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Charlesworth D, Harkess A. Why should we study plant sex chromosomes? THE PLANT CELL 2024; 36:1242-1256. [PMID: 38163640 PMCID: PMC11062472 DOI: 10.1093/plcell/koad278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/10/2023] [Indexed: 01/03/2024]
Abstract
Understanding plant sex chromosomes involves studying interactions between developmental and physiological genetics, genome evolution, and evolutionary ecology. We focus on areas of overlap between these. Ideas about how species with separate sexes (dioecious species, in plant terminology) can evolve are even more relevant to plants than to most animal taxa because dioecy has evolved many times from ancestral functionally hermaphroditic populations, often recently. One aim of studying plant sex chromosomes is to discover how separate males and females evolved from ancestors with no such genetic sex-determining polymorphism, and the diversity in the genetic control of maleness vs femaleness. Different systems share some interesting features, and their differences help to understand why completely sex-linked regions may evolve. In some dioecious plants, the sex-determining genome regions are physically small. In others, regions without crossing over have evolved sometimes extensive regions with properties very similar to those of the familiar animal sex chromosomes. The differences also affect the evolutionary changes possible when the environment (or pollination environment, for angiosperms) changes, as dioecy is an ecologically risky strategy for sessile organisms. Dioecious plants have repeatedly reverted to cosexuality, and hermaphroditic strains of fruit crops such as papaya and grapes are desired by plant breeders. Sex-linked regions are predicted to become enriched in genes with sex differences in expression, especially when higher expression benefits one sex function but harms the other. Such trade-offs may be important for understanding other plant developmental and physiological processes and have direct applications in plant breeding.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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2
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Sacchi B, Humphries Z, Kružlicová J, Bodláková M, Pyne C, Choudhury BI, Gong Y, Bačovský V, Hobza R, Barrett SCH, Wright SI. Phased Assembly of Neo-Sex Chromosomes Reveals Extensive Y Degeneration and Rapid Genome Evolution in Rumex hastatulus. Mol Biol Evol 2024; 41:msae074. [PMID: 38606901 PMCID: PMC11057207 DOI: 10.1093/molbev/msae074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/31/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024] Open
Abstract
Y chromosomes are thought to undergo progressive degeneration due to stepwise loss of recombination and subsequent reduction in selection efficiency. However, the timescales and evolutionary forces driving degeneration remain unclear. To investigate the evolution of sex chromosomes on multiple timescales, we generated a high-quality phased genome assembly of the massive older (<10 MYA) and neo (<200,000 yr) sex chromosomes in the XYY cytotype of the dioecious plant Rumex hastatulus and a hermaphroditic outgroup Rumex salicifolius. Our assemblies, supported by fluorescence in situ hybridization, confirmed that the neo-sex chromosomes were formed by two key events: an X-autosome fusion and a reciprocal translocation between the homologous autosome and the Y chromosome. The enormous sex-linked regions of the X (296 Mb) and two Y chromosomes (503 Mb) both evolved from large repeat-rich genomic regions with low recombination; however, the complete loss of recombination on the Y still led to over 30% gene loss and major rearrangements. In the older sex-linked region, there has been a significant increase in transposable element abundance, even into and near genes. In the neo-sex-linked regions, we observed evidence of extensive rearrangements without gene degeneration and loss. Overall, we inferred significant degeneration during the first 10 million years of Y chromosome evolution but not on very short timescales. Our results indicate that even when sex chromosomes emerge from repetitive regions of already-low recombination, the complete loss of recombination on the Y chromosome still leads to a substantial increase in repetitive element content and gene degeneration.
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Affiliation(s)
- Bianca Sacchi
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Zoë Humphries
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Jana Kružlicová
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Markéta Bodláková
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Cassandre Pyne
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Baharul I Choudhury
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
- Department of Biology, Queen’s University, Kingston, Canada
| | - Yunchen Gong
- Centre for Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
| | - Václav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
- Centre for Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
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3
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Razumova OV, Divashuk MG, Alexandrov OS, Karlov GI. GISH painting of the Y chromosomes suggests advanced phases of sex chromosome evolution in three dioecious Cannabaceae species (Humulus lupulus, H. japonicus, and Cannabis sativa). PROTOPLASMA 2023; 260:249-256. [PMID: 35595927 DOI: 10.1007/s00709-022-01774-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
In plants, dioecy is relatively rare, and it involves sex chromosome systems that often developed independently over time. These characteristics make dioecious plants an attractive model to study sex chromosome evolution. To clarify the patterns of plant sex chromosome evolution, studies should be performed on a wide range of dioecious species. It is interesting to study the sex chromosomes in related species that evolved during a long period of independent sex chromosome evolution. The Cannabaceae family includes three dioecious species with heteromorphic sex chromosomes. Cannabis sativa and Humulus lupulus use the XX/XY chromosome system, whereas Humulus japonicus contains multiple sex chromosomes (XX/XY1Y2). To better understand sex chromosome evolution and the level of genomic divergence of these three related species, we undertook self-GISH and comparative GISH analyses. The self-GISH allowed visualization of the Y chromosomes of C. sativa, H. lupulus, and H. japonicus. The self-GISH signal was distributed along the entire Y chromosome, excluding the pseudo-autosomal region (PAR). Our results indicate that the male-specific region of the Y chromosome (MSY) spans the overwhelming majority of the Y chromosomes of all three species studied. The self-GISH results reveal the accumulation of repetitive DNA sequences in the Y chromosomes of all three species studied. This sequences presented in autosomes and/or chromosome X at a lower copy number than in Y. In comparative GISH experiments where the probe DNA of one species was applied to another species, a weak signal was exclusively detected on 45S rDNA sites, indicating a high level of genomic differentiation of the species used in this study. We demonstrate small PAR size and opposing large MSY and its positions on Y chromosomes. We also found that these genomes are highly differentiated. Furthermore, the data obtained in this study indicate a long period of independent and advanced sex chromosome evolution. Our study provides a valuable basis for future genomic studies of sex and suggests that the Cannabaceae family offers a promising model to study sex chromosome evolution.
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Affiliation(s)
- Olga V Razumova
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, Moscow, 127550, Russia
| | - Mikhail G Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, Moscow, 127550, Russia
| | - Oleg S Alexandrov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, Moscow, 127550, Russia
| | - Gennady I Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, Moscow, 127550, Russia.
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4
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An Overview of Molecular Basis and Genetic Modification of Floral Organs Genes: Impact of Next-Generation Sequencing. Mol Biotechnol 2022; 65:833-848. [DOI: 10.1007/s12033-022-00633-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022]
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5
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Balant M, Rodríguez González R, Garcia S, Garnatje T, Pellicer J, Vallès J, Vitales D, Hidalgo O. Novel Insights into the Nature of Intraspecific Genome Size Diversity in Cannabis sativa L. PLANTS (BASEL, SWITZERLAND) 2022; 11:2736. [PMID: 36297761 PMCID: PMC9607409 DOI: 10.3390/plants11202736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/08/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Cannabis sativa has been used for millennia in traditional medicine for ritual purposes and for the production of food and fibres, thus, providing important and versatile services to humans. The species, which currently has a worldwide distribution, strikes out for displaying a huge morphological and chemical diversity. Differences in Cannabis genome size have also been found, suggesting it could be a useful character to differentiate between accessions. We used flow cytometry to investigate the extent of genome size diversity across 483 individuals belonging to 84 accessions, with a wide range of wild/feral, landrace, and cultivated accessions. We also carried out sex determination using the MADC2 marker and investigated the potential of flow cytometry as a method for early sex determination. All individuals were diploid, with genome sizes ranging from 1.810 up to 2.152 pg/2C (1.189-fold variation), apart from a triploid, with 2.884 pg/2C. Our results suggest that the geographical expansion of Cannabis and its domestication had little impact on its overall genome size. We found significant differences between the genome size of male and female individuals. Unfortunately, differences were, however, too small to be discriminated using flow cytometry through the direct processing of combined male and female individuals.
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Affiliation(s)
- Manica Balant
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., 08038 Barcelona, Catalonia, Spain
| | - Roi Rodríguez González
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., 08038 Barcelona, Catalonia, Spain
| | - Sònia Garcia
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., 08038 Barcelona, Catalonia, Spain
| | - Teresa Garnatje
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., 08038 Barcelona, Catalonia, Spain
| | - Jaume Pellicer
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., 08038 Barcelona, Catalonia, Spain
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK
| | - Joan Vallès
- Laboratori de Botànica (UB), Unitat Associada al CSIC, Facultat de Farmàcia i Ciències de l’Alimentació–Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Joan XXIII 27–31, 08028 Barcelona, Catalonia, Spain
| | - Daniel Vitales
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica (UB), Unitat Associada al CSIC, Facultat de Farmàcia i Ciències de l’Alimentació–Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Joan XXIII 27–31, 08028 Barcelona, Catalonia, Spain
| | - Oriane Hidalgo
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., 08038 Barcelona, Catalonia, Spain
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK
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6
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Joachimiak AJ, Libik-Konieczny M, Wójtowicz T, Sliwinska E, Grabowska-Joachimiak A. Physiological aspects of sex differences and Haldane's rule in Rumex hastatulus. Sci Rep 2022; 12:11145. [PMID: 35778518 PMCID: PMC9249882 DOI: 10.1038/s41598-022-15219-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 06/21/2022] [Indexed: 11/08/2022] Open
Abstract
Haldane's rule (HR, impairment of fertility and/or viability of interracial hybrids) seems to be one of few generalizations in evolutionary biology. The validity of HR has been confirmed in animals, and more recently in some dioecious plants (Silene and Rumex). Dioecious Rumex hastatulus has two races differing in the sex chromosome system: Texas (T) and North Carolina (NC), and T × NC males showed both reduced pollen fertility and rarity-two classical symptoms of Haldane's rule (HR). The reduced fertility of these plants has a simple mechanistic explanation, but the reason for their rarity was not elucidated. Here, we measured selected physiological parameters related to the antioxidant defense system in parental races and reciprocal hybrids of R. hastatulus. We showed that the X-autosome configurations, as well as asymmetries associated with Y chromosomes and cytoplasm, could modulate this system in hybrids. The levels and quantitative patterns of the measured parameters distinguish the T × NC hybrid from the other analyzed forms. Our observations suggest that the rarity of T × NC males is caused postzygotically and most likely related to the higher level of oxidative stress induced by the chromosomal incompatibilities. It is the first report on the physiological aspects of HR in plants.
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Affiliation(s)
- Andrzej J Joachimiak
- Department of Plant Cytology and Embryology, Faculty of Biology, Institute of Botany, Jagiellonian University, Gronostajowa 9, 30-387, Kraków, Poland
| | - Marta Libik-Konieczny
- Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Kraków, Poland
| | - Tomasz Wójtowicz
- Department of Plant Breeding, Physiology and Seed Science, Faculty of Agriculture and Economics, University of Agriculture in Krakow, Łobzowska 24, 31-140, Kraków, Poland
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, Bydgoszcz University of Science and Technology, Kaliskiego Ave. 7, 85-789, Bydgoszcz, Poland
| | - Aleksandra Grabowska-Joachimiak
- Department of Plant Breeding, Physiology and Seed Science, Faculty of Agriculture and Economics, University of Agriculture in Krakow, Łobzowska 24, 31-140, Kraków, Poland.
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7
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Rifkin JL, Hnatovska S, Yuan M, Sacchi BM, Choudhury BI, Gong Y, Rastas P, Barrett SCH, Wright SI. Recombination landscape dimorphism and sex chromosome evolution in the dioecious plant Rumex hastatulus. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210226. [PMID: 35306892 PMCID: PMC8935318 DOI: 10.1098/rstb.2021.0226] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
There is growing evidence from diverse taxa for sex differences in the genomic landscape of recombination, but the causes and consequences of these differences remain poorly understood. Strong recombination landscape dimorphism between the sexes could have important implications for the dynamics of sex chromosome evolution because low recombination in the heterogametic sex can favour the spread of sexually antagonistic alleles. Here, we present a sex-specific linkage map and revised genome assembly of Rumex hastatulus and provide the first evidence and characterization of sex differences in recombination landscape in a dioecious plant. We present data on significant sex differences in recombination, with regions of very low recombination in males covering over half of the genome. This pattern is evident on both sex chromosomes and autosomes, suggesting that pre-existing differences in recombination may have contributed to sex chromosome formation and divergence. Our analysis of segregation distortion suggests that haploid selection due to pollen competition occurs disproportionately in regions with low male recombination. We hypothesize that sex differences in the recombination landscape have contributed to the formation of a large heteromorphic pair of sex chromosomes in R. hastatulus, but more comparative analyses of recombination will be important to investigate this hypothesis further. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.
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Affiliation(s)
- Joanna L Rifkin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2
| | - Solomiya Hnatovska
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2
| | - Meng Yuan
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2
| | - Bianca M Sacchi
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2
| | - Baharul I Choudhury
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2.,Department of Biology, Queen's University, Kingston, ON, Canada K7L 396
| | - Yunchen Gong
- Centre for Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada M5S 3B2
| | - Pasi Rastas
- Institute of Biotechnology, 00014 University of Helsinki, Helsinki, Finland
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2.,Centre for Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada M5S 3B2
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8
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Charlesworth D. When and how do sex-linked regions become sex chromosomes? Evolution 2021; 75:569-581. [PMID: 33592115 DOI: 10.1111/evo.14196] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 12/22/2022]
Abstract
The attention given to heteromorphism and genetic degeneration of "classical sex chromosomes" (Y chromosomes in XY systems, and the W in ZW systems that were studied first and are best described) has perhaps created the impression that the absence of recombination between sex chromosomes is inevitable. I here argue that continued recombination is often to be expected, that absence of recombination is surprising and demands further study, and that the involvement of selection in reduced recombination is not yet well understood. Despite a long history of investigations of sex chromosome pairs, there is a need for more quantitative approaches to studying sex-linked regions. I describe a scheme to help understand the relationships between different properties of sex-linked regions. Specifically, I focus on their sizes (differentiating between small regions and extensive fully sex-linked ones), the times when they evolved, and their differentiation, and review studies using DNA sequencing in nonmodel organisms that are providing information about the processes causing these properties.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
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9
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Rifkin JL, Beaudry FEG, Humphries Z, Choudhury BI, Barrett SCH, Wright SI. Widespread Recombination Suppression Facilitates Plant Sex Chromosome Evolution. Mol Biol Evol 2021; 38:1018-1030. [PMID: 33095227 PMCID: PMC7947811 DOI: 10.1093/molbev/msaa271] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Classical models suggest that recombination rates on sex chromosomes evolve in a stepwise manner to localize sexually antagonistic variants in the sex in which they are beneficial, thereby lowering rates of recombination between X and Y chromosomes. However, it is also possible that sex chromosome formation occurs in regions with preexisting recombination suppression. To evaluate these possibilities, we constructed linkage maps and a chromosome-scale genome assembly for the dioecious plant Rumex hastatulus. This species has a polymorphic karyotype with a young neo-sex chromosome, resulting from a Robertsonian fusion between the X chromosome and an autosome, in part of its geographic range. We identified the shared and neo-sex chromosomes using comparative genetic maps of the two cytotypes. We found that sex-linked regions of both the ancestral and the neo-sex chromosomes are embedded in large regions of low recombination. Furthermore, our comparison of the recombination landscape of the neo-sex chromosome to its autosomal homolog indicates that low recombination rates mainly preceded sex linkage. These patterns are not unique to the sex chromosomes; all chromosomes were characterized by massive regions of suppressed recombination spanning most of each chromosome. This represents an extreme case of the periphery-biased recombination seen in other systems with large chromosomes. Across all chromosomes, gene and repetitive sequence density correlated with recombination rate, with patterns of variation differing by repetitive element type. Our findings suggest that ancestrally low rates of recombination may facilitate the formation and subsequent evolution of heteromorphic sex chromosomes.
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Affiliation(s)
- Joanna L Rifkin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Felix E G Beaudry
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Zoë Humphries
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Baharul I Choudhury
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
- Centre for Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
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10
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Jesionek W, Bodláková M, Kubát Z, Čegan R, Vyskot B, Vrána J, Šafář J, Puterova J, Hobza R. Fundamentally different repetitive element composition of sex chromosomes in Rumex acetosa. ANNALS OF BOTANY 2021; 127:33-47. [PMID: 32902599 PMCID: PMC7750719 DOI: 10.1093/aob/mcaa160] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIMS Dioecious species with well-established sex chromosomes are rare in the plant kingdom. Most sex chromosomes increase in size but no comprehensive analysis of the kind of sequences that drive this expansion has been presented. Here we analyse sex chromosome structure in common sorrel (Rumex acetosa), a dioecious plant with XY1Y2 sex determination, and we provide the first chromosome-specific repeatome analysis for a plant species possessing sex chromosomes. METHODS We flow-sorted and separately sequenced sex chromosomes and autosomes in R. acetosa using the two-dimensional fluorescence in situ hybridization in suspension (FISHIS) method and Illumina sequencing. We identified and quantified individual repeats using RepeatExplorer, Tandem Repeat Finder and the Tandem Repeats Analysis Program. We employed fluorescence in situ hybridization (FISH) to analyse the chromosomal localization of satellites and transposons. KEY RESULTS We identified a number of novel satellites, which have, in a fashion similar to previously known satellites, significantly expanded on the Y chromosome but not as much on the X or on autosomes. Additionally, the size increase of Y chromosomes is caused by non-long terminal repeat (LTR) and LTR retrotransposons, while only the latter contribute to the enlargement of the X chromosome. However, the X chromosome is populated by different LTR retrotransposon lineages than those on Y chromosomes. CONCLUSIONS The X and Y chromosomes have significantly diverged in terms of repeat composition. The lack of recombination probably contributed to the expansion of diverse satellites and microsatellites and faster fixation of newly inserted transposable elements (TEs) on the Y chromosomes. In addition, the X and Y chromosomes, despite similar total counts of TEs, differ significantly in the representation of individual TE lineages, which indicates that transposons proliferate preferentially in either the paternal or the maternal lineage.
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Affiliation(s)
- Wojciech Jesionek
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice, Brno, Czech Republic
- For correspondence. E-mail: or
| | - Markéta Bodláková
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
| | - Zdeněk Kubát
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
| | - Radim Čegan
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
| | - Boris Vyskot
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů, Olomouc-Holice, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů, Olomouc-Holice, Czech Republic
| | - Janka Puterova
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
- Brno University of Technology, Faculty of Information Technology, Centre of Excellence IT4Innovations, Bozetechova, Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, The Czech Academy of Sciences, Institute of Biophysics, Královopolská, Brno, Czech Republic
- For correspondence. E-mail: or
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11
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Bačovský V, Čegan R, Šimoníková D, Hřibová E, Hobza R. The Formation of Sex Chromosomes in Silene latifolia and S. dioica Was Accompanied by Multiple Chromosomal Rearrangements. FRONTIERS IN PLANT SCIENCE 2020; 11:205. [PMID: 32180787 PMCID: PMC7059608 DOI: 10.3389/fpls.2020.00205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 02/11/2020] [Indexed: 05/02/2023]
Abstract
The genus Silene includes a plethora of dioecious and gynodioecious species. Two species, Silene latifolia (white campion) and Silene dioica (red campion), are dioecious plants, having heteromorphic sex chromosomes with an XX/XY sex determination system. The X and Y chromosomes differ mainly in size, DNA content and posttranslational histone modifications. Although it is generally assumed that the sex chromosomes evolved from a single pair of autosomes, it is difficult to distinguish the ancestral pair of chromosomes in related gynodioecious and hermaphroditic plants. We designed an oligo painting probe enriched for X-linked scaffolds from currently available genomic data and used this probe on metaphase chromosomes of S. latifolia (2n = 24, XY), S. dioica (2n = 24, XY), and two gynodioecious species, S. vulgaris (2n = 24) and S. maritima (2n = 24). The X chromosome-specific oligo probe produces a signal specifically on the X and Y chromosomes in S. latifolia and S. dioica, mainly in the subtelomeric regions. Surprisingly, in S. vulgaris and S. maritima, the probe hybridized to three pairs of autosomes labeling their p-arms. This distribution suggests that sex chromosome evolution was accompanied by extensive chromosomal rearrangements in studied dioecious plants.
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Affiliation(s)
- Václav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
- *Correspondence: Václav Bačovský,
| | - Radim Čegan
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Denisa Šimoníková
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Eva Hřibová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- Roman Hobza,
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12
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Beaudry FEG, Barrett SCH, Wright SI. Ancestral and neo-sex chromosomes contribute to population divergence in a dioecious plant. Evolution 2019; 74:256-269. [PMID: 31808547 DOI: 10.1111/evo.13892] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 10/16/2019] [Accepted: 11/11/2019] [Indexed: 12/18/2022]
Abstract
Empirical evidence from several animal groups suggests sex chromosomes disproportionately contribute to reproductive isolation. This effect may be enhanced when sex chromosomes are associated with turnover of sex determination systems resulting from structural rearrangements to the chromosomes. We investigated these predictions in the dioecious plant Rumex hastatulus, which is composed of populations of two different sex chromosome cytotypes caused by an X-autosome fusion. Using population genomic analyses, we investigated the demographic history of R. hastatulus and explored the contributions of ancestral and neo-sex chromosomes to population genetic divergence. Our study revealed that the cytotypes represent genetically divergent populations with evidence for historical but not contemporary gene flow between them. In agreement with classical predictions, we found that the ancestral X chromosome was disproportionately divergent compared with the rest of the genome. Excess differentiation was also observed on the Y chromosome, even when we used measures of differentiation that control for differences in effective population size. Our estimates of the timing of the origin of neo-sex chromosomes in R. hastatulus are coincident with cessation of gene flow, suggesting that the chromosomal fusion event that gave rise to the origin of the XYY cytotype may have also contributed to reproductive isolation.
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Affiliation(s)
- Felix E G Beaudry
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
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13
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Toups MA, Rodrigues N, Perrin N, Kirkpatrick M. A reciprocal translocation radically reshapes sex-linked inheritance in the common frog. Mol Ecol 2019; 28:1877-1889. [PMID: 30576024 DOI: 10.1111/mec.14990] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 12/04/2018] [Accepted: 12/04/2018] [Indexed: 12/22/2022]
Abstract
X and Y chromosomes can diverge when rearrangements block recombination between them. Here we present the first genomic view of a reciprocal translocation that causes two physically unconnected pairs of chromosomes to be coinherited as sex chromosomes. In a population of the common frog (Rana temporaria), both pairs of X and Y chromosomes show extensive sequence differentiation, but not degeneration of the Y chromosomes. A new method based on gene trees shows both chromosomes are sex-linked. Furthermore, the gene trees from the two Y chromosomes have identical topologies, showing they have been coinherited since the reciprocal translocation occurred. Reciprocal translocations can thus reshape sex linkage on a much greater scale compared with inversions, the type of rearrangement that is much better known in sex chromosome evolution, and they can greatly amplify the power of sexually antagonistic selection to drive genomic rearrangement. Two more populations show evidence of other rearrangements, suggesting that this species has unprecedented structural polymorphism in its sex chromosomes.
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Affiliation(s)
- Melissa A Toups
- Department of Integrative Biology, University of Texas, Austin, Texas.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Rodrigues
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, Texas
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14
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Kasjaniuk M, Grabowska-Joachimiak A, Joachimiak AJ. Testing the translocation hypothesis and Haldane's rule in Rumex hastatulus. PROTOPLASMA 2019; 256:237-247. [PMID: 30073414 PMCID: PMC6349804 DOI: 10.1007/s00709-018-1295-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 07/25/2018] [Indexed: 05/16/2023]
Abstract
The translocation hypothesis regarding the origin of the XX/XY1Y2 sex chromosome system was tested with reference to the F1 hybrids between two chromosomal races of Rumex hastatulus. The hybrids derived from reciprocal crossing between the Texas (T) race and the North Carolina (NC) race were investigated for the first time with respect to the meiotic chromosome configuration in the pollen mother cells, pollen viability, and sex ratio. A sex chromosome trivalent in the NC × T males and two sex chromosome bivalents in the T × NC males were detected. The observed conjugation patterns confirmed the autosomal origin of the extra chromosome segments occurring in the North Carolina neo-sex chromosomes. Decreased pollen viability was found in the T × NC hybrid in contrast to the NC × T hybrid and the parental forms. Moreover, only in the T × NC hybrid sex ratio was significantly female-biased (1:1.72). Thus, Haldane's rule for both male fertility and male rarity was shown in this hybrid. According to the authors' knowledge, R. hastatulus is just the second plant with sex chromosomes in which Haldane's rule was evidenced.
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Affiliation(s)
- Magdalena Kasjaniuk
- Department of Plant Breeding and Seed Science, University of Agriculture in Kraków, Łobzowska 24, 31-140, Kraków, Poland
| | | | - Andrzej J Joachimiak
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, Gronostajowa 9, 30-387, Kraków, Poland.
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15
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Hobza R, Hudzieczek V, Kubat Z, Cegan R, Vyskot B, Kejnovsky E, Janousek B. Sex and the flower - developmental aspects of sex chromosome evolution. ANNALS OF BOTANY 2018; 122:1085-1101. [PMID: 30032185 PMCID: PMC6324748 DOI: 10.1093/aob/mcy130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/13/2018] [Indexed: 05/07/2023]
Abstract
Background The evolution of dioecious plants is occasionally accompanied by the establishment of sex chromosomes: both XY and ZW systems have been found in plants. Structural studies of sex chromosomes are now being followed up by functional studies that are gradually shedding light on the specific genetic and epigenetic processes that shape the development of separate sexes in plants. Scope This review describes sex determination diversity in plants and the genetic background of dioecy, summarizes recent progress in the investigation of both classical and emerging model dioecious plants and discusses novel findings. The advantages of interspecies hybrids in studies focused on sex determination and the role of epigenetic processes in sexual development are also overviewed. Conclusions We integrate the genic, genomic and epigenetic levels of sex determination and stress the impact of sex chromosome evolution on structural and functional aspects of plant sexual development. We also discuss the impact of dioecy and sex chromosomes on genome structure and expression.
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Affiliation(s)
- Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Vojtech Hudzieczek
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Zdenek Kubat
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Radim Cegan
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Boris Vyskot
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Eduard Kejnovsky
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
| | - Bohuslav Janousek
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska, Brno, Czech Republic
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16
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Veltsos P, Cossard G, Beaudoing E, Beydon G, Savova Bianchi D, Roux C, C González-Martínez S, R Pannell J. Size and Content of the Sex-Determining Region of the Y Chromosome in Dioecious Mercurialis annua, a Plant with Homomorphic Sex Chromosomes. Genes (Basel) 2018; 9:E277. [PMID: 29844299 PMCID: PMC6027223 DOI: 10.3390/genes9060277] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/16/2018] [Accepted: 05/23/2018] [Indexed: 01/01/2023] Open
Abstract
Dioecious plants vary in whether their sex chromosomes are heteromorphic or homomorphic, but even homomorphic sex chromosomes may show divergence between homologues in the non-recombining, sex-determining region (SDR). Very little is known about the SDR of these species, which might represent particularly early stages of sex-chromosome evolution. Here, we assess the size and content of the SDR of the diploid dioecious herb Mercurialis annua, a species with homomorphic sex chromosomes and mild Y-chromosome degeneration. We used RNA sequencing (RNAseq) to identify new Y-linked markers for M. annua. Twelve of 24 transcripts showing male-specific expression in a previous experiment could be amplified by polymerase chain reaction (PCR) only from males, and are thus likely to be Y-linked. Analysis of genome-capture data from multiple populations of M. annua pointed to an additional six male-limited (and thus Y-linked) sequences. We used these markers to identify and sequence 17 sex-linked bacterial artificial chromosomes (BACs), which form 11 groups of non-overlapping sequences, covering a total sequence length of about 1.5 Mb. Content analysis of this region suggests that it is enriched for repeats, has low gene density, and contains few candidate sex-determining genes. The BACs map to a subset of the sex-linked region of the genetic map, which we estimate to be at least 14.5 Mb. This is substantially larger than estimates for other dioecious plants with homomorphic sex chromosomes, both in absolute terms and relative to their genome sizes. Our data provide a rare, high-resolution view of the homomorphic Y chromosome of a dioecious plant.
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Affiliation(s)
- Paris Veltsos
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
- Department of Biology, Jordan Hall, 1001 East Third Street, Indiana University, Bloomington, IN 47405, USA.
| | - Guillaume Cossard
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Emmanuel Beaudoing
- Faculty of Biology and Medicine, University of Lausanne, Bâtiment Génopode, 1014 Lausanne, Switzerland.
| | - Genséric Beydon
- National Centre for Genomic Resources (CNRGV), 24 Chemin de Borde Rouge-Auzeville-CS52627, 31326 Castanet Tolosan Cedex, France.
| | | | - Camille Roux
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
- CNRS, University of Lille, UMR 8198-Evo-Eco-Paleo, F-59000 Lille, France.
| | - Santiago C González-Martínez
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
- BIOGECO, INRA, University of Bordeaux, 33610 Cestas, France.
| | - John R Pannell
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
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17
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Hill-Robertson Interference Reduces Genetic Diversity on a Young Plant Y-Chromosome. Genetics 2017; 207:685-695. [PMID: 28811388 DOI: 10.1534/genetics.117.300142] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 08/03/2017] [Indexed: 11/18/2022] Open
Abstract
X and Y chromosomes differ in effective population size (Ne ), rates of recombination, and exposure to natural selection, all of which can affect patterns of genetic diversity. On Y chromosomes with suppressed recombination, natural selection is expected to eliminate linked neutral variation, and lower the Ne of Y compared to X chromosomes or autosomes. However, female-biased sex ratios and high variance in male reproductive success can also reduce Y-linked Ne , making it difficult to infer the causes of low Y-diversity. Here, we investigate the factors affecting levels of polymorphism during sex chromosome evolution in the dioecious plant Rumexhastatulus (Polygonaceae). Strikingly, we find that neutral diversity for genes on the Y chromosome is, on average, 2.1% of the value for their X-linked homologs, corresponding to a chromosome-wide reduction of 93% compared to the standard neutral expectation. We demonstrate that the magnitude of this diversity loss is inconsistent with reduced male Ne caused by neutral processes. Instead, using forward simulations and estimates of the distribution of deleterious fitness effects, we show that Y chromosome diversity loss can be explained by purifying selection acting in aggregate over a large number of genetically linked sites. Simulations also suggest that our observed level of Y-diversity is consistent with the joint action of purifying and positive selection, but only for models in which there were fewer constrained sites than we empirically estimated. Given the relatively recent origin of R. hastatulus sex chromosomes, our results imply that Y-chromosome degeneration in the early stages may be largely driven by selective interference rather than by neutral genetic drift of silenced Y-linked genes.
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18
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Harkess A, Leebens-Mack J. A Century of Sex Determination in Flowering Plants. J Hered 2016; 108:69-77. [PMID: 27974487 DOI: 10.1093/jhered/esw060] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 09/07/2016] [Indexed: 11/14/2022] Open
Abstract
Plants have evolved a diverse array of strategies for sexual reproduction, particularly through the modification of male and female organs at distinct points in development. The immense variation in sexual systems across the land plants provides a unique opportunity to study the genetic, epigenetic, phylogenetic, and ecological underpinnings of sex determination. Here, we reflect on more than a century of research into flowering plant sex determination, placing a particular focus on the foundational genetic and cytogenetic observations, experiments, and hypotheses. Building on the seminal work on the genetics of plant sex, modern comparative genomic analyses now allow us to address longstanding questions about sex determination and the origins of sex chromosomes.
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Affiliation(s)
- Alex Harkess
- From the Department of Plant Biology, University of Georgia, Athens, GA 30602 (Harkess and Leebens-Mack), Alex Harkess is now at the Donald Danforth Plant Science Center, St. Louis MO 63132.
| | - Jim Leebens-Mack
- From the Department of Plant Biology, University of Georgia, Athens, GA 30602 (Harkess and Leebens-Mack), Alex Harkess is now at the Donald Danforth Plant Science Center, St. Louis MO 63132
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19
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Campos JL, Qiu S, Guirao-Rico S, Bergero R, Charlesworth D. Recombination changes at the boundaries of fully and partially sex-linked regions between closely related Silene species pairs. Heredity (Edinb) 2016; 118:395-403. [PMID: 27827389 DOI: 10.1038/hdy.2016.113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/05/2016] [Accepted: 10/05/2016] [Indexed: 11/09/2022] Open
Abstract
The establishment of a region of suppressed recombination is a critical change during sex chromosome evolution, leading to such properties as Y (and W) chromosome genetic degeneration, accumulation of repetitive sequences and heteromorphism. Although chromosome inversions can cause large regions to have suppressed recombination, and inversions are sometimes involved in sex chromosome evolution, gradual expansion of the non-recombining region could potentially sometimes occur. We here test whether closer linkage has recently evolved between the sex-determining region and several genes that are partially sex-linked in Silene latifolia, using Silene dioica, a closely related dioecious plants whose XY sex chromosome system is inherited from a common ancestor. The S. latifolia pseudoautosomal region (PAR) includes several genes extremely closely linked to the fully Y-linked region. These genes were added to an ancestral PAR of the sex chromosome pair in two distinct events probably involving translocations of autosomal genome regions causing multiple genes to become partially sex-linked. Close linkage with the PAR boundary must have evolved since these additions, because some genes added in both events now show almost complete sex linkage in S. latifolia. We compared diversity patterns of five such S. latifolia PAR boundary genes with their orthologues in S. dioica, including all three regions of the PAR (one gene that was in the ancestral PAR and two from each of the added regions). The results suggest recent recombination suppression in S. latifolia, since its split from S. dioica.
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Affiliation(s)
- J L Campos
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - S Qiu
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - S Guirao-Rico
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - R Bergero
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - D Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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20
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A Survey of Genetic Variation and Genome Evolution within the Invasive Fallopia Complex. PLoS One 2016; 11:e0161854. [PMID: 27575805 PMCID: PMC5004975 DOI: 10.1371/journal.pone.0161854] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 08/13/2016] [Indexed: 11/24/2022] Open
Abstract
The knotweed taxa Fallopia japonica, F. sachalinensis and their interspecific hybrid F. × bohemica are some of the most aggressive invaders in Europe and North America and they are serious threats to native biodiversity. At the same time, they constitute a unique model system for the creation of hybrids and studies of the initiation of evolutionary processes. In the presented study, we focused on (i) examining genetic diversity in selected populations of three Fallopia taxa in the invaded (Poland) and native ranges (Japan), (ii) establishing genome size and ploidy levels and (iii) identifying ribosomal DNA (rDNA)-bearing chromosomes in all of the taxa from the invaded range. We found that the genetic diversity within particular taxa was generally low regardless of their geographical origin. A higher level of clonality was observed for the Polish populations compared to the Japanese populations. Our study suggests that the co-occurrence of F. sachalinensis together with the other two taxa in the same stand may be the source of the higher genetic variation within the F. × bohemica hybrid. Some shift towards the contribution of F. japonica alleles was also observed for selected F. × bohemica individuals, which indicates the possibility of producing more advanced generations of F. × bohemica hybrids. All of the F. sachalinensis individuals were hexaploid (2n = 6x = 66; 2C = 6.01 pg), while those of F. japonica were mostly octoploid (2n = 8x = 88; 2C = 8.87 pg) and all of the F. × bohemica plants except one were hexaploid (2n = 6x = 66; 2C = 6.46 pg). Within the chromosome complement of F. japonica, F. sachalinensis and F. × bohemica, the physical mapping of the rDNA loci provided markers for 16, 13 and 10 chromosomes, respectively. In F. × bohemica, a loss of some of rDNA loci was observed, which indicates the occurrence of genome changes in the hybrid.
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21
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Razumova OV, Alexandrov OS, Divashuk MG, Sukhorada TI, Karlov GI. Molecular cytogenetic analysis of monoecious hemp (Cannabis sativa L.) cultivars reveals its karyotype variations and sex chromosomes constitution. PROTOPLASMA 2016; 253:895-901. [PMID: 26149370 DOI: 10.1007/s00709-015-0851-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Accepted: 06/19/2015] [Indexed: 05/21/2023]
Abstract
Hemp (Cannabis sativa L., 2n = 20) is a dioecious plant. Sex expression is controlled by an X-to-autosome balance system consisting of the heteromorphic sex chromosomes XY for males and XX for females. Genetically monoecious hemp offers several agronomic advantages compared to the dioecious cultivars that are widely used in hemp cultivation. The male or female origin of monoecious maternal plants is unknown. Additionally, the sex chromosome composition of monoecious hemp forms remains unknown. In this study, we examine the sex chromosome makeup in monoecious hemp using a cytogenetic approach. Eight monoecious and two dioecious cultivars were used. The DNA of 210 monoecious plants was used for PCR analysis with the male-associated markers MADC2 and SCAR323. All monoecious plants showed female amplification patterns. Fluorescence in situ hybridization (FISH) with the subtelomeric CS-1 probe to chromosomes plates and karyotyping revealed a lack of Y chromosome and presence of XX sex chromosomes in monoecious cultivars with the chromosome number 2n = 20. There was a high level of intra- and intercultivar karyotype variation detected. The results of this study can be used for further analysis of the genetic basis of sex expression in plants.
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Affiliation(s)
- Olga V Razumova
- Center for Molecular Biotechnology, Russian State Agrarian University-MTAA, Timiryazevskaya St. 49, Moscow, 127550, Russia
| | - Oleg S Alexandrov
- Center for Molecular Biotechnology, Russian State Agrarian University-MTAA, Timiryazevskaya St. 49, Moscow, 127550, Russia
| | - Mikhail G Divashuk
- Center for Molecular Biotechnology, Russian State Agrarian University-MTAA, Timiryazevskaya St. 49, Moscow, 127550, Russia
| | - Tatiana I Sukhorada
- Krasnodar Lukyanenko Research Institute of Agriculture, C/U KNIISH, Krasnodar, 350012, Russia
| | - Gennady I Karlov
- Center for Molecular Biotechnology, Russian State Agrarian University-MTAA, Timiryazevskaya St. 49, Moscow, 127550, Russia.
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22
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Abstract
Although individuals in most flowering plant species, and in many haploid plants, have both sex functions, dioecious species-in which individuals have either male or female functions only-are scattered across many taxonomic groups, and many species have genetic sex determination. Among these, some have visibly heteromorphic sex chromosomes, and molecular genetic studies are starting to uncover sex-linked markers in others, showing that they too have fully sex-linked regions that are either too small or are located in chromosomes that are too small to be cytologically detectable from lack of pairing, lack of visible crossovers, or accumulation of heterochromatin. Detailed study is revealing that, like animal sex chromosomes, plant sex-linked regions show evidence for accumulation of repetitive sequences and genetic degeneration. Estimating when recombination stopped confirms the view that many plants have young sex-linked regions, making plants of great interest for studying the timescale of these changes.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
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23
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Rodrigues N, Vuille Y, Brelsford A, Merilä J, Perrin N. The genetic contribution to sex determination and number of sex chromosomes vary among populations of common frogs (Rana temporaria). Heredity (Edinb) 2016; 117:25-32. [PMID: 27071845 DOI: 10.1038/hdy.2016.22] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 02/24/2016] [Accepted: 02/26/2016] [Indexed: 01/18/2023] Open
Abstract
The patterns of sex determination and sex differentiation have been shown to differ among geographic populations of common frogs. Notably, the association between phenotypic sex and linkage group 2 (LG2) has been found to be perfect in a northern Swedish population, but weak and variable among families in a southern one. By analyzing these populations with markers from other linkage groups, we bring two new insights: (1) the variance in phenotypic sex not accounted for by LG2 in the southern population could not be assigned to genetic factors on other linkage groups, suggesting an epigenetic component to sex determination; (2) a second linkage group (LG7) was found to co-segregate with sex and LG2 in the northern population. Given the very short timeframe since post-glacial colonization (in the order of 1000 generations) and its seemingly localized distribution, this neo-sex chromosome system might be the youngest one described so far. It does not result from a fusion, but more likely from a reciprocal translocation between the original Y chromosome (LG2) and an autosome (LG7), causing their co-segregation during male meiosis. By generating a strict linkage between several important genes from the sex-determination cascade (Dmrt1, Amh and Amhr2), this neo-sex chromosome possibly contributes to the 'differentiated sex race' syndrome (strictly genetic sex determination and early gonadal development) that characterizes this northern population.
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Affiliation(s)
- N Rodrigues
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Y Vuille
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - A Brelsford
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - J Merilä
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - N Perrin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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24
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Bhowmick BK, Yamamoto M, Jha S. Chromosomal localization of 45S rDNA, sex-specific C values, and heterochromatin distribution in Coccinia grandis (L.) Voigt. PROTOPLASMA 2016; 253:201-209. [PMID: 25795278 DOI: 10.1007/s00709-015-0797-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/05/2015] [Indexed: 06/04/2023]
Abstract
Coccinia grandis is a widely distributed dioecious cucurbit in India, with heteromorphic sex chromosomes and X-Y sex determination mode. The present study aids in the cytogenetic characterization of four native populations of this plant employing distribution patterns of 45S rDNA on chromosomes and guanine-cytosine (GC)-rich heterochromatin in the genome coupled with flow cytometric determination of genome sizes. Existence of four nucleolar chromosomes could be confirmed by the presence of four telomeric 45S rDNA signals in both male and female plants. All four 45S rDNA sites are rich in heterochromatin evident from the co-localization of telomeric chromomycin A (CMA)(+ve) signals. The size of 45S rDNA signal was found to differ between the homologues of one nucleolar chromosome pair. The distribution of heterochromatin is found to differ among the male and female populations. The average GC-rich heterochromatin content of male and female populations is 23.27 and 29.86 %, respectively. Moreover, the male plants have a genome size of 0.92 pg/2C while the female plants have a size of 0.73 pg/2C, reflecting a huge genomic divergence between the genders. The great variation in genome size is owing to the presence of Y chromosome in the male populations, playing a multifaceted role in sexual divergence in C. grandis.
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Affiliation(s)
- Biplab Kumar Bhowmick
- Center of Advanced Study, Department of Botany, University of Calcutta 35, Ballygunge Circular Road, Kolkata, West Bengal, 700019, India.
| | - Masashi Yamamoto
- Faculty of Agriculture, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan.
| | - Sumita Jha
- Center of Advanced Study, Department of Botany, University of Calcutta 35, Ballygunge Circular Road, Kolkata, West Bengal, 700019, India.
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25
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Garrido-Ramos MA. Satellite DNA in Plants: More than Just Rubbish. Cytogenet Genome Res 2015; 146:153-170. [PMID: 26202574 DOI: 10.1159/000437008] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2015] [Indexed: 11/19/2022] Open
Abstract
For decades, satellite DNAs have been the hidden part of genomes. Initially considered as junk DNA, there is currently an increasing appreciation of the functional significance of satellite DNA repeats and of their sequences. Satellite DNA families accumulate in the heterochromatin in different parts of the eukaryotic chromosomes, mainly in pericentromeric and subtelomeric regions, but they also span the functional centromere. Tandem repeat sequences may spread from subtelomeric to interstitial loci, leading to the formation of chromosome-specific loci or to the accumulation in equilocal sites in different chromosomes. They also appear as the main components of the heterochromatin in the sex-specific region of sex chromosomes. Satellite DNA, required for chromosome organization, also plays a role in pairing and segregation. Some satellite repeats are transcribed and can participate in the formation and maintenance of heterochromatin structure and in the modulation of gene expression. In addition to the identification of the different satellite DNA families, their characteristics and location, we are interested in determining their impact on the genomes, by identifying the mechanisms leading to their appearance and amplification as well as in understanding how they change over time, the factors affecting these changes, and the influence exerted by the evolutionary history of the organisms. On the other hand, satellite DNA sequences are rapidly evolving sequences that may cause reproductive barriers between organisms and promote speciation. The accumulation of experimental data collected in recent years and the emergence of new approaches based on next-generation sequencing and high-throughput genome analysis are opening new perspectives that are changing our understanding of satellite DNA. This review examines recent data to provide a timely update on the overall information gathered about this part of the genome, focusing on the advances in the knowledge of its origin, its evolution, and its potential functional roles.
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