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Tavernier EK, Perroud PF, Lockwood E, Nogué F, McDaniel SF. Establishing CRISPR-Cas9 in the sexually dimorphic moss, Ceratodon purpureus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39154335 DOI: 10.1111/tpj.16946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 07/07/2024] [Accepted: 07/13/2024] [Indexed: 08/20/2024]
Abstract
The development of CRISPR technologies provides a powerful tool for understanding the evolution and functionality of essential biological processes. Here we demonstrate successful CRISPR-Cas9 genome editing in the dioecious moss species, Ceratodon purpureus. Using an existing selection system from the distantly related hermaphroditic moss, Physcomitrium patens, we generated knock-outs of the APT reporter gene by employing CRISPR-targeted mutagenesis under expression of native U6 snRNA promoters. Next, we used the native homology-directed repair (HDR) pathway, combined with CRISPR-Cas9, to knock in two reporter genes under expression of an endogenous RPS5A promoter in a newly developed landing site in C. purpureus. Our results show that the molecular tools developed in P. patens can be extended to other mosses across this ecologically important and developmentally variable group. These findings pave the way for precise and powerful experiments aimed at identifying the genetic basis of key functional variation within the bryophytes and between the bryophytes and other land plants.
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Affiliation(s)
- Emilie-Katherine Tavernier
- Department of Biology, University of Florida, Gainesville, Florida, USA
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
| | - Pierre-François Perroud
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
| | - Emily Lockwood
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Fabien Nogué
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
| | - Stuart F McDaniel
- Department of Biology, University of Florida, Gainesville, Florida, USA
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2
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Sandler G, Agrawal AF, Wright SI. Population Genomics of the Facultatively Sexual Liverwort Marchantia polymorpha. Genome Biol Evol 2023; 15:evad196. [PMID: 37883717 PMCID: PMC10667032 DOI: 10.1093/gbe/evad196] [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: 12/16/2022] [Revised: 10/15/2023] [Accepted: 10/18/2023] [Indexed: 10/28/2023] Open
Abstract
The population genomics of facultatively sexual organisms are understudied compared with their abundance across the tree of life. We explore patterns of genetic diversity in two subspecies of the facultatively sexual liverwort Marchantia polymorpha using samples from across Southern Ontario, Canada. Despite the ease with which M. polymorpha should be able to propagate asexually, we find no evidence of strictly clonal descent among our samples and little to no signal of isolation by distance. Patterns of identity-by-descent tract sharing further showed evidence of recent recombination and close relatedness between geographically distant isolates, suggesting long distance gene flow and at least a modest frequency of sexual reproduction. However, the M. polymorpha genome contains overall very low levels of nucleotide diversity and signs of inefficient selection evidenced by a relatively high fraction of segregating deleterious variants. We interpret these patterns as possible evidence of the action of linked selection and a small effective population size due to past generations of asexual propagation. Overall, the M. polymorpha genome harbors signals of a complex history of both sexual and asexual reproduction.
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Affiliation(s)
- George Sandler
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Aneil F Agrawal
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Center for Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Center for Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
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3
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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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4
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Carey SB, Jenkins J, Lovell JT, Maumus F, Sreedasyam A, Payton AC, Shu S, Tiley GP, Fernandez-Pozo N, Healey A, Barry K, Chen C, Wang M, Lipzen A, Daum C, Saski CA, McBreen JC, Conrad RE, Kollar LM, Olsson S, Huttunen S, Landis JB, Burleigh JG, Wickett NJ, Johnson MG, Rensing SA, Grimwood J, Schmutz J, McDaniel SF. Gene-rich UV sex chromosomes harbor conserved regulators of sexual development. SCIENCE ADVANCES 2021; 7:7/27/eabh2488. [PMID: 34193417 PMCID: PMC8245031 DOI: 10.1126/sciadv.abh2488] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/14/2021] [Indexed: 05/19/2023]
Abstract
Nonrecombining sex chromosomes, like the mammalian Y, often lose genes and accumulate transposable elements, a process termed degeneration. The correlation between suppressed recombination and degeneration is clear in animal XY systems, but the absence of recombination is confounded with other asymmetries between the X and Y. In contrast, UV sex chromosomes, like those found in bryophytes, experience symmetrical population genetic conditions. Here, we generate nearly gapless female and male chromosome-scale reference genomes of the moss Ceratodon purpureus to test for degeneration in the bryophyte UV sex chromosomes. We show that the moss sex chromosomes evolved over 300 million years ago and expanded via two chromosomal fusions. Although the sex chromosomes exhibit weaker purifying selection than autosomes, we find that suppressed recombination alone is insufficient to drive degeneration. Instead, the U and V sex chromosomes harbor thousands of broadly expressed genes, including numerous key regulators of sexual development across land plants.
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Affiliation(s)
- Sarah B Carey
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - John T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Florian Maumus
- Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
| | - Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Adam C Payton
- Department of Biology, University of Florida, Gainesville, FL, USA
- RAPiD Genomics, Gainesville, FL, USA
| | - Shengqiang Shu
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | | | - Adam Healey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cindy Chen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mei Wang
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Daum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christopher A Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Jordan C McBreen
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Roth E Conrad
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Leslie M Kollar
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Sanna Olsson
- Department of Forest Ecology and Genetics, INIA-CIFOR, Madrid, Spain
| | - Sanna Huttunen
- Department of Biology and Biodiversity Unit, University of Turku, Turku, Finland
| | - Jacob B Landis
- L.H. Bailey Hortorium and Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | | | - Norman J Wickett
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, USA
| | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Stefan A Rensing
- Plant Cell Biology, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Hans-Meerwein-Straße 6, 35032 Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104 Freiburg im Breisgau, Germany
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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5
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Sousa A, Schubert V, Renner SS. Centromere organization and UU/V sex chromosome behavior in a liverwort. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:133-141. [PMID: 33372295 DOI: 10.1111/tpj.15150] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/15/2020] [Accepted: 12/23/2020] [Indexed: 06/12/2023]
Abstract
In 1917, sex chromosomes in plants were discovered in a liverwort with hetermorphic U and V chromosomes. Such heteromorphy is unexpected because, unlike the XY chromosomes in diploid-dominant plants, in haploid-dominant plants the female U and the male V chromosomes experience largely symmetrical potential recombination environments. Here we use molecular cytogenetics and super-resolution microscopy to study Frullania dilatata, a liverwort with one male and two female sex chromosomes. We applied a pipeline to Illumina sequences to detect abundant types of repetitive DNA and developed FISH probes to microscopically distinguish the sex chromosomes. We also determined the phenotypic population sex ratio because biased ratios have been reported from other liverworts with heteromorphic sex chromosomes. Populations had male-biased sex ratios. The sex chromosomes are monocentric, and of 14 probes studied (eight satellites, five transposable elements and one plastid region), four resulted in unique signals that differentiated the sex chromosomes from the autosomes and from each other. One FISH probe selectively marked the centromeres of both U chromosomes, so we could prove that during meiosis each U chromosome associates with one of the opposite telomeres of the V chromosome, resulting in a head-to-head trivalent. The similarity of the two U chromosomes to each other in size and in their centromere FISH signal positions points to their origin via a non-disjunction event (aneuploidy), which would fit with the general picture of sex chromosomes rarely crossing-over and being prone to suffer from non-disjunction.
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Affiliation(s)
- Aretuza Sousa
- Systematic Botany and Mycology, Department of Biology, University of Munich (LMU), Munich, 80638, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, 06466, Germany
| | - Susanne S Renner
- Systematic Botany and Mycology, Department of Biology, University of Munich (LMU), Munich, 80638, Germany
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6
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Marks RA, Smith JJ, Cronk Q, Grassa CJ, McLetchie DN. Genome of the tropical plant Marchantia inflexa: implications for sex chromosome evolution and dehydration tolerance. Sci Rep 2019; 9:8722. [PMID: 31217536 PMCID: PMC6584576 DOI: 10.1038/s41598-019-45039-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 05/29/2019] [Indexed: 01/29/2023] Open
Abstract
We present a draft genome assembly for the tropical liverwort, Marchantia inflexa, which adds to a growing body of genomic resources for bryophytes and provides an important perspective on the evolution and diversification of land plants. We specifically address questions related to sex chromosome evolution, sexual dimorphisms, and the genomic underpinnings of dehydration tolerance. This assembly leveraged the recently published genome of related liverwort, M. polymorpha, to improve scaffolding and annotation, aid in the identification of sex-linked sequences, and quantify patterns of sequence differentiation within Marchantia. We find that genes on sex chromosomes are under greater diversifying selection than autosomal and organellar genes. Interestingly, this is driven primarily by divergence of male-specific genes, while divergence of other sex-linked genes is similar to autosomal genes. Through analysis of sex-specific read coverage, we identify and validate genetic sex markers for M. inflexa, which will enable diagnosis of sex for non-reproductive individuals. To investigate dehydration tolerance, we capitalized on a difference between genetic lines, which allowed us to identify multiple dehydration associated genes two of which were sex-linked, suggesting that dehydration tolerance may be impacted by sex-specific genes.
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Affiliation(s)
- Rose A Marks
- Department of Biology, University of Kentucky, 101 Thomas Hunt Morgan Building, Lexington, KY, 40506, USA.
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, 101 Thomas Hunt Morgan Building, Lexington, KY, 40506, USA
| | - Quentin Cronk
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - Christopher J Grassa
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA, 02138, USA
| | - D Nicholas McLetchie
- Department of Biology, University of Kentucky, 101 Thomas Hunt Morgan Building, Lexington, KY, 40506, USA
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7
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Abstract
Levels and patterns of genetic diversity can provide insights into a population’s history. In species with sex chromosomes, differences between genomic regions with unique inheritance patterns can be used to distinguish between different sets of possible demographic and selective events. This review introduces the differences in population history for sex chromosomes and autosomes, provides the expectations for genetic diversity across the genome under different evolutionary scenarios, and gives an introductory description for how deviations in these expectations are calculated and can be interpreted. Predominantly, diversity on the sex chromosomes has been used to explore and address three research areas: 1) Mating patterns and sex-biased variance in reproductive success, 2) signatures of selection, and 3) evidence for modes of speciation and introgression. After introducing the theory, this review catalogs recent studies of genetic diversity on the sex chromosomes across species within the major research areas that sex chromosomes are typically applied to, arguing that there are broad similarities not only between male-heterogametic (XX/XY) and female-heterogametic (ZZ/ZW) sex determination systems but also any mating system with reduced recombination in a sex-determining region. Further, general patterns of reduced diversity in nonrecombining regions are shared across plants and animals. There are unique patterns across populations with vastly different patterns of mating and speciation, but these do not tend to cluster by taxa or sex determination system.
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Affiliation(s)
- Melissa A Wilson Sayres
- School of Life Sciences, Center for Evolution and Medicine, The Biodesign Institute, Arizona State University
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8
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Coelho SM, Gueno J, Lipinska AP, Cock JM, Umen JG. UV Chromosomes and Haploid Sexual Systems. TRENDS IN PLANT SCIENCE 2018; 23:794-807. [PMID: 30007571 PMCID: PMC6128410 DOI: 10.1016/j.tplants.2018.06.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/04/2018] [Accepted: 06/07/2018] [Indexed: 05/20/2023]
Abstract
The evolution of sex determination continues to pose major questions in biology. Sex-determination mechanisms control reproductive cell differentiation and development of sexual characteristics in all organisms, from algae to animals and plants. While the underlying processes defining sex (meiosis and recombination) are conserved, sex-determination mechanisms are highly labile. In particular, a flow of new discoveries has highlighted several fascinating features of the previously understudied haploid UV sex determination and related mating systems found in diverse photosynthetic taxa including green algae, bryophytes, and brown algae. Analyses integrating information from these systems and contrasting them with classical XY and ZW systems are providing exciting insights into both the universality and the diversity of sex-determining chromosomes across eukaryotes.
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Affiliation(s)
- Susana Margarida Coelho
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France.
| | - Josselin Gueno
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Agnieszka Paulina Lipinska
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Jeremy Mark Cock
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - James G Umen
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
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9
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Nieto-Lugilde M, Werner O, McDaniel SF, Koutecký P, Kučera J, Rizk SM, Ros RM. Peripatric speciation associated with genome expansion and female-biased sex ratios in the moss genus Ceratodon. AMERICAN JOURNAL OF BOTANY 2018; 105:1009-1020. [PMID: 29957852 DOI: 10.1002/ajb2.1107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 03/21/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY A period of allopatry is widely believed to be essential for the evolution of reproductive isolation. However, strict allopatry may be difficult to achieve in some cosmopolitan, spore-dispersed groups, like mosses. We examined the genetic and genome size diversity in Mediterranean populations of the moss Ceratodon purpureus s.l. to evaluate the role of allopatry and ploidy change in population divergence. METHODS We sampled populations of the genus Ceratodon from mountainous areas and lowlands of the Mediterranean region, and from Western and Central Europe. We performed phylogenetic and coalescent analyses on sequences from five nuclear introns and a chloroplast locus to reconstruct their evolutionary history. We also estimated genome size using flow cytometry (employing propidium iodide) and determined the sex of samples using a sex-linked PCR marker. KEY RESULTS Two well-differentiated clades were resolved, discriminating two homogeneous groups: the widespread C. purpureus and a local group mostly restricted to the mountains in Southern Spain. The latter also possessed a genome size 25% larger than the widespread C. purpureus, and the samples of this group consist entirely of females. We also found hybrids, and some of them had a genome size equivalent to the sum of the C. purpureus and Spanish genome, suggesting that they arose by allopolyploidy. CONCLUSIONS These data suggest that a new species of Ceratodon arose via peripatric speciation, potentially involving a genome size change and a strong female-biased sex ratio. The new species has hybridized in the past with C. purpureus.
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Affiliation(s)
- Marta Nieto-Lugilde
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Murcia, Campus de Espinardo, 30100, Murcia, Spain
| | - Olaf Werner
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Murcia, Campus de Espinardo, 30100, Murcia, Spain
| | - Stuart F McDaniel
- Biology Department, University of Florida, Gainesville, Florida, 32611, USA
| | - Petr Koutecký
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-370 05, České Budějovice, Czech Republic
| | - Jan Kučera
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-370 05, České Budějovice, Czech Republic
| | - Samah Mohamed Rizk
- Genetics Department, Faculty of Agriculture, Ain Shams University, 68 Hadayek Shubra, 11241, Cairo, Egypt
| | - Rosa M Ros
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Murcia, Campus de Espinardo, 30100, Murcia, Spain
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10
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Muyle A, Shearn R, Marais GA. The Evolution of Sex Chromosomes and Dosage Compensation in Plants. Genome Biol Evol 2017; 9:627-645. [PMID: 28391324 PMCID: PMC5629387 DOI: 10.1093/gbe/evw282] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2017] [Indexed: 12/17/2022] Open
Abstract
Plant sex chromosomes can be vastly different from those of the few historical animal model organisms from which most of our understanding of sex chromosome evolution is derived. Recently, we have seen several advancements from studies on green algae, brown algae, and land plants that are providing a broader understanding of the variable ways in which sex chromosomes can evolve in distant eukaryotic groups. Plant sex-determining genes are being identified and, as expected, are completely different from those in animals. Species with varying levels of differentiation between the X and Y have been found in plants, and these are hypothesized to be representing different stages of sex chromosome evolution. However, we are also finding that sex chromosomes can remain morphologically unchanged over extended periods of time. Where degeneration of the Y occurs, it appears to proceed similarly in plants and animals. Dosage compensation (a phenomenon that compensates for the consequent loss of expression from the Y) has now been documented in a plant system, its mechanism, however, remains unknown. Research has also begun on the role of sex chromosomes in sexual conflict resolution, and it appears that sex-biased genes evolve similarly in plants and animals, although the functions of these genes remain poorly studied. Because the difficulty in obtaining sex chromosome sequences is increasingly being overcome by methodological developments, there is great potential for further discovery within the field of plant sex chromosome evolution.
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Affiliation(s)
- Aline Muyle
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
| | - Rylan Shearn
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
| | - Gabriel Ab Marais
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
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11
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Yamazaki T, Ichihara K, Suzuki R, Oshima K, Miyamura S, Kuwano K, Toyoda A, Suzuki Y, Sugano S, Hattori M, Kawano S. Genomic structure and evolution of the mating type locus in the green seaweed Ulva partita. Sci Rep 2017; 7:11679. [PMID: 28916791 PMCID: PMC5601483 DOI: 10.1038/s41598-017-11677-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 08/29/2017] [Indexed: 01/08/2023] Open
Abstract
The evolution of sex chromosomes and mating loci in organisms with UV systems of sex/mating type determination in haploid phases via genes on UV chromosomes is not well understood. We report the structure of the mating type (MT) locus and its evolutionary history in the green seaweed Ulva partita, which is a multicellular organism with an isomorphic haploid-diploid life cycle and mating type determination in the haploid phase. Comprehensive comparison of a total of 12.0 and 16.6 Gb of genomic next-generation sequencing data for mt- and mt+ strains identified highly rearranged MT loci of 1.0 and 1.5 Mb in size and containing 46 and 67 genes, respectively, including 23 gametologs. Molecular evolutionary analyses suggested that the MT loci diverged over a prolonged period in the individual mating types after their establishment in an ancestor. A gene encoding an RWP-RK domain-containing protein was found in the mt- MT locus but was not an ortholog of the chlorophycean mating type determination gene MID. Taken together, our results suggest that the genomic structure and its evolutionary history in the U. partita MT locus are similar to those on other UV chromosomes and that the MT locus genes are quite different from those of Chlorophyceae.
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Affiliation(s)
- Tomokazu Yamazaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Kensuke Ichihara
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Ryogo Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Kenshiro Oshima
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Shinichi Miyamura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Kazuyoshi Kuwano
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Japan
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Masahira Hattori
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Shigeyuki Kawano
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan.
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12
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Baughman JT, Payton AC, Paasch AE, Fisher KM, McDaniel SF. Multiple factors influence population sex ratios in the Mojave Desert moss Syntrichia caninervis. AMERICAN JOURNAL OF BOTANY 2017; 104:733-742. [PMID: 28490519 DOI: 10.3732/ajb.1700045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/27/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF RESEARCH Natural populations of many mosses appear highly female-biased based on the presence of reproductive structures. This bias could be caused by increased male mortality, lower male growth rate, or a higher threshold for achieving sexual maturity in males. Here we test these hypotheses using samples from two populations of the Mojave Desert moss Syntrichia caninervis. METHODS We used double-digest restriction-site associated DNA (RAD) sequencing to identify candidate sex-associated loci in a panel of sex-expressing plants. Next, we used putative sex-associated markers to identify the sex of individuals without sex structures. KEY RESULTS We found a 17:1 patch-level phenotypic female to male sex ratio in the higher elevation site (Wrightwood) and no sex expression at the low elevation site (Phelan). In contrast, on the basis of genetic data, we found a 2:1 female bias at the Wrightwood site and only females at the Phelan site. The relative area occupied by male and female genets was indistinguishable, but males were less genetically diverse. CONCLUSIONS Our data suggest that both male-biased mortality and sexual dimorphism in thresholds for sex expression could explain genetic and phenotypic sex ratio biases and that phenotypic sex expression alone over-estimates the extent of actual sex ratio bias present in these two populations of S. caninervis.
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Affiliation(s)
- Jenna T Baughman
- Department of Biological Sciences, California State University, 5151 State University Drive, Los Angeles, California 90032 USA
| | - Adam C Payton
- Department of Biology, University of Florida, 876 Newell Drive, Gainesville, Florida 32611 USA
| | - Amber E Paasch
- Department of Biological Sciences, California State University, 5151 State University Drive, Los Angeles, California 90032 USA
| | - Kirsten M Fisher
- Department of Biological Sciences, California State University, 5151 State University Drive, Los Angeles, California 90032 USA
| | - Stuart F McDaniel
- Department of Biology, University of Florida, 876 Newell Drive, Gainesville, Florida 32611 USA
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Sequence of the Gonium pectorale Mating Locus Reveals a Complex and Dynamic History of Changes in Volvocine Algal Mating Haplotypes. G3-GENES GENOMES GENETICS 2016; 6:1179-89. [PMID: 26921294 PMCID: PMC4856071 DOI: 10.1534/g3.115.026229] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sex-determining regions (SDRs) or mating-type (MT) loci in two sequenced volvocine algal species, Chlamydomonas reinhardtii and Volvox carteri, exhibit major differences in size, structure, gene content, and gametolog differentiation. Understanding the origin of these differences requires investigation of MT loci from related species. Here, we determined the sequences of the minus and plus MT haplotypes of the isogamous 16-celled volvocine alga, Gonium pectorale, which is more closely related to the multicellular V. carteri than to C. reinhardtii. Compared to C. reinhardtii MT, G. pectorale MT is moderately larger in size, and has a less complex structure, with only two major syntenic blocs of collinear gametologs. However, the gametolog content of G. pectorale MT has more overlap with that of V. carteri MT than with C. reinhardtii MT, while the allelic divergence between gametologs in G. pectorale is even lower than that in C. reinhardtii. Three key sex-related genes are conserved in G. pectorale MT: GpMID and GpMTD1 in MT–, and GpFUS1 in MT+. GpFUS1 protein exhibited specific localization at the plus-gametic mating structure, indicating a conserved function in fertilization. Our results suggest that the G. pectorale–V. carteri common ancestral MT experienced at least one major reformation after the split from C. reinhardtii, and that the V. carteri ancestral MT underwent a subsequent expansion and loss of recombination after the divergence from G. pectorale. These data begin to polarize important changes that occurred in volvocine MT loci, and highlight the potential for discontinuous and dynamic evolution in SDRs.
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14
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Abstract
The nonrecombining regions of animal Y chromosomes are known to undergo genetic degeneration, but previous work has failed to reveal large-scale gene degeneration on plant Y chromosomes. Here, we uncover rapid and extensive degeneration of Y-linked genes in a plant species, Silene latifolia, that evolved sex chromosomes de novo in the last 10 million years. Previous transcriptome-based studies of this species missed unexpressed, degenerate Y-linked genes. To identify sex-linked genes, regardless of their expression, we sequenced male and female genomes of S. latifolia and integrated the genomic contigs with a high-density genetic map. This revealed that 45% of Y-linked genes are not expressed, and 23% are interrupted by premature stop codons. This contrasts with X-linked genes, in which only 1.3% of genes contained stop codons and 4.3% of genes were not expressed in males. Loss of functional Y-linked genes is partly compensated for by gene-specific up-regulation of X-linked genes. Our results demonstrate that the rate of genetic degeneration of Y-linked genes in S. latifolia is as fast as in animals, and that the evolutionary trajectories of sex chromosomes are similar in the two kingdoms.
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15
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Charlesworth D. Plant contributions to our understanding of sex chromosome evolution. THE NEW PHYTOLOGIST 2015; 208:52-65. [PMID: 26053356 DOI: 10.1111/nph.13497] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 05/01/2015] [Indexed: 05/06/2023]
Abstract
A minority of angiosperms have male and female flowers separated in distinct individuals (dioecy), and most dioecious plants do not have cytologically different (heteromorphic) sex chromosomes. Plants nevertheless have several advantages for the study of sex chromosome evolution, as genetic sex determination has evolved repeatedly and is often absent in close relatives. I review sex-determining regions in non-model plant species, which may help us to understand when and how (and, potentially, test hypotheses about why) recombination suppression evolves within young sex chromosomes. I emphasize high-throughput sequencing approaches that are increasingly being applied to plants to test for non-recombining regions. These data are particularly illuminating when combined with sequence data that allow phylogenetic analyses, and estimates of when these regions evolved. Together with comparative genetic mapping, this has revealed that sex-determining loci and sex-linked regions evolved independently in many plant lineages, sometimes in closely related dioecious species, and often within the past few million years. In reviewing recent progress, I suggest areas for future work, such as the use of phylogenies to allow the informed choice of outgroup species suitable for inferring the directions of changes, including testing whether Y chromosome-like regions are undergoing genetic degeneration, a predicted consequence of losing recombination.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Lab, King's Buildings, W. Mains Road, Edinburgh, EH9 3FL, UK
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16
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Chaos of Rearrangements in the Mating-Type Chromosomes of the Anther-Smut Fungus Microbotryum lychnidis-dioicae. Genetics 2015; 200:1275-84. [PMID: 26044594 PMCID: PMC4574255 DOI: 10.1534/genetics.115.177709] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 06/02/2015] [Indexed: 12/02/2022] Open
Abstract
Sex chromosomes in plants and animals and fungal mating-type chromosomes often show exceptional genome features, with extensive suppression of homologous recombination and cytological differentiation between members of the diploid chromosome pair. Despite strong interest in the genetics of these chromosomes, their large regions of suppressed recombination often are enriched in transposable elements and therefore can be challenging to assemble. Here we show that the latest improvements of the PacBio sequencing yield assembly of the whole genome of the anther-smut fungus, Microbotryum lychnidis-dioicae (the pathogenic fungus causing anther-smut disease of Silene latifolia), into finished chromosomes or chromosome arms, even for the repeat-rich mating-type chromosomes and centromeres. Suppressed recombination of the mating-type chromosomes is revealed to span nearly 90% of their lengths, with extreme levels of rearrangements, transposable element accumulation, and differentiation between the two mating types. We observed no correlation between allelic divergence and physical position in the nonrecombining regions of the mating-type chromosomes. This may result from gene conversion or from rearrangements of ancient evolutionary strata, i.e., successive steps of suppressed recombination. Centromeres were found to be composed mainly of copia-like transposable elements and to possess specific minisatellite repeats identical between the different chromosomes. We also identified subtelomeric motifs. In addition, extensive signs of degeneration were detected in the nonrecombining regions in the form of transposable element accumulation and of hundreds of gene losses on each mating-type chromosome. Furthermore, our study highlights the potential of the latest breakthrough PacBio chemistry to resolve complex genome architectures.
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Hedenäs L, Bisang I. Infraspecific diversity in a spore-dispersed species with limited distribution range. SYST BIODIVERS 2014. [DOI: 10.1080/14772000.2014.968234] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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