2n = 12) and sugar beet (Beta vulgaris, 2n = 18) are important crop members of the family Chenopodiaceae ss Sugar beet has a basic chromosome number of 9 and a cosexual breeding system, as do most members of the Chenopodiaceae ss. family. By contrast, spinach has a basic chromosome number of 6 and, although certain cultivars and genotypes produce monoecious plants, is considered to be a dioecious species. The loci determining male and monoecious sexual expression were mapped to different loci on the spinach sex chromosomes. In this study, a linkage map with 46 mapped protein-coding sequences was constructed for the spinach sex chromosomes. Comparison of the linkage map with a reference genome sequence of sugar beet revealed that the spinach sex chromosomes exhibited extensive synteny with sugar beet chromosomes 4 and 9. Tightly linked protein-coding genes linked to the male-determining locus in spinach corresponded to genes located in or around the putative pericentromeric and centromeric regions of sugar beet chromosomes 4 and 9, supporting the observation that recombination rates were low in the vicinity of the male-determining locus. The locus for monoecism was confined to a chromosomal segment corresponding to a region of approximately 1.7Mb on sugar beet chromosome 9, which may facilitate future positional cloning of the locus.
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Affiliation(s)
- Satoshi Takahata
- From the Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Sapporo 060-8589, Japan (Takahata, Yago, Iwabuchi, and Onodera); the Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan (Hirakawa); and the Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8568, Japan (Suzuki)
| | - Takumi Yago
- From the Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Sapporo 060-8589, Japan (Takahata, Yago, Iwabuchi, and Onodera); the Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan (Hirakawa); and the Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8568, Japan (Suzuki)
| | - Keisuke Iwabuchi
- From the Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Sapporo 060-8589, Japan (Takahata, Yago, Iwabuchi, and Onodera); the Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan (Hirakawa); and the Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8568, Japan (Suzuki)
| | - Hideki Hirakawa
- From the Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Sapporo 060-8589, Japan (Takahata, Yago, Iwabuchi, and Onodera); the Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan (Hirakawa); and the Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8568, Japan (Suzuki)
| | - Yutaka Suzuki
- From the Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Sapporo 060-8589, Japan (Takahata, Yago, Iwabuchi, and Onodera); the Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan (Hirakawa); and the Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8568, Japan (Suzuki)
| | - Yasuyuki Onodera
- From the Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Sapporo 060-8589, Japan (Takahata, Yago, Iwabuchi, and Onodera); the Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan (Hirakawa); and the Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8568, Japan (Suzuki).
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24
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Bailey SF, Bataillon T. Can the experimental evolution programme help us elucidate the genetic basis of adaptation in nature? Mol Ecol 2016; 25:203-18. [PMID: 26346808 PMCID: PMC5019151 DOI: 10.1111/mec.13378] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 08/26/2015] [Accepted: 09/04/2015] [Indexed: 02/04/2023]
Abstract
There have been a variety of approaches taken to try to characterize and identify the genetic basis of adaptation in nature, spanning theoretical models, experimental evolution studies and direct tests of natural populations. Theoretical models can provide formalized and detailed hypotheses regarding evolutionary processes and patterns, from which experimental evolution studies can then provide important proofs of concepts and characterize what is biologically reasonable. Genetic and genomic data from natural populations then allow for the identification of the particular factors that have and continue to play an important role in shaping adaptive evolution in the natural world. Further to this, experimental evolution studies allow for tests of theories that may be difficult or impossible to test in natural populations for logistical and methodological reasons and can even generate new insights, suggesting further refinement of existing theories. However, as experimental evolution studies often take place in a very particular set of controlled conditions--that is simple environments, a small range of usually asexual species, relatively short timescales--the question remains as to how applicable these experimental results are to natural populations. In this review, we discuss important insights coming from experimental evolution, focusing on four key topics tied to the evolutionary genetics of adaptation, and within those topics, we discuss the extent to which the experimental work compliments and informs natural population studies. We finish by making suggestions for future work in particular a need for natural population genomic time series data, as well as the necessity for studies that combine both experimental evolution and natural population approaches.
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Affiliation(s)
- Susan F. Bailey
- Bioinformatics Research CentreAarhus UniversityC.F. Møllers Allé 8DK‐8000Aarhus CDenmark
| | - Thomas Bataillon
- Bioinformatics Research CentreAarhus UniversityC.F. Møllers Allé 8DK‐8000Aarhus CDenmark
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25
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Abstract
Background Silene latifolia represents one of the best-studied plant sex chromosome systems. A new approach using RNA-seq data has recently identified hundreds of new sex-linked genes in this species. However, this approach is expected to miss genes that are either not expressed or are expressed at low levels in the tissue(s) used for RNA-seq. Therefore other independent approaches are needed to discover such sex-linked genes. Results Here we used 10 well-characterized S. latifolia sex-linked genes and their homologs in Silene vulgaris, a species without sex chromosomes, to screen BAC libraries of both species. We isolated and sequenced 4 Mb of BAC clones of S. latifolia X and Y and S. vulgaris genomic regions, which yielded 59 new sex-linked genes (with S. vulgaris homologs for some of them). We assembled sequences that we believe represent the tip of the Xq arm. These sequences are clearly not pseudoautosomal, so we infer that the S. latifolia X has a single pseudoautosomal region (PAR) on the Xp arm. The estimated mean gene density in X BACs is 2.2 times lower than that in S. vulgaris BACs, agreeing with the genome size difference between these species. Gene density was estimated to be extremely low in the Y BAC clones. We compared our BAC-located genes with the sex-linked genes identified in previous RNA-seq studies, and found that about half of them (those with low expression in flower buds) were not identified as sex-linked in previous RNA-seq studies. We compiled a set of ~70 validated X/Y genes and X-hemizygous genes (without Y copies) from the literature, and used these genes to show that X-hemizygous genes have a higher probability of being undetected by the RNA-seq approach, compared with X/Y genes; we used this to estimate that about 30 % of our BAC-located genes must be X-hemizygous. The estimate is similar when we use BAC-located genes that have S. vulgaris homologs, which excludes genes that were gained by the X chromosome. Conclusions Our BAC sequencing identified 59 new sex-linked genes, and our analysis of these BAC-located genes, in combination with RNA-seq data suggests that gene losses from the S. latifolia Y chromosome could be as high as 30 %, higher than previous estimates of 10-20 %. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1698-7) contains supplementary material, which is available to authorized users.
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