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Hayashi S, Abe T, Igawa T, Katsura Y, Kazama Y, Nozawa M. Sex chromosome cycle as a mechanism of stable sex determination. J Biochem 2024; 176:81-95. [PMID: 38982631 PMCID: PMC11289310 DOI: 10.1093/jb/mvae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/27/2024] [Indexed: 07/11/2024] Open
Abstract
Recent advances in DNA sequencing technology have enabled the precise decoding of genomes in non-model organisms, providing a basis for unraveling the patterns and mechanisms of sex chromosome evolution. Studies of different species have yielded conflicting results regarding the traditional theory that sex chromosomes evolve from autosomes via the accumulation of deleterious mutations and degeneration of the Y (or W) chromosome. The concept of the 'sex chromosome cycle,' emerging from this context, posits that at any stage of the cycle (i.e., differentiation, degeneration, or loss), sex chromosome turnover can occur while maintaining stable sex determination. Thus, understanding the mechanisms that drive both the persistence and turnover of sex chromosomes at each stage of the cycle is crucial. In this review, we integrate recent findings on the mechanisms underlying maintenance and turnover, with a special focus on several organisms having unique sex chromosomes. Our review suggests that the diversity of sex chromosomes in the maintenance of stable sex determination is underappreciated and emphasizes the need for more research on the sex chromosome cycle.
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Affiliation(s)
- Shun Hayashi
- Amphibian Research Center, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Takuya Abe
- Division of Biochemistry, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aobaku, Sendai, Miyagi 981-8558, Japan
| | - Takeshi Igawa
- Amphibian Research Center, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Yukako Katsura
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, 41-2 Kanrin, Inuyama, Aichi 484-8506, Japan
| | - Yusuke Kazama
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Kenjojima, Matsuoka, Eiheiji, Fukui 910-1195, Japan
| | - Masafumi Nozawa
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0397, Japan
- Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0397, Japan
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2
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Khachaturyan M, Santer M, Reusch TBH, Dagan T. Heteroplasmy Is Rare in Plant Mitochondria Compared with Plastids despite Similar Mutation Rates. Mol Biol Evol 2024; 41:msae135. [PMID: 38934796 PMCID: PMC11245704 DOI: 10.1093/molbev/msae135] [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: 11/17/2023] [Revised: 06/11/2024] [Accepted: 06/20/2024] [Indexed: 06/28/2024] Open
Abstract
Plant cells harbor two membrane-bound organelles containing their own genetic material-plastids and mitochondria. Although the two organelles coexist and coevolve within the same plant cells, they differ in genome copy number, intracellular organization, and mode of segregation. How these attributes affect the time to fixation or, conversely, loss of neutral alleles is currently unresolved. Here, we show that mitochondria and plastids share the same mutation rate, yet plastid alleles remain in a heteroplasmic state significantly longer compared with mitochondrial alleles. By analyzing genetic variants across populations of the marine flowering plant Zostera marina and simulating organelle allele dynamics, we examine the determinants of allele segregation and allele fixation. Our results suggest that the bottlenecks on the cell population, e.g. during branching or seeding, and stratification of the meristematic tissue are important determinants of mitochondrial allele dynamics. Furthermore, we suggest that the prolonged plastid allele dynamics are due to a yet unknown active plastid partition mechanism. The dissimilarity between plastid and mitochondrial novel allele fixation at different levels of organization may manifest in differences in adaptation processes. Our study uncovers fundamental principles of organelle population genetics that are essential for further investigations of long-term evolution and molecular dating of divergence events.
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Affiliation(s)
- Marina Khachaturyan
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Institute of General Microbiology, University of Kiel, Kiel, Germany
| | - Mario Santer
- Institute of General Microbiology, University of Kiel, Kiel, Germany
| | - Thorsten B H Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Tal Dagan
- Institute of General Microbiology, University of Kiel, Kiel, Germany
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3
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Choi TY, Son DC, Oh A, Lee SR. Unveiling a potential threat to forest ecosystems: molecular diagnosis of Alliaria petiolata, a newly introduced alien plant in Korea. FRONTIERS IN PLANT SCIENCE 2024; 15:1395676. [PMID: 39011305 PMCID: PMC11246967 DOI: 10.3389/fpls.2024.1395676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 06/14/2024] [Indexed: 07/17/2024]
Abstract
Identifying stages of a species invasion in a new habitat (i.e., colonization, establishment, and landscape spread) and their primary determinants in biological invasion warrants attention, as it provides vital insights for preventing non-native species from becoming pervasive invaders. However, delineating invasion stages and their associated factors can pose significant challenges due to the ambiguous distinctions between these stages. Alliaria petiolata, one of the most noxious weeds in woodland habitats, has recently been introduced to Korea and observed in a few distant locations. Although the plant's spread has been relatively slow thus far, rapid spread is highly likely in the future, given the high invasive potential reported elsewhere. We indirectly diagnose the current status of A. petiolata invasion in Korea through the assessment of genetic diversity and phylogenetic inferences using genome-wide molecular markers and cytological data. We analyzed 86 individual samples collected from two native and six introduced populations, employing 1,172 SNPs. Our analysis estimated within- and among-population genetic diversity and included two clustering analyses. Furthermore, we investigated potential gene flow and reticulation events among the sampled populations. Our data unraveled that Korean garlic mustard exhibits a hexaploid ploidy level with two distinct chromosome numbers, 2n = 36 and 42. The extent of genetic diversity measured in Korean populations was comparable to that of native populations. Using genome-wide SNP data, we identified three distinct clusters with minor gene flow, while failing to detect indications of reticulation among Korean populations. Based on the multifaceted analyses, our study provides valuable insights into the colonization process and stressed the importance of closely monitoring A. petiolata populations in Korea.
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Affiliation(s)
- Tae-Young Choi
- Department of Biology Education, College of Education, Chosun University, Gwangju, Republic of Korea
| | - Dong Chan Son
- Division of Forest Biodiversity and Herbarium, Korea National Arboretum, Pocheon, Republic of Korea
| | - Ami Oh
- Department of Biology Education, College of Education, Chosun University, Gwangju, Republic of Korea
| | - Soo-Rang Lee
- Department of Biology Education, College of Education, Chosun University, Gwangju, Republic of Korea
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4
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Lee S, Choi T, Son D. Multiple introductions of divergent lineages and admixture conferred the high invasiveness in a widespread weed ( Hypochaeris radicata). Evol Appl 2024; 17:e13740. [PMID: 38911265 PMCID: PMC11192970 DOI: 10.1111/eva.13740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 05/21/2024] [Accepted: 05/27/2024] [Indexed: 06/25/2024] Open
Abstract
Biological invasion consists of spatially and temporally varying stages, accompanied by ecological and evolutionary changes. Understanding the genomics underlying invasion dynamics provides critical insights into the geographic sources and genetic diversity, contributing to successful invasions across space and time. Here, we used genomic data and model-based approaches to characterize the invasion dynamics of Hypochaeris radicata L., a noxious weed in Korea. Genetic diversity and assignment patterns were investigated using 3563 SNPs of 283 individuals sampled from 22 populations. We employed a coalescent-based simulation method to estimate demographic changes for each population and inferred colonization history using both phylogenetic and population genetic model-based approaches. Our data suggest that H. radicata has been repeatedly been introduced to Korea from multiple genetic sources within the last 50 years, experiencing weak population bottlenecks followed by subsequent population expansions. These findings highlight the potential for further range expansion, particularly in the presence of human-mediated dispersal. Our study represents the first population-level genomic research documenting the invasion dynamics of the successful worldwide invader, H. radicata, outside of Europe.
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Affiliation(s)
- Soo‐Rang Lee
- Department of Biology Education, College of EducationChosun UniversityGwangjuSouth Korea
| | - Tae‐Young Choi
- Department of Biology Education, College of EducationChosun UniversityGwangjuSouth Korea
| | - Dong‐Chan Son
- Division of Forest Biodiversity and HerbariumKorea National ArboretumPocheonKorea
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5
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Nevado B, Atchison GW, Bridges EL, Orzell S, Filatov D, Hughes CE. Pleistocene diversification of unifoliolate-leaved Lupinus (Leguminosae: Papilionoideae) in Florida. Mol Ecol 2024; 33:e17232. [PMID: 38205900 DOI: 10.1111/mec.17232] [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: 08/02/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 01/12/2024]
Abstract
The importance and prevalence of recent ice-age and post-glacial speciation and species diversification during the Pleistocene across many organismal groups and physiographic settings are well established. However, the extent to which Pleistocene diversification can be attributed to climatic oscillations and their effects on distribution ranges and population structure remains debatable. In this study, we use morphologic, geographic and genetic (RADseq) data to document Pleistocene speciation and intra-specific diversification of the unifoliolate-leaved clade of Florida Lupinus, a small group of species largely restricted to inland and coastal sand ridges across the Florida peninsula and panhandle. Phylogenetic and demographic analyses alongside morphological and geographic evidence suggest that recent speciation and intra-specific divergence within this clade were driven by a combination of non-adaptive allopatric divergence caused by edaphic niche conservatism and opportunities presented by the emergence of new post-glacial sand ridge habitats. These results highlight the central importance of even modest geographic isolation and short periods of allopatric divergence following range expansion in the emergence of new taxa and add to the growing evidence that Pleistocene climatic oscillations may contribute to rapid diversification in a myriad of physiographic settings. Furthermore, our results shed new light on long-standing taxonomic debate surrounding the number of species in the Florida unifoliate Lupinus clade providing support for recognition of five species and a set of intra-specific variants. The important conservation implications for the narrowly restricted, highly endangered species Lupinus aridorum, which we show to be genetically distinct from its sister species Lupinus westianus, are discussed.
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Affiliation(s)
- Bruno Nevado
- Faculty of Sciences, cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, University of Lisbon, Lisbon, Portugal
- Department of Animal Biology, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Guy W Atchison
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Edwin L Bridges
- Botanical and Ecological Consultant, Gig Harbor, Washington, USA
| | - Steve Orzell
- Avon Park Air Force Range, Avon Park, Florida, USA
| | | | - Colin E Hughes
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
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6
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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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7
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Wong ELY, Filatov DA. Pericentromeric recombination suppression and the 'large X effect' in plants. Sci Rep 2023; 13:21682. [PMID: 38066067 PMCID: PMC10709461 DOI: 10.1038/s41598-023-48870-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
X chromosome was reported to be a major contributor to isolation between closely related species-the 'large X' effect (LXE). The causes of LXE are not clear, but the leading theory is that it is caused by recessive species incompatibilities exposed in the phenotype due to the hemizygosity of X-linked genes in the heterogametic sex. However, the LXE was also reported in species with relatively recently evolved sex chromosomes where Y chromosome is not completely degenerate and X-linked genes are not hemizygous, such as the plant Silene latifolia. Recent genome sequencing and detailed genetic mapping in this species revealed a massive (> 330 Mb) non- or rarely-recombining pericentromeric region on the X chromosome (Xpr) that comprises ~ 90% of the chromosome and over 13% of the entire genome. If any of the Xpr genes are involved in species incompatibilities, this would oppose interspecific gene flow for other genes tightly linked in the Xpr. Here we test the hypothesis that the previously reported LXE in S. latifolia is caused by the lack of recombination on most of the X chromosome. Based on genome-wide analysis of DNA polymorphism and gene expression in S. latifolia and its close cross-compatible relative S. dioica, we report that the rarely-recombining regions represent a significant barrier for interspecific gene flow. We found little evidence for any additional factors contributing to the LXE, suggesting that extensive pericentromeric recombination suppression on the X-chromosome is the major if not the only cause of the LXE in S. latifolia and S. dioica.
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Affiliation(s)
- Edgar L Y Wong
- Department of Biology, University of Oxford, Oxford, UK
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
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8
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Fields PD, Weber MM, Waneka G, Broz AK, Sloan DB. Chromosome-Level Genome Assembly for the Angiosperm Silene conica. Genome Biol Evol 2023; 15:evad192. [PMID: 37862134 PMCID: PMC10630074 DOI: 10.1093/gbe/evad192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/28/2023] [Accepted: 10/16/2023] [Indexed: 10/22/2023] Open
Abstract
The angiosperm genus Silene has been the subject of extensive study in the field of ecology and evolution, but the availability of high-quality reference genome sequences has been limited for this group. Here, we report a chromosome-level assembly for the genome of Silene conica based on Pacific Bioscience HiFi, Hi-C, and Bionano technologies. The assembly produced 10 scaffolds (1 per chromosome) with a total length of 862 Mb and only ∼1% gap content. These results confirm previous observations that S. conica and its relatives have a reduced base chromosome number relative to the genus's ancestral state of 12. Silene conica has an exceptionally large mitochondrial genome (>11 Mb), predominantly consisting of sequence of unknown origins. Analysis of shared sequence content suggests that it is unlikely that transfer of nuclear DNA is the primary driver of this mitochondrial genome expansion. More generally, this assembly should provide a valuable resource for future genomic studies in Silene, including comparative analyses with related species that recently evolved sex chromosomes.
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Affiliation(s)
- Peter D Fields
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
- Mammalian Genetics, The Jackson Laboratory, Bar Harbor, Maine, USA
| | - Melody M Weber
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Gus Waneka
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
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9
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Fields PD, Weber MM, Waneka G, Broz AK, Sloan DB. Chromosome-level genome assembly for the angiosperm Silene conica. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.05.556365. [PMID: 37732249 PMCID: PMC10508779 DOI: 10.1101/2023.09.05.556365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The angiosperm genus Silene has been the subject of extensive study in the field of ecology and evolution, but the availability of high-quality reference genome sequences has been limited for this group. Here, we report a chromosome-level assembly for the genome of Silene conica based on PacBio HiFi, Hi-C and Bionano technologies. The assembly produced 10 scaffolds (one per chromosome) with a total length of 862 Mb and only ~1% gap content. These results confirm previous observations that S. conica and its relatives have a reduced base chromosome number relative to the genus's ancestral state of 12. Silene conica has an exceptionally large mitochondrial genome (>11 Mb), predominantly consisting of sequence of unknown origins. Analysis of shared sequence content suggests that it is unlikely that transfer of nuclear DNA is the primary driver of this mitochondrial genome expansion. More generally, this assembly should provide a valuable resource for future genomic studies in Silene, including comparative analyses with related species that recently evolved sex chromosomes. Significance Whole-genome sequences have been largely lacking for species in the genus Silene even though these flowering plants have been used for studying ecology, evolution, and genetics for over a century. Here, we address this gap by providing a high-quality nuclear genome assembly for S. conica, a species known to have greatly accelerated rates of sequence and structural divergence in its mitochondrial and plastid genomes. This resource will be valuable in understanding the coevolutionary interactions between nuclear and cytoplasmic genomes and in comparative analyses across this highly diverse genus.
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Affiliation(s)
- Peter D. Fields
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
- Mammalian Genetics, The Jackson Laboratory, Bar Harbor, Maine, USA
| | - Melody M. Weber
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Gus Waneka
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Amanda K. Broz
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
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10
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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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11
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Krasovec M, Hoshino M, Zheng M, Lipinska AP, Coelho SM. Low Spontaneous Mutation Rate in Complex Multicellular Eukaryotes with a Haploid-Diploid Life Cycle. Mol Biol Evol 2023; 40:msad105. [PMID: 37140022 PMCID: PMC10254074 DOI: 10.1093/molbev/msad105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/22/2023] [Accepted: 05/01/2023] [Indexed: 05/05/2023] Open
Abstract
The spontaneous mutation rate µ is a crucial parameter to understand evolution and biodiversity. Mutation rates are highly variable across species, suggesting that µ is susceptible to selection and drift and that species life cycle and life history may impact its evolution. In particular, asexual reproduction and haploid selection are expected to affect the mutation rate, but very little empirical data are available to test this expectation. Here, we sequence 30 genomes of a parent-offspring pedigree in the model brown alga Ectocarpus sp.7, and 137 genomes of an interspecific cross of the closely related brown alga Scytosiphon to have access to the spontaneous mutation rate of representative organisms of a complex multicellular eukaryotic lineage outside animals and plants, and to evaluate the potential impact of life cycle on the mutation rate. Brown algae alternate between a haploid and a diploid stage, both multicellular and free living, and utilize both sexual and asexual reproduction. They are, therefore, excellent models to empirically test expectations of the effect of asexual reproduction and haploid selection on mutation rate evolution. We estimate that Ectocarpus has a base substitution rate of µbs = 4.07 × 10-10 per site per generation, whereas the Scytosiphon interspecific cross had µbs = 1.22 × 10-9. Overall, our estimations suggest that these brown algae, despite being multicellular complex eukaryotes, have unusually low mutation rates. In Ectocarpus, effective population size (Ne) could not entirely explain the low µbs. We propose that the haploid-diploid life cycle, combined with extensive asexual reproduction, may be additional key drivers of the mutation rate in these organisms.
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Affiliation(s)
- Marc Krasovec
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Masakazu Hoshino
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Min Zheng
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Agnieszka P Lipinska
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Susana M Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
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12
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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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13
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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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14
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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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15
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Gramlich S, Liu X, Favre A, Buerkle CA, Karrenberg S. A polygenic architecture with habitat-dependent effects underlies ecological differentiation in Silene. THE NEW PHYTOLOGIST 2022; 235:1641-1652. [PMID: 35586969 PMCID: PMC9544174 DOI: 10.1111/nph.18260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 05/04/2022] [Indexed: 05/27/2023]
Abstract
Ecological differentiation can drive speciation but it is unclear how the genetic architecture of habitat-dependent fitness contributes to lineage divergence. We investigated the genetic architecture of cumulative flowering, a fitness component, in second-generation hybrids between Silene dioica and Silene latifolia transplanted into the natural habitat of each species. We used reduced-representation sequencing and Bayesian sparse linear mixed models (BSLMMs) to analyze the genetic control of cumulative flowering in each habitat. Our results point to a polygenic architecture of cumulative flowering. Allelic effects were mostly beneficial or deleterious in one habitat and neutral in the other. Positive-effect alleles often were derived from the native species, whereas negative-effect alleles, at other loci, tended to originate from the non-native species. We conclude that ecological differentiation is governed and maintained by many loci with small, habitat-dependent effects consistent with conditional neutrality. This pattern may result from differences in selection targets in the two habitats and from environmentally dependent deleterious load. Our results further suggest that selection for native alleles and against non-native alleles acts as a barrier to gene flow between species.
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Affiliation(s)
- Susanne Gramlich
- Department of Ecology and Genetics, Plant Ecology and EvolutionUppsala UniversityNorbyvägen 18D75267UppsalaSweden
| | - Xiaodong Liu
- Department of Ecology and Genetics, Plant Ecology and EvolutionUppsala UniversityNorbyvägen 18D75267UppsalaSweden
- Department of Biology, The Bioinformatics CenterUniversity of CopenhagenOle Maaløes Vej 52200CopenhagenDenmark
| | - Adrien Favre
- Senckenberg Research Institute and Natural History MuseumSenckenberganlage 2560325Frankfurt/MainGermany
| | - C. Alex Buerkle
- Department of BotanyUniversity of Wyoming1000 E. University AveLaramieWY82071USA
| | - Sophie Karrenberg
- Department of Ecology and Genetics, Plant Ecology and EvolutionUppsala UniversityNorbyvägen 18D75267UppsalaSweden
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16
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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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17
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Abstract
We discuss the genetic, demographic, and selective forces that are likely to be at play in restricting observed levels of DNA sequence variation in natural populations to a much smaller range of values than would be expected from the distribution of census population sizes alone-Lewontin's Paradox. While several processes that have previously been strongly emphasized must be involved, including the effects of direct selection and genetic hitchhiking, it seems unlikely that they are sufficient to explain this observation without contributions from other factors. We highlight a potentially important role for the less-appreciated contribution of population size change; specifically, the likelihood that many species and populations may be quite far from reaching the relatively high equilibrium diversity values that would be expected given their current census sizes.
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Affiliation(s)
- Brian Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
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18
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Mao Y, Cui X, Wang H, Qin X, Liu Y, Yin Y, Su X, Tang J, Wang F, Ma F, Duan N, Zhang D, Hu Y, Wang W, Wei S, Chen X, Mao Z, Chen X, Shen X. De novo assembly provides new insights into the evolution of Elaeagnus angustifolia L. PLANT METHODS 2022; 18:84. [PMID: 35717244 PMCID: PMC9206267 DOI: 10.1186/s13007-022-00915-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/26/2022] [Indexed: 05/04/2023]
Abstract
BACKGROUND Elaeagnus angustifolia L. is a deciduous tree in the family Elaeagnaceae. It is widely used to study abiotic stress tolerance in plants and to improve desertification-affected land because of its ability to withstand diverse types of environmental stress, such as drought, salt, cold, and wind. However, no studies have examined the mechanisms underlying the resistance of E. angustifolia to environmental stress and its adaptive evolution. METHODS Here, we used PacBio, Hi-C, resequencing, and RNA-seq to construct the genome and transcriptome of E. angustifolia and explore its adaptive evolution. RESULTS The reconstructed genome of E. angustifolia was 526.80 Mb, with a contig N50 of 12.60 Mb and estimated divergence time of 84.24 Mya. Gene family expansion and resequencing analyses showed that the evolution of E. angustifolia was closely related to environmental conditions. After exposure to salt stress, GO pathway analysis showed that new genes identified from the transcriptome were related to ATP-binding, metal ion binding, and nucleic acid binding. CONCLUSION The genome sequence of E. angustifolia could be used for comparative genomic analyses of Elaeagnaceae family members and could help elucidate the mechanisms underlying the response of E. angustifolia to drought, salt, cold, and wind stress. Generally, these results provide new insights that could be used to improve desertification-affected land.
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Affiliation(s)
- Yunfei Mao
- College of Horticultural Science and Engineering/State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Xueli Cui
- College of Horticultural Science and Engineering/State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Haiyan Wang
- College of Horticultural Science and Engineering/State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Xin Qin
- College of Horticultural Science and Engineering/State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Yangbo Liu
- College of Horticultural Science and Engineering/State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Yijun Yin
- College of Horticultural Science and Engineering/State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Xiafei Su
- College of Horticultural Science and Engineering/State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Juan Tang
- Biomarker Technologies Corporation, Beijing, China
| | | | - Fengwang Ma
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
| | - Naibin Duan
- Germplasm Resource Center of Shandong Province, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Donglin Zhang
- Department of Horticulture, University of Georgia, Athens, USA
| | - Yanli Hu
- College of Horticultural Science and Engineering/State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Wenli Wang
- College of Horticultural Science and Engineering/State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Shaochong Wei
- College of Horticultural Science and Engineering/State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Xiaoliu Chen
- College of Horticultural Science and Engineering/State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Zhiquan Mao
- College of Horticultural Science and Engineering/State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Xuesen Chen
- College of Horticultural Science and Engineering/State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Xiang Shen
- College of Horticultural Science and Engineering/State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China.
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19
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Delph LF, Brown KE, Ríos LD, Kelly JK. Sex‐specific natural selection on SNPs in
Silene latifolia. Evol Lett 2022; 6:308-318. [PMID: 35937470 PMCID: PMC9346077 DOI: 10.1002/evl3.283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 02/24/2022] [Accepted: 03/13/2022] [Indexed: 01/15/2023] Open
Affiliation(s)
- Lynda F. Delph
- Department of Biology Indiana University Bloomington Indiana USA
| | - Keely E. Brown
- Department of Ecology and Evolutionary Biology University of Kansas Lawrence Kansas USA
| | - Luis Diego Ríos
- Department of Biology Indiana University Bloomington Indiana USA
| | - John K. Kelly
- Department of Ecology and Evolutionary Biology University of Kansas Lawrence Kansas USA
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20
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Carey SB, Lovell JT, Jenkins J, Leebens-Mack J, Schmutz J, Wilson MA, Harkess A. Representing sex chromosomes in genome assemblies. CELL GENOMICS 2022; 2. [PMID: 35720975 PMCID: PMC9205529 DOI: 10.1016/j.xgen.2022.100132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Sex chromosomes have evolved hundreds of independent times across eukaryotes. As genome sequencing, assembly, and scaffolding techniques rapidly improve, it is now feasible to build fully phased sex chromosome assemblies. Despite technological advances enabling phased assembly of whole chromosomes, there are currently no standards for representing sex chromosomes when publicly releasing a genome. Furthermore, most computational analysis tools are unable to efficiently investigate their unique biology relative to autosomes. We discuss a diversity of sex chromosome systems and consider the challenges of representing sex chromosome pairs in genome assemblies. By addressing these issues now as technologies for full phasing of chromosomal assemblies are maturing, we can collectively ensure that future genome analysis toolkits can be broadly applied to all eukaryotes with diverse types of sex chromosome systems. Here we provide best practice guidelines for presenting a genome assembly that contains sex chromosomes. These guidelines can also be applied to other non-recombining genomic regions, such as S-loci in plants and mating-type loci in fungi and algae.
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Affiliation(s)
- Sarah B Carey
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - John T Lovell
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.,US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Melissa A Wilson
- School of Life Sciences, Center for Evolution and Medicine, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Alex Harkess
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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21
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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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22
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Carey SB, Aközbek L, Harkess A. The contributions of Nettie Stevens to the field of sex chromosome biology. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210215. [PMID: 35306894 PMCID: PMC8941642 DOI: 10.1098/rstb.2021.0215] [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: 12/31/2022] Open
Abstract
The early 1900s delivered many foundational discoveries in genetics, including re-discovery of Mendel's research and the chromosomal theory of inheritance. Following these insights, many focused their research on whether the development of separate sexes had a chromosomal basis or if instead it was caused by environmental factors. It is Dr Nettie M. Stevens' Studies in spermatogenesis (1905) that provided the unequivocal evidence that the inheritance of the Y chromosome initiated male development in mealworms. This result established that sex is indeed a Mendelian trait with a genetic basis and that the sex chromosomes play a critical role. In Part II of Studies in spermatogenesis (1906), an XY pair was identified in dozens of additional species, further validating the function of sex chromosomes. Since this formative work, a wealth of studies in animals and plants have examined the genetic basis of sex. The goal of this review is to shine a light again on Stevens’ Studies in spermatogenesis and the lasting impact of this work. We additionally focus on key findings in plant systems over the last century and open questions that are best answered, as in Stevens' work, by synthesizing across many systems. This article is part of the theme issue ‘Sex determination and sex chromosome evolution in land plants’.
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Affiliation(s)
- Sarah B Carey
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Laramie Aközbek
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Alex Harkess
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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23
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Käfer J, Méndez M, Mousset S. Labile sex expression in angiosperm species with sex chromosomes. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210216. [PMID: 35306891 PMCID: PMC8935303 DOI: 10.1098/rstb.2021.0216] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/26/2022] [Indexed: 12/18/2022] Open
Abstract
Here, we review the literature on sexual lability in dioecious angiosperm species with well-studied sex chromosomes. We distinguish three types of departures from strict dioecy, concerning either a minority of flowers in some individuals (leakiness) or the entire individual, which can constantly be bisexual or change sex. We found that for only four of the 22 species studied, reports of lability are lacking. The occurrence of lability is only weakly related to sex chromosome characteristics (number of sex-linked genes, age of the non-recombining region). These results contradict the naive idea that lability is an indication of the absence or the recent evolution of sex chromosomes, and thereby contribute to a growing consensus that sex chromosomes do not necessarily fix sex determination once and for all. We discuss some implications of these findings for the evolution of sex chromosomes, and suggest that more species with well-characterized lability should be studied with genomic data and tools. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.
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Affiliation(s)
- Jos Käfer
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS UMR 5558, 69622 Villeurbanne, France
- CESAB–FRB, 34000 Montpellier, France
| | - Marcos Méndez
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Tulipán s/n, 28933 Móstoles (Madrid), Spain
| | - Sylvain Mousset
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS UMR 5558, 69622 Villeurbanne, France
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24
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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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/06/2021] [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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25
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New Geometric Models for Shape Quantification of the Dorsal View in Seeds of Silene Species. PLANTS 2022; 11:plants11070958. [PMID: 35406938 PMCID: PMC9002935 DOI: 10.3390/plants11070958] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 11/23/2022]
Abstract
The description of shape in Silene seeds is based on adjectives coined by naturalists in the 19th century. The expressions reniform, dorso plana, and dorso canaliculata were applied in reference to lateral or dorsal views of seeds, but the characters described can be submitted now to an analytical description by quantitative methods, allowing shape quantification and the comparison between species or populations. A quantitative morphological analysis is based on the comparison with geometric models that adjust to the shape of seeds. Morphological analysis of the dorsal view of Silene seeds based on geometric models is applied here to 26 seed populations belonging to 12 species. According to their dorsal views, the seeds are classified as convex and non-convex. New geometric models are presented for both types, including figures such as super-ellipses and modified ellipses. The values of J index (percent of similarity of a seed image with the model) are obtained in representative seed samples from diverse populations and species. The quantitative description of seed shape based on the comparison with geometric models allows the study of variation in shape between species and in populations, as well as the identification of seeds in Silene species. The method is of application to other plant species.
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26
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Carpentier F, Rodríguez de la Vega RC, Jay P, Duhamel M, Shykoff JA, Perlin MH, Wallen RM, Hood ME, Giraud T. Tempo of degeneration across independently evolved non-recombining regions. Mol Biol Evol 2022; 39:6553583. [PMID: 35325190 PMCID: PMC9004411 DOI: 10.1093/molbev/msac060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Recombination is beneficial over the long term, allowing more effective selection. Despite long-term advantages of recombination, local recombination suppression can evolve and lead to genomic degeneration, in particular on sex chromosomes. Here, we investigated the tempo of degeneration in nonrecombining regions, that is, the function curve for the accumulation of deleterious mutations over time, leveraging on 22 independent events of recombination suppression identified on mating-type chromosomes of anther-smut fungi, including newly identified ones. Using previously available and newly generated high-quality genome assemblies of alternative mating types of 13 Microbotryum species, we estimated degeneration levels in terms of accumulation of nonoptimal codons and nonsynonymous substitutions in nonrecombining regions. We found a reduced frequency of optimal codons in the nonrecombining regions compared with autosomes, that was not due to less frequent GC-biased gene conversion or lower ancestral expression levels compared with recombining regions. The frequency of optimal codons rapidly decreased following recombination suppression and reached an asymptote after ca. 3 Ma. The strength of purifying selection remained virtually constant at dN/dS = 0.55, that is, at an intermediate level between purifying selection and neutral evolution. Accordingly, nonsynonymous differences between mating-type chromosomes increased linearly with stratum age, at a rate of 0.015 per My. We thus develop a method for disentangling effects of reduced selection efficacy from GC-biased gene conversion in the evolution of codon usage and we quantify the tempo of degeneration in nonrecombining regions, which is important for our knowledge on genomic evolution and on the maintenance of regions without recombination.
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Affiliation(s)
- Fantin Carpentier
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
- Université de Lille, CNRS, UMR 8198-Evo-Eco-Paleo F-59000, Lille, France
| | - Ricardo C. Rodríguez de la Vega
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
- Corresponding authors: E-mails: ;
| | - Paul Jay
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
| | - Marine Duhamel
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
- Evolution der Pflanzen und Pilze, Ruhr-Universität Bochum, Universitätsstraße 150, 44780, Bochum, Germany
| | - Jacqui A. Shykoff
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
| | - Michael H. Perlin
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY 40292, USA
| | - R. Margaret Wallen
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY 40292, USA
| | | | - Tatiana Giraud
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
- Corresponding authors: E-mails: ;
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Masuda K, Ikeda Y, Matsuura T, Kawakatsu T, Tao R, Kubo Y, Ushijima K, Henry IM, Akagi T. Reinvention of hermaphroditism via activation of a RADIALIS-like gene in hexaploid persimmon. NATURE PLANTS 2022; 8:217-224. [PMID: 35301445 DOI: 10.1038/s41477-022-01107-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 02/10/2022] [Indexed: 05/29/2023]
Abstract
In flowering plants, different lineages have independently transitioned from the ancestral hermaphroditic state into and out of various sexual systems1. Polyploidizations are often associated with this plasticity in sexual systems2,3. Persimmons (the genus Diospyros) have evolved dioecy via lineage-specific palaeoploidizations. More recently, hexaploid D. kaki has established monoecy and also exhibits reversions from male to hermaphrodite flowers in response to natural environmental signals (natural hermaphroditism, NH), or to artificial cytokinin treatment (artificial hermaphroditism, AH). We sought to identify the molecular pathways underlying these polyploid-specific reversions to hermaphroditism. Co-expression network analyses identified regulatory pathways specific to NH or AH transitions. Surprisingly, the two pathways appeared to be antagonistic, with abscisic acid and cytokinin signalling for NH and AH, respectively. Among the genes common to both pathways leading to hermaphroditic flowers, we identified a small-Myb RADIALIS-like gene, named DkRAD, which is specifically activated in hexaploid D. kaki. Consistently, ectopic overexpression of DkRAD in two model plants resulted in hypergrowth of the gynoecium. These results suggest that production of hermaphrodite flowers via polyploidization depends on DkRAD activation, which is not associated with a loss-of-function within the existing sex determination pathway, but rather represents a new path to (or reinvention of) hermaphroditism.
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Affiliation(s)
- Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Yoko Ikeda
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Takakazu Matsuura
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Taiji Kawakatsu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yasutaka Kubo
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Koichiro Ushijima
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Isabelle M Henry
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA, USA
| | - Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
- JST-PRESTO, Saitama, Japan.
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28
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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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29
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Coelho SM, Umen J. Switching it up: algal insights into sexual transitions. PLANT REPRODUCTION 2021; 34:287-296. [PMID: 34181073 PMCID: PMC8566403 DOI: 10.1007/s00497-021-00417-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/02/2021] [Indexed: 05/03/2023]
Abstract
While the process of meiosis is highly conserved across eukaryotes, the sexual systems that govern life cycle phase transitions are surprisingly labile. Switches between sexual systems have profound evolutionary and ecological consequences, in particular for plants, but our understanding of the fundamental mechanisms and ultimate causes underlying these transitions is still surprisingly incomplete. We explore here the idea that brown and green algae may be interesting comparative models that can increase our understanding of relevant processes in plant reproductive biology, from evolution of gamete dimorphism, gametogenesis, sex determination and transitions in sex-determining systems.
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Affiliation(s)
- Susana M Coelho
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
| | - James Umen
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
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30
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Mattick J, Libro S, Bromley R, Chaicumpa W, Chung M, Cook D, Khan MB, Kumar N, Lau YL, Misra-Bhattacharya S, Rao R, Sadzewicz L, Saeung A, Shahab M, Sparklin BC, Steven A, Turner JD, Tallon LJ, Taylor MJ, Moorhead AR, Michalski M, Foster JM, Dunning Hotopp JC. X-treme loss of sequence diversity linked to neo-X chromosomes in filarial nematodes. PLoS Negl Trop Dis 2021; 15:e0009838. [PMID: 34705823 PMCID: PMC8575316 DOI: 10.1371/journal.pntd.0009838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 11/08/2021] [Accepted: 09/24/2021] [Indexed: 11/19/2022] Open
Abstract
The sequence diversity of natural and laboratory populations of Brugia pahangi and Brugia malayi was assessed with Illumina resequencing followed by mapping in order to identify single nucleotide variants and insertions/deletions. In natural and laboratory Brugia populations, there is a lack of sequence diversity on chromosome X relative to the autosomes (πX/πA = 0.2), which is lower than the expected (πX/πA = 0.75). A reduction in diversity is also observed in other filarial nematodes with neo-X chromosome fusions in the genera Onchocerca and Wuchereria, but not those without neo-X chromosome fusions in the genera Loa and Dirofilaria. In the species with neo-X chromosome fusions, chromosome X is abnormally large, containing a third of the genetic material such that a sizable portion of the genome is lacking sequence diversity. Such profound differences in genetic diversity can be consequential, having been associated with drug resistance and adaptability, with the potential to affect filarial eradication.
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Affiliation(s)
- John Mattick
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
| | - Silvia Libro
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Robin Bromley
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
| | - Wanpen Chaicumpa
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Matthew Chung
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
| | - Darren Cook
- Centre for Neglected Tropical Diseases, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Mohammad Behram Khan
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Nikhil Kumar
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
| | - Yee-Ling Lau
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Ramakrishna Rao
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Lisa Sadzewicz
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
| | - Atiporn Saeung
- Center of Insect Vector Study, Department of Parasitology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Mohd Shahab
- Division of Parasitology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Benjamin C. Sparklin
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
| | - Andrew Steven
- Centre for Neglected Tropical Diseases, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Joseph D. Turner
- Centre for Neglected Tropical Diseases, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Luke J. Tallon
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
| | - Mark J. Taylor
- Centre for Neglected Tropical Diseases, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Andrew R. Moorhead
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Michelle Michalski
- University of Wisconsin Oshkosh, Oshkosh, Wisconsin, United States of America
| | - Jeremy M. Foster
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Julie C. Dunning Hotopp
- Institute for Genome Science, University of Maryland, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland, Baltimore, Maryland, United States of America
- Greenebaum Cancer Center, University of Maryland, Baltimore, Maryland, United States of America
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31
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Warren JM, Salinas-Giegé T, Triant DA, Taylor DR, Drouard L, Sloan DB. Rapid shifts in mitochondrial tRNA import in a plant lineage with extensive mitochondrial tRNA gene loss. Mol Biol Evol 2021; 38:5735-5751. [PMID: 34436590 PMCID: PMC8662596 DOI: 10.1093/molbev/msab255] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In most eukaryotes, transfer RNAs (tRNAs) are one of the very few classes of genes remaining in the mitochondrial genome, but some mitochondria have lost these vestiges of their prokaryotic ancestry. Sequencing of mitogenomes from the flowering plant genus Silene previously revealed a large range in tRNA gene content, suggesting rapid and ongoing gene loss/replacement. Here, we use this system to test longstanding hypotheses about how mitochondrial tRNA genes are replaced by importing nuclear-encoded tRNAs. We traced the evolutionary history of these gene loss events by sequencing mitochondrial genomes from key outgroups (Agrostemma githago and Silene [=Lychnis] chalcedonica). We then performed the first global sequencing of purified plant mitochondrial tRNA populations to characterize the expression of mitochondrial-encoded tRNAs and the identity of imported nuclear-encoded tRNAs. We also confirmed the utility of high-throughput sequencing methods for the detection of tRNA import by sequencing mitochondrial tRNA populations in a species (Solanum tuberosum) with known tRNA trafficking patterns. Mitochondrial tRNA sequencing in Silene revealed substantial shifts in the abundance of some nuclear-encoded tRNAs in conjunction with their recent history of mt-tRNA gene loss and surprising cases where tRNAs with anticodons still encoded in the mitochondrial genome also appeared to be imported. These data suggest that nuclear-encoded counterparts are likely replacing mitochondrial tRNAs even in systems with recent mitochondrial tRNA gene loss, and the redundant import of a nuclear-encoded tRNA may provide a mechanism for functional replacement between translation systems separated by billions of years of evolutionary divergence.
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Affiliation(s)
- Jessica M Warren
- Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA
| | - Thalia Salinas-Giegé
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, Strasbourg, F-67084, France
| | - Deborah A Triant
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Douglas R Taylor
- Department of Biology, University of Virginia, Charlottesville, VA, 22904-4328, USA
| | - Laurence Drouard
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, Strasbourg, F-67084, France
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA
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32
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Papadopulos AST, Helmstetter AJ, Osborne OG, Comeault AA, Wood DP, Straw EA, Mason L, Fay MF, Parker J, Dunning LT, Foote AD, Smith RJ, Lighten J. Rapid Parallel Adaptation to Anthropogenic Heavy Metal Pollution. Mol Biol Evol 2021; 38:3724-3736. [PMID: 33950261 PMCID: PMC8382892 DOI: 10.1093/molbev/msab141] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The impact of human-mediated environmental change on the evolutionary trajectories of wild organisms is poorly understood. In particular, capacity of species to adapt rapidly (in hundreds of generations or less), reproducibly and predictably to extreme environmental change is unclear. Silene uniflora is predominantly a coastal species, but it has also colonized isolated, disused mines with phytotoxic, zinc-contaminated soils. To test whether rapid, parallel adaptation to anthropogenic pollution has taken place, we used reduced representation sequencing (ddRAD) to reconstruct the evolutionary history of geographically proximate mine and coastal population pairs and found largely independent colonization of mines from different coastal sites. Furthermore, our results show that parallel evolution of zinc tolerance has occurred without gene flow spreading adaptive alleles between mine populations. In genomic regions where signatures of selection were detected across multiple mine-coast pairs, we identified genes with functions linked to physiological differences between the putative ecotypes, although genetic differentiation at specific loci is only partially shared between mine populations. Our results are consistent with a complex, polygenic genetic architecture underpinning rapid adaptation. This shows that even under a scenario of strong selection and rapid adaptation, evolutionary responses to human activities (and other environmental challenges) may be idiosyncratic at the genetic level and, therefore, difficult to predict from genomic data.
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Affiliation(s)
- Alexander S T Papadopulos
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Andrew J Helmstetter
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- FRB-CESAB, Institut Bouisson Bertrand, Rue de l'École de Médecine, Montpellier, France
| | - Owen G Osborne
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Aaron A Comeault
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Daniel P Wood
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Edward A Straw
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Centre for Ecology, Evolution & Behaviour, Department of Biological Sciences, School for Life Sciences and the Environment, Royal Holloway University of London, Egham, United Kingdom
| | | | - Michael F Fay
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- School of Plant Biology, University of Western Australia, Crawley, WA, Australia
| | - Joe Parker
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- National Biofilms Innovation Centre, Department of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Luke T Dunning
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Andrew D Foote
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Department of Natural History, Norwegian University of Science and Technology, NTNU University Museum, Trondheim, Norway
| | - Rhian J Smith
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Jackie Lighten
- Biosciences, University of Exeter, Exeter, United Kingdom
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33
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Williams AM, Itgen MW, Broz AK, Carter OG, Sloan DB. Long-read transcriptome and other genomic resources for the angiosperm Silene noctiflora. G3 (BETHESDA, MD.) 2021; 11:jkab189. [PMID: 34849814 PMCID: PMC8496259 DOI: 10.1093/g3journal/jkab189] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/20/2021] [Indexed: 01/04/2023]
Abstract
The angiosperm genus Silene is a model system for several traits of ecological and evolutionary significance in plants, including breeding system and sex chromosome evolution, host-pathogen interactions, invasive species biology, heavy metal tolerance, and cytonuclear interactions. Despite its importance, genomic resources for this large genus of approximately 850 species are scarce, with only one published whole-genome sequence (from the dioecious species Silene latifolia). Here, we provide genomic and transcriptomic resources for a hermaphroditic representative of this genus (S. noctiflora), including a PacBio Iso-Seq transcriptome, which uses long-read, single-molecule sequencing technology to analyze full-length mRNA transcripts. Using these data, we have assembled and annotated high-quality full-length cDNA sequences for approximately 14,126 S. noctiflora genes and 25,317 isoforms. We demonstrated the utility of these data to distinguish between recent and highly similar gene duplicates by identifying novel paralogous genes in an essential protease complex. Furthermore, we provide a draft assembly for the approximately 2.7-Gb genome of this species, which is near the upper range of genome-size values reported for diploids in this genus and threefold larger than the 0.9-Gb genome of Silene conica, another species in the same subgenus. Karyotyping confirmed that S. noctiflora is a diploid, indicating that its large genome size is not due to polyploidization. These resources should facilitate further study and development of this genus as a model in plant ecology and evolution.
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Affiliation(s)
- Alissa M Williams
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO 80523, USA
| | - Michael W Itgen
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Olivia G Carter
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
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34
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Prentout D, Stajner N, Cerenak A, Tricou T, Brochier-Armanet C, Jakse J, Käfer J, Marais GAB. Plant genera Cannabis and Humulus share the same pair of well-differentiated sex chromosomes. THE NEW PHYTOLOGIST 2021; 231:1599-1611. [PMID: 33978992 DOI: 10.1111/nph.17456] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
We recently described, in Cannabis sativa, the oldest sex chromosome system documented so far in plants (12-28 Myr old). Based on the estimated age, we predicted that it should be shared by its sister genus Humulus, which is known also to possess XY chromosomes. Here, we used transcriptome sequencing of an F1 family of H. lupulus to identify and study the sex chromosomes in this species using the probabilistic method SEX-DETector. We identified 265 sex-linked genes in H. lupulus, which preferentially mapped to the C. sativa X chromosome. Using phylogenies of sex-linked genes, we showed that a region of the sex chromosomes had already stopped recombining in an ancestor of both species. Furthermore, as in C. sativa, Y-linked gene expression reduction is correlated to the position on the X chromosome, and highly Y degenerated genes showed dosage compensation. We report, for the first time in Angiosperms, a sex chromosome system that is shared by two different genera. Thus, recombination suppression started at least 21-25 Myr ago, and then (either gradually or step-wise) spread to a large part of the sex chromosomes (c. 70%), leading to a degenerated Y chromosome.
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Affiliation(s)
- Djivan Prentout
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, F-69622, France
| | - Natasa Stajner
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana, SI-1000, Slovenia
| | - Andreja Cerenak
- Slovenian Institute of Hop Research and Brewing, Cesta Zalskega Tabora 2, Zalec, SI-3310, Slovenia
| | - Theo Tricou
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, F-69622, France
| | - Celine Brochier-Armanet
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, F-69622, France
| | - Jernej Jakse
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana, SI-1000, Slovenia
| | - Jos Käfer
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, F-69622, France
| | - Gabriel A B Marais
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, F-69622, France
- LEAF- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, 1349-017, Portugal
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35
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Wang Z, Zhang J, Xu X, Witt C, Deng Y, Chen G, Meng G, Feng S, Xu L, Szekely T, Zhang G, Zhou Q. Phylogeny and sex chromosome evolution of palaeognathae. J Genet Genomics 2021; 49:109-119. [PMID: 34872841 DOI: 10.1016/j.jgg.2021.06.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 06/10/2021] [Accepted: 06/17/2021] [Indexed: 12/30/2022]
Abstract
Many paleognaths (ratites and tinamous) have a pair of homomorphic ZW sex chromosomes in contrast to the highly differentiated sex chromosomes of most other birds. To understand the evolutionary causes for the different tempos of sex chromosome evolution, we produced female genomes of 12 paleognathous species and reconstructed the phylogeny and the evolutionary history of paleognathous sex chromosomes. We uncovered that Palaeognathae sex chromosomes had undergone stepwise recombination suppression and formed a pattern of "evolutionary strata". Nine of the 15 studied species' sex chromosomes have maintained homologous recombination in their long pseudoautosomal regions extending more than half of the entire chromosome length. We found that in older strata, the W chromosome suffered more serious functional gene loss. Their homologous Z-linked regions, compared with other genomic regions, have produced an excess of species-specific autosomal duplicated genes that evolved female-specific expression, in contrast to their broadly expressed progenitors. We speculate the "defeminization" of Z chromosome with underrepresentation of female-biased genes and slow divergence of sex chromosomes of paleognaths might be related to their distinctive mode of sexual selection targeting females that evolved in their common ancestors.
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Affiliation(s)
- 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, Zhejiang 310058, China; Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1090, Austria; Institute of Animal Sex and Development, Zhejiang Wanli University, Ningbo, Zhejiang 315100, China; BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Jilin Zhang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Xiaoman Xu
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Christopher Witt
- Department of Biology and the Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Yuan Deng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Guangji Chen
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Guanliang Meng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Shaohong Feng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Luohao Xu
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1090, Austria
| | - Tamas Szekely
- State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Milner Center for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA1 7AY, UK
| | - Guojie Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1090, Austria; Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, China.
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36
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Krasovec M, Rickaby REM, Filatov DA. Evolution of Mutation Rate in Astronomically Large Phytoplankton Populations. Genome Biol Evol 2021; 12:1051-1059. [PMID: 32645145 PMCID: PMC7486954 DOI: 10.1093/gbe/evaa131] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2020] [Indexed: 02/06/2023] Open
Abstract
Genetic diversity is expected to be proportional to population size, yet, there is a well-known, but unexplained lack of genetic diversity in large populations-the "Lewontin's paradox." Larger populations are expected to evolve lower mutation rates, which may help to explain this paradox. Here, we test this conjecture by measuring the spontaneous mutation rate in a ubiquitous unicellular marine phytoplankton species Emiliania huxleyi (Haptophyta) that has modest genetic diversity despite an astronomically large population size. Genome sequencing of E. huxleyi mutation accumulation lines revealed 455 mutations, with an unusual GC-biased mutation spectrum. This yielded an estimate of the per site mutation rate µ = 5.55×10-10 (CI 95%: 5.05×10-10 - 6.09×10-10), which corresponds to an effective population size Ne ∼ 2.7×106. Such a modest Ne is surprising for a ubiquitous and abundant species that accounts for up to 10% of global primary productivity in the oceans. Our results indicate that even exceptionally large populations do not evolve mutation rates lower than ∼10-10 per nucleotide per cell division. Consequently, the extreme disparity between modest genetic diversity and astronomically large population size in the plankton species cannot be explained by an unusually low mutation rate.
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Affiliation(s)
- Marc Krasovec
- Department of Plant Sciences, University of Oxford, United Kingdom
| | | | - Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, United Kingdom
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Charlesworth D. The timing of genetic degeneration of sex chromosomes. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200093. [PMID: 34247501 DOI: 10.1098/rstb.2020.0093] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genetic degeneration is an extraordinary feature of sex chromosomes, with the loss of functions of Y-linked genes in species with XY systems, and W-linked genes in ZW systems, eventually affecting almost all genes. Although degeneration is familiar to most biologists, important aspects are not yet well understood, including how quickly a Y or W chromosome can become completely degenerated. I review the current understanding of the time-course of degeneration. Degeneration starts after crossing over between the sex chromosome pair stops, and theoretical models predict an initially fast degeneration rate and a later much slower one. It has become possible to estimate the two quantities that the models suggest are the most important in determining degeneration rates-the size of the sex-linked region, and the time when recombination became suppressed (which can be estimated using Y-X or W-Z sequence divergence). However, quantifying degeneration is still difficult. I review evidence on gene losses (based on coverage analysis) or loss of function (by classifying coding sequences into functional alleles and pseudogenes). I also review evidence about whether small genome regions degenerate, or only large ones, whether selective constraints on the genes in a sex-linked region also strongly affect degeneration rates, and about how long it takes before all (or almost all) genes are lost. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, EH9 3LF, UK
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38
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Käfer J, Lartillot N, Marais GAB, Picard F. Detecting sex-linked genes using genotyped individuals sampled in natural populations. Genetics 2021; 218:iyab053. [PMID: 33764439 PMCID: PMC8225351 DOI: 10.1093/genetics/iyab053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/21/2021] [Indexed: 12/20/2022] Open
Abstract
We propose a method, SDpop, able to infer sex-linkage caused by recombination suppression typical of sex chromosomes. The method is based on the modeling of the allele and genotype frequencies of individuals of known sex in natural populations. It is implemented in a hierarchical probabilistic framework, accounting for different sources of error. It allows statistical testing for the presence or absence of sex chromosomes, and detection of sex-linked genes based on the posterior probabilities in the model. Furthermore, for gametologous sequences, the haplotype and level of nucleotide polymorphism of each copy can be inferred, as well as the divergence between them. We test the method using simulated data, as well as data from both a relatively recent and an old sex chromosome system (the plant Silene latifolia and humans) and show that, for most cases, robust predictions are obtained with 5 to 10 individuals per sex.
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Affiliation(s)
- Jos Käfer
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR 5558, Université Lyon 1, Université de Lyon, Villeurbanne F-69622, France
| | - Nicolas Lartillot
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR 5558, Université Lyon 1, Université de Lyon, Villeurbanne F-69622, France
| | - Gabriel A B Marais
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR 5558, Université Lyon 1, Université de Lyon, Villeurbanne F-69622, France
| | - Franck Picard
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR 5558, Université Lyon 1, Université de Lyon, Villeurbanne F-69622, France
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39
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Märkle H, John S, Cornille A, Fields PD, Tellier A. Novel genomic approaches to study antagonistic coevolution between hosts and parasites. Mol Ecol 2021; 30:3660-3676. [PMID: 34038012 DOI: 10.1111/mec.16001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/09/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022]
Abstract
Host-parasite coevolution is ubiquitous, shaping genetic and phenotypic diversity and the evolutionary trajectory of interacting species. With the advances of high throughput sequencing technologies applicable to model and non-model organisms alike, it is now feasible to study in greater detail (a) the genetic underpinnings of coevolution, (b) the speed and type of dynamics at coevolving loci, and (c) the genomic consequences of coevolution. This review focuses on three recently developed approaches that leverage information from host and parasite full genome data simultaneously to pinpoint coevolving loci and draw inference on the coevolutionary history. First, co-genome-wide association study (co-GWAS) methods allow pinpointing the loci underlying host-parasite interactions. These methods focus on detecting associations between genetic variants and the outcome of experimental infection tests or on correlations between genomes of naturally infected hosts and their infecting parasites. Second, extensions to population genomics methods can detect genes under coevolution and infer the coevolutionary history, such as fitness costs. Third, correlations between host and parasite population size in time are indicative of coevolution, and polymorphism levels across independent spatially distributed populations of hosts and parasites can reveal coevolutionary loci and infer coevolutionary history. We describe the principles of these three approaches and discuss their advantages and limitations based on coevolutionary theory. We present recommendations for their application to various host (prokaryotes, fungi, plants, and animals) and parasite (viruses, bacteria, fungi, and macroparasites) species. We conclude by pointing out methodological and theoretical gaps to be filled to extract maximum information from full genome data and thereby to shed light on the molecular underpinnings of coevolution.
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Affiliation(s)
- Hanna Märkle
- Professorship for Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany.,Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Sona John
- Professorship for Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Amandine Cornille
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Peter D Fields
- Department of Environmental Sciences, University of Basel, Zoology, Basel, Switzerland
| | - Aurélien Tellier
- Professorship for Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
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40
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Stability across the Whole Nuclear Genome in the Presence and Absence of DNA Mismatch Repair. Cells 2021; 10:cells10051224. [PMID: 34067668 PMCID: PMC8156620 DOI: 10.3390/cells10051224] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 01/06/2023] Open
Abstract
We describe the contribution of DNA mismatch repair (MMR) to the stability of the eukaryotic nuclear genome as determined by whole-genome sequencing. To date, wild-type nuclear genome mutation rates are known for over 40 eukaryotic species, while measurements in mismatch repair-defective organisms are fewer in number and are concentrated on Saccharomyces cerevisiae and human tumors. Well-studied organisms include Drosophila melanogaster and Mus musculus, while less genetically tractable species include great apes and long-lived trees. A variety of techniques have been developed to gather mutation rates, either per generation or per cell division. Generational rates are described through whole-organism mutation accumulation experiments and through offspring–parent sequencing, or they have been identified by descent. Rates per somatic cell division have been estimated from cell line mutation accumulation experiments, from systemic variant allele frequencies, and from widely spaced samples with known cell divisions per unit of tissue growth. The latter methods are also used to estimate generational mutation rates for large organisms that lack dedicated germlines, such as trees and hyphal fungi. Mechanistic studies involving genetic manipulation of MMR genes prior to mutation rate determination are thus far confined to yeast, Arabidopsis thaliana, Caenorhabditis elegans, and one chicken cell line. A great deal of work in wild-type organisms has begun to establish a sound baseline, but far more work is needed to uncover the variety of MMR across eukaryotes. Nonetheless, the few MMR studies reported to date indicate that MMR contributes 100-fold or more to genome stability, and they have uncovered insights that would have been impossible to obtain using reporter gene assays.
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41
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Smith CI, McKain MR, Guimond A, Flatz R. Genome-scale data resolves the timing of divergence in Joshua trees. AMERICAN JOURNAL OF BOTANY 2021; 108:647-663. [PMID: 33846972 DOI: 10.1002/ajb2.1633] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Joshua trees (Yucca brevifolia and Y. jaegeriana) and their yucca moth pollinators (Tegeticula synthetica and T. antithetica) are a model system for studies of plant-pollinator coevolution and, they are thought to be one of the only cases in which there is compelling evidence for cospeciation driven by coevolution. Previous work attempted to evaluate whether divergence between the plant and their pollinators was contemporaneous. That work concluded that the trees diverged more than 5 million years ago-well before the pollinators. However, clear inferences were hampered by a lack of data from the nuclear genome and low genetic variation in chloroplast genes. As a result, divergence times in the trees could not be confidently estimated. METHODS We present an analysis of whole chloroplast genome sequence data and RADseq data from >5000 loci in the nuclear genome. We developed a molecular clock for the Asparagales and the Agavoideae using multiple fossil calibration points. Using Bayesian inference, we produced new estimates for the age of the genus Yucca and for Joshua trees. We used calculated summary statistics describing genetic variation and used coalescent-based methods to estimate population genetic parameters. RESULTS We find that the Joshua trees are moderately genetically differentiated, but that they diverged quite recently (~100-200 kya), and much more recently than their pollinators. CONCLUSIONS The results argue against the notion that coevolution directly contributed to speciation in this system, suggesting instead that coevolution with pollinators may have reinforced reproductive isolation following initial divergence in allopatry.
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Affiliation(s)
| | - Michael R McKain
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL
| | - Austin Guimond
- Department of Biology, Willamette University, 900 State Street, Salem, OR
| | - Ramona Flatz
- Department of Biology, Willamette University, 900 State Street, Salem, OR
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42
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Transcriptional regulation of dosage compensation in Carica papaya. Sci Rep 2021; 11:5854. [PMID: 33712672 PMCID: PMC7971000 DOI: 10.1038/s41598-021-85480-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/22/2021] [Indexed: 12/13/2022] Open
Abstract
Sex chromosome evolution results in the disparity in gene content between heterogametic sex chromosomes and creates the need for dosage compensation to counteract the effects of gene dose imbalance of sex chromosomes in males and females. It is not known at which stage of sex chromosome evolution dosage compensation would evolve. We used global gene expression profiling in male and female papayas to assess gene expression patterns of sex-linked genes on the papaya sex chromosomes. By analyzing expression ratios of sex-linked genes to autosomal genes and sex-linked genes in males relative to females, our results showed that dosage compensation was regulated on a gene-by-gene level rather than whole sex-linked region in papaya. Seven genes on the papaya X chromosome exhibited dosage compensation. We further compared gene expression ratios in the two evolutionary strata. Y alleles in the older evolutionary stratum showed reduced expression compared to X alleles, while Y alleles in the younger evolutionary stratum showed elevated expression compared to X alleles. Reduced expression of Y alleles in the older evolutionary stratum might be caused by accumulation of deleterious mutations in regulatory regions or transposable element-mediated methylation spreading. Most X-hemizygous genes exhibited either no or very low expression, suggesting that gene silencing might play a role in maintaining transcriptional balance between females and males.
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43
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Muyle A, Martin H, Zemp N, Mollion M, Gallina S, Tavares R, Silva A, Bataillon T, Widmer A, Glémin S, Touzet P, Marais GAB. Dioecy Is Associated with High Genetic Diversity and Adaptation Rates in the Plant Genus Silene. Mol Biol Evol 2021; 38:805-818. [PMID: 32926156 PMCID: PMC7947750 DOI: 10.1093/molbev/msaa229] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
About 15,000 angiosperm species (∼6%) have separate sexes, a phenomenon known as dioecy. Why dioecious taxa are so rare is still an open question. Early work reported lower species richness in dioecious compared with nondioecious sister clades, raising the hypothesis that dioecy may be an evolutionary dead-end. This hypothesis has been recently challenged by macroevolutionary analyses that detected no or even positive effect of dioecy on diversification. However, the possible genetic consequences of dioecy at the population level, which could drive the long-term fate of dioecious lineages, have not been tested so far. Here, we used a population genomics approach in the Silene genus to look for possible effects of dioecy, especially for potential evidence of evolutionary handicaps of dioecy underlying the dead-end hypothesis. We collected individual-based RNA-seq data from several populations in 13 closely related species with different sexual systems: seven dioecious, three hermaphroditic, and three gynodioecious species. We show that dioecy is associated with increased genetic diversity, as well as higher selection efficacy both against deleterious mutations and for beneficial mutations. The results hold after controlling for phylogenetic inertia, differences in species census population sizes and geographic ranges. We conclude that dioecious Silene species neither show signs of increased mutational load nor genetic evidence for extinction risk. We discuss these observations in the light of the possible demographic differences between dioecious and self-compatible hermaphroditic species and how this could be related to alternatives to the dead-end hypothesis to explain the rarity of dioecy.
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Affiliation(s)
- Aline Muyle
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA
| | - Hélène Martin
- University of Lille, CNRS, UMR 8198—Evo-Eco-Paleo, F-59000 Lille, France
- Département de Biologie, Institut de Biologie Integrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Niklaus Zemp
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Genetic Diversity Centre (GDC), ETH Zurich, Zurich, Switzerland
| | - Maéva Mollion
- Bioinformatics Research Centre, Aarhus University, Aarhus C, Denmark
| | - Sophie Gallina
- University of Lille, CNRS, UMR 8198—Evo-Eco-Paleo, F-59000 Lille, France
| | - Raquel Tavares
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
| | - Alexandre Silva
- Centro de Interpretação da Serra da Estrela (CISE), Seia, Portugal
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus C, Denmark
| | - Alex Widmer
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Sylvain Glémin
- CNRS, ECOBIO [(Ecosystèmes, Biodiversité, Évolution)]—UMR 6553, University of Rennes, Rennes, France
- Department of Ecology and Genetics, Evolutionary Biology Center and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Pascal Touzet
- University of Lille, CNRS, UMR 8198—Evo-Eco-Paleo, F-59000 Lille, France
| | - Gabriel A B Marais
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
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Florez-Rueda AM, Scharmann M, Roth M, Städler T. Population Genomics of the "Arcanum" Species Group in Wild Tomatoes: Evidence for Separate Origins of Two Self-Compatible Lineages. FRONTIERS IN PLANT SCIENCE 2021; 12:624442. [PMID: 33815438 PMCID: PMC8018279 DOI: 10.3389/fpls.2021.624442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/24/2021] [Indexed: 05/07/2023]
Abstract
Given their diverse mating systems and recent divergence, wild tomatoes (Solanum section Lycopersicon) have become an attractive model system to study ecological divergence, the build-up of reproductive barriers, and the causes and consequences of the breakdown of self-incompatibility. Here we report on a lesser-studied group of species known as the "Arcanum" group, comprising the nominal species Solanum arcanum, Solanum chmielewskii, and Solanum neorickii. The latter two taxa are self-compatible but are thought to self-fertilize at different rates, given their distinct manifestations of the morphological "selfing syndrome." Based on experimental crossings and transcriptome sequencing of a total of 39 different genotypes from as many accessions representing each species' geographic range, we provide compelling evidence for deep genealogical divisions within S. arcanum; only the self-incompatible lineage known as "var. marañón" has close genealogical ties to the two self-compatible species. Moreover, there is evidence under multiple inference schemes for different geographic subsets of S. arcanum var. marañón being closest to S. chmielewskii and S. neorickii, respectively. To broadly characterize the population-genomic consequences of these recent mating-system transitions and their associated speciation events, we fit demographic models indicating strong reductions in effective population size, congruent with reduced nucleotide and S-locus diversity in the two independently derived self-compatible species.
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45
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Beaudry FE, Rifkin JL, Barrett SC, Wright SI. Evolutionary Genomics of Plant Gametophytic Selection. PLANT COMMUNICATIONS 2020; 1:100115. [PMID: 33367268 PMCID: PMC7748008 DOI: 10.1016/j.xplc.2020.100115] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/17/2020] [Accepted: 10/22/2020] [Indexed: 05/26/2023]
Abstract
It has long been recognized that natural selection during the haploid gametophytic phase of the plant life cycle may have widespread importance for rates of evolution and the maintenance of genetic variation. Recent theoretical advances have further highlighted the significance of gametophytic selection for diverse evolutionary processes. Genomic approaches offer exciting opportunities to address key questions about the extent and effects of gametophytic selection on plant evolution and adaptation. Here, we review the progress and prospects for integrating functional and evolutionary genomics to test theoretical predictions, and to examine the importance of gametophytic selection on genetic diversity and rates of evolution. There is growing evidence that selection during the gametophyte phase of the plant life cycle has important effects on both gene and genome evolution and is likely to have important pleiotropic effects on the sporophyte. We discuss the opportunities to integrate comparative population genomics, genome-wide association studies, and experimental approaches to further distinguish how differential selection in the two phases of the plant life cycle contributes to genetic diversity and adaptive evolution.
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Affiliation(s)
- Felix E.G. Beaudry
- Department of Ecology and Evolutionary Biology, The University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Joanna L. Rifkin
- Department of Ecology and Evolutionary Biology, The University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Spencer C.H. Barrett
- Department of Ecology and Evolutionary Biology, The University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Stephen I. Wright
- Department of Ecology and Evolutionary Biology, The University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
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46
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Estimation of the SNP Mutation Rate in Two Vegetatively Propagating Species of Duckweed. G3-GENES GENOMES GENETICS 2020; 10:4191-4200. [PMID: 32973000 PMCID: PMC7642947 DOI: 10.1534/g3.120.401704] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mutation rate estimates for vegetatively reproducing organisms are rare, despite their frequent occurrence across the tree of life. Here we report mutation rate estimates in two vegetatively reproducing duckweed species, Lemna minor and Spirodela polyrhiza We use a modified approach to estimating mutation rates by taking into account the reduction in mutation detection power that occurs when new individuals are produced from multiple cell lineages. We estimate an extremely low per generation mutation rate in both species of duckweed and note that allelic coverage at de novo mutation sites is very skewed. We also find no substantial difference in mutation rate between mutation accumulation lines propagated under benign conditions and those grown under salt stress. Finally, we discuss the implications of interpreting mutation rate estimates in vegetatively propagating organisms.
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47
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Liu X, Glémin S, Karrenberg S. Evolution of putative barrier loci at an intermediate stage of speciation with gene flow in campions (Silene). Mol Ecol 2020; 29:3511-3525. [PMID: 32740990 PMCID: PMC7540528 DOI: 10.1111/mec.15571] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 07/09/2020] [Accepted: 07/16/2020] [Indexed: 12/22/2022]
Abstract
Understanding the origin of new species is a central goal in evolutionary biology. Diverging lineages often evolve highly heterogeneous patterns of genetic differentiation; however, the underlying mechanisms are not well understood. We investigated evolutionary processes governing genetic differentiation between the hybridizing campions Silene dioica (L.) Clairv. and S. latifolia Poiret. Demographic modelling indicated that the two species diverged with gene flow. The best‐supported scenario with heterogeneity in both migration rate and effective population size suggested that a small proportion of the loci evolved without gene flow. Differentiation (FST) and sequence divergence (dXY) were correlated and both tended to peak in the middle of most linkage groups, consistent with reduced gene flow at highly differentiated loci. Highly differentiated loci further exhibited signatures of selection. In between‐species population pairs, isolation by distance was stronger for genomic regions with low between‐species differentiation than for highly differentiated regions that may contain barrier loci. Moreover, differentiation landscapes within and between species were only weakly correlated, suggesting that linked selection due to shared recombination and gene density landscapes is not the dominant determinant of genetic differentiation in these lineages. Instead, our results suggest that divergent selection shaped the genomic landscape of differentiation between the two Silene species, consistent with predictions for speciation in the face of gene flow.
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Affiliation(s)
- Xiaodong Liu
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Sylvain Glémin
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,UMR CNRS 6553 ECOBIO, Université de Rennes I, Rennes Cedex, France
| | - Sophie Karrenberg
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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48
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Fruchard C, Badouin H, Latrasse D, Devani RS, Muyle A, Rhoné B, Renner SS, Banerjee AK, Bendahmane A, Marais GAB. Evidence for Dosage Compensation in Coccinia grandis, a Plant with a Highly Heteromorphic XY System. Genes (Basel) 2020; 11:E787. [PMID: 32668777 PMCID: PMC7397054 DOI: 10.3390/genes11070787] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/01/2020] [Accepted: 07/08/2020] [Indexed: 01/17/2023] Open
Abstract
About 15,000 angiosperms are dioecious, but the mechanisms of sex determination in plants remain poorly understood. In particular, how Y chromosomes evolve and degenerate, and whether dosage compensation evolves as a response, are matters of debate. Here, we focus on Coccinia grandis, a dioecious cucurbit with the highest level of X/Y heteromorphy recorded so far. We identified sex-linked genes using RNA sequences from a cross and a model-based method termed SEX-DETector. Parents and F1 individuals were genotyped, and the transmission patterns of SNPs were then analyzed. In the >1300 sex-linked genes studied, maximum X-Y divergence was 0.13-0.17, and substantial Y degeneration is implied by an average Y/X expression ratio of 0.63 and an inferred gene loss on the Y of ~40%. We also found reduced Y gene expression being compensated by elevated expression of corresponding genes on the X and an excess of sex-biased genes on the sex chromosomes. Molecular evolution of sex-linked genes in C. grandis is thus comparable to that in Silene latifolia, another dioecious plant with a strongly heteromorphic XY system, and cucurbits are the fourth plant family in which dosage compensation is described, suggesting it might be common in plants.
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Affiliation(s)
- Cécile Fruchard
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR5558, Université Lyon 1, 69622 Villeurbanne, France; (C.F.); (H.B.); (B.R.)
| | - Hélène Badouin
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR5558, Université Lyon 1, 69622 Villeurbanne, France; (C.F.); (H.B.); (B.R.)
| | - David Latrasse
- Institute of Plant Sciences Paris Saclay (IPS2), University of Paris Saclay, 91405 Orsay, France; (D.L.); (R.S.D.); (A.B.)
| | - Ravi S. Devani
- Institute of Plant Sciences Paris Saclay (IPS2), University of Paris Saclay, 91405 Orsay, France; (D.L.); (R.S.D.); (A.B.)
- Biology Division, Indian Institute of Science Education and Research (IISER), Pune 411008, Maharashtra, India;
| | - Aline Muyle
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA;
| | - Bénédicte Rhoné
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR5558, Université Lyon 1, 69622 Villeurbanne, France; (C.F.); (H.B.); (B.R.)
- Institut de Recherche pour le Développement (IRD), Université Montpellier, DIADE, F-34394 Montpellier, France
| | - Susanne S. Renner
- Systematic Botany and Mycology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany;
| | - Anjan K. Banerjee
- Biology Division, Indian Institute of Science Education and Research (IISER), Pune 411008, Maharashtra, India;
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris Saclay (IPS2), University of Paris Saclay, 91405 Orsay, France; (D.L.); (R.S.D.); (A.B.)
| | - Gabriel A. B. Marais
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR5558, Université Lyon 1, 69622 Villeurbanne, France; (C.F.); (H.B.); (B.R.)
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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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50
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Van Buskirk J, Jansen van Rensburg A. Relative importance of isolation‐by‐environment and other determinants of gene flow in an alpine amphibian. Evolution 2020; 74:962-978. [DOI: 10.1111/evo.13955] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/26/2020] [Accepted: 03/09/2020] [Indexed: 02/07/2023]
Affiliation(s)
- Josh Van Buskirk
- Department of Evolutionary Biology and Environmental StudiesUniversity of Zurich Zurich 8057 Switzerland
| | - Alexandra Jansen van Rensburg
- Department of Evolutionary Biology and Environmental StudiesUniversity of Zurich Zurich 8057 Switzerland
- School of Biological SciencesUniversity of Bristol Bristol BS8 1TQ United Kingdom
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