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Qiao Q, Cao Q, Zhang R, Wu M, Zheng Y, Xue L, Lei J, Sun H, Liston A, Zhang T. Genomic analyses provide insights into sex differentiation of tetraploid strawberry (Fragaria moupinensis). PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1552-1565. [PMID: 38184782 PMCID: PMC11123429 DOI: 10.1111/pbi.14286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/08/2024]
Abstract
The strawberry genus, Fragaria, exhibits a wide range of sexual systems and natural ploidy variation. Nearly, all polyploid strawberry species exhibit separate sexes (dioecy). Research has identified the sex-determining sequences as roughly conserved but with repeatedly changed genomic locations across octoploid strawberries. However, it remains unclear whether tetraploid wild strawberries evolved dioecy independently or shared a common origin with octoploid strawberries. In this study, we investigated the sex determinants of F. moupinensis, a dioecious plant with heterogametic females (ZW). Utilizing a combination of haplotype-resolved genome sequencing of the female F. moupinensis, k-mer-based and coverage-based genome-wide association studies (GWAS), and transcriptomic analysis, we discovered a non-recombining, approximately 33.6 kb W-specific region on chromosome 2a. Within this region, only one candidate sex-determining gene (FmoAFT) was identified. Furthermore, an extensive resequencing of the entire Fragaria genus indicated that the W-specific region displays conservative female specificity across all tetraploid species. This observation suggests that dioecy evolved independently in tetraploid and octoploid strawberries. Moreover, employing virus-induced gene silencing (VIGS), we knocked down the expression of the FmoAFT homologue transcript in cultivated strawberries, revealing its potential role in promoting female functions during early carpel development. We also applied DNA affinity purification sequencing (DAP-seq) and yeast one-hybrid assays to identify potential direct targets of FmoAFT. These insights shed new light on the genetic basis and evolutionary history of sex determination in strawberries, thereby facilitating the formulation of strategies to manipulate sex determination in breeding programs.
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Affiliation(s)
- Qin Qiao
- College of Horticulture and LandscapeYunnan Agricultural UniversityKunmingChina
| | - Qiang Cao
- College of Horticulture and LandscapeYunnan Agricultural UniversityKunmingChina
| | - Rengang Zhang
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
| | - Mingzhao Wu
- School of AgricultureYunnan UniversityKunmingChina
| | | | - Li Xue
- College of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Jiajun Lei
- College of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
| | - Aaron Liston
- Department of Botany and Plant PathologyOregon State UniversityCorvallisOregonUSA
| | - Ticao Zhang
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
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Osterman WHA, Hill A, Hagan JG, Whitton J, Bacon CD, Bjorkman AD. Rethinking pathways to the dioecy-polyploidy association: Genera with many dioecious species have fewer polyploids. AMERICAN JOURNAL OF BOTANY 2024:e16318. [PMID: 38654555 DOI: 10.1002/ajb2.16318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/19/2024] [Accepted: 03/19/2024] [Indexed: 04/26/2024]
Abstract
PREMISE Numerous studies have found a positive association between dioecy and polyploidy; however, this association presents a theoretical conflict: While polyploids are predicted to benefit from self-reproduction for successful establishment, dioecious species cannot self-reproduce. We propose a theoretical framework to resolve this apparent conflict. We hypothesize that the inability of dioecious species to self-reproduce hinders their establishment as polyploids. We therefore expect that genera with many dioecious species have fewer polyploids, leading to a negative association between polyploidy and dioecy across genera. METHODS We used three publicly available databases to determine ploidy and sexual systems for 131 genera and 546 species. We quantified (1) the relationship between the frequency of polyploid species and the frequency of dioecious species across genera, and (2) the proportion of polyploids with hermaphroditism and dioecy across species, adjusting for phylogenetic history. RESULTS Across genera, we found a negative relationship between the proportion of polyploids and the proportion of dioecious species, a consistent trend across clades. Across all species, we found that sexual system (dioecious or not) was not associated with polyploidy. CONCLUSIONS Polyploids are rare in genera in which the majority of species are dioecious, consistent with the theory that self-reproduction favors polyploid establishment. The low frequency of polyploidy among dioecious species indicates the association is not as widespread as previously suggested. Our findings are consistent with previous studies identifying a positive relationship between the two traits, but only if polyploidy promotes a transition to dioecy, and not the reverse.
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Affiliation(s)
- Wilhelm H A Osterman
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Adrian Hill
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - James G Hagan
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Jeannette Whitton
- Department of Botany and Biodiversity Research Centre, The University of British Columbia, Vancouver, Canada
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Anne D Bjorkman
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
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3
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Valdés-Florido A, Tan L, Maguilla E, Simón-Porcar VI, Zhou YH, Arroyo J, Escudero M. Drivers of diversification in Linum (Linaceae) by means of chromosome evolution: correlations with biogeography, breeding system and habit. ANNALS OF BOTANY 2023; 132:949-962. [PMID: 37738171 PMCID: PMC10808019 DOI: 10.1093/aob/mcad139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
BACKGROUND AND AIMS Chromosome evolution leads to hybrid dysfunction and recombination patterns and has thus been proposed as a major driver of diversification in all branches of the tree of life, including flowering plants. In this study we used the genus Linum (flax species) to evaluate the effects of chromosomal evolution on diversification rates and on traits that are important for sexual reproduction. Linum is a useful study group because it has considerable reproductive polymorphism (heterostyly) and chromosomal variation (n = 6-36) and a complex pattern of biogeographical distribution. METHODS We tested several traditional hypotheses of chromosomal evolution. We analysed changes in chromosome number across the phylogenetic tree (ChromEvol model) in combination with diversification rates (ChromoSSE model), biogeographical distribution, heterostyly and habit (ChromePlus model). KEY RESULTS Chromosome number evolved across the Linum phylogeny from an estimated ancestral chromosome number of n = 9. While there were few apparent incidences of cladogenesis through chromosome evolution, we inferred up to five chromosomal speciation events. Chromosome evolution was not related to heterostyly but did show significant relationships with habit and geographical range. Polyploidy was negatively correlated with perennial habit, as expected from the relative commonness of perennial woodiness and absence of perennial clonality in the genus. The colonization of new areas was linked to genome rearrangements (polyploidy and dysploidy), which could be associated with speciation events during the colonization process. CONCLUSIONS Chromosome evolution is a key trait in some clades of the Linum phylogeny. Chromosome evolution directly impacts speciation and indirectly influences biogeographical processes and important plant traits.
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Affiliation(s)
- Ana Valdés-Florido
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes no. 6, 41012, Seville, Spain
| | - Lu Tan
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, Xichang University, Xichang, Sichuan, 615000, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Enrique Maguilla
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes no. 6, 41012, Seville, Spain
- Área de Botánica, Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Ctra de Utrera km 1 sn, 41013, Seville, Spain
| | - Violeta I Simón-Porcar
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes no. 6, 41012, Seville, Spain
| | - Yong-Hong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Juan Arroyo
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes no. 6, 41012, Seville, Spain
| | - Marcial Escudero
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Avenida Reina Mercedes no. 6, 41012, Seville, Spain
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Masuda K, Akagi T. Evolution of sex in crops: recurrent scrap and rebuild. BREEDING SCIENCE 2023; 73:95-107. [PMID: 37404348 PMCID: PMC10316312 DOI: 10.1270/jsbbs.22082] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/20/2022] [Indexed: 07/06/2023]
Abstract
Sexuality is the main strategy for maintaining genetic diversity within a species. In flowering plants (angiosperms), sexuality is derived from ancestral hermaphroditism and multiple sexualities can be expressed in an individual. The mechanisms conferring chromosomal sex determination in plants (or dioecy) have been studied for over a century by both biologists and agricultural scientists, given the importance of this field for crop cultivation and breeding. Despite extensive research, the sex determining gene(s) in plants had not been identified until recently. In this review, we dissect plant sex evolution and determining systems, with a focus on crop species. We introduced classic studies with theoretical, genetic, and cytogenic approaches, as well as more recent research using advanced molecular and genomic techniques. Plants have undergone very frequent transitions into, and out of, dioecy. Although only a few sex determinants have been identified in plants, an integrative viewpoint on their evolutionary trends suggests that recurrent neofunctionalization events are potentially common, in a "scrap and (re)build" cycle. We also discuss the potential association between crop domestication and transitions in sexual systems. We focus on the contribution of duplication events, which are particularly frequent in plant taxa, as a trigger for the creation of new sexual systems.
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Affiliation(s)
- Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
- JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan
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5
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Godin VN. Trioecy in Flowering Plants. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2022; 507:301-311. [PMID: 36781527 DOI: 10.1134/s0012496622060023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/15/2022] [Accepted: 07/20/2022] [Indexed: 02/15/2023]
Abstract
Populations of trioecious plants consists of individuals with staminate, pistillate, and hermaphrodite flowers. Trioecy is extremely rare in angiosperms, and relevant data are scarce. A list of trioecious plants found in the global flora was compiled on the basis of literature data and original research. The list includes 80 species of 46 genera, which represent 33 families and 21 orders of flowering plants. Trioecy is found in 7.9% of families, 0.3% of genera, and 0.03% of species in angiosperms. Trioecious species are now unknown in basal angiosperms, uncommon in magnoliids, and rather rare in monocots. The overwhelming majority (87.5%) of trioecious plants belong to Superrosids (30 species) and Superasterids (40 species). The greatest numbers of trioecious species are found in the families Rosaceae (nine species of two genera), Caprifoliaceae (seven species of one genus), Scrophulariaceae (seven species of one genus), Caryophyllaceae (six species of two genera), and Celastraceae (six species of two genera). Almost half of the identified trioecious species represent five genera: Fragaria L. (eight species), Valeriana L. (seven species), Buddleja L. (seven species), Maytenus Molina (five species), and Silene L. (five species). An association with trioecy was analyzed for several biological and ecological factors, such as the life form, the method of pollination, the perianth color, the pericarp consistency, the presence of related dioecious species in the same genus, the latitudinal position, and the distribution through floristic phytochoria. A lability of sex differentiation in certain trioecious plants, the proportion of sex forms in a population, a possible association with polyploidy, and mechanisms of trioecy maintenance and evolution in flowering plants are discussed.
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Affiliation(s)
- V N Godin
- Moscow Pedagogical State University, Moscow, Russia. .,Central Siberian Botanical Garden, Novosibirsk, Russia.
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6
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He L, Hörandl E. Does polyploidy inhibit sex chromosome evolution in angiosperms? FRONTIERS IN PLANT SCIENCE 2022; 13:976765. [PMID: 36212292 PMCID: PMC9541106 DOI: 10.3389/fpls.2022.976765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Dioecy is rare in flowering plants (5-6% of species), but is often controlled genetically by sex-linked regions (SLRs). It has so far been unclear whether, polyploidy affects sex chromosome evolution, as it does in animals, though polyploidy is quite common in angiosperms, including in dioecious species. Plants could be different, as, unlike many animal systems, degenerated sex chromosomes, are uncommon in plants. Here we consider sex determination in plants and plant-specific factors, and propose that constraints created at the origin of polyploids limit successful polyploidization of species with SLRs. We consider the most likely case of a polyploid of a dioecious diploid with an established SLR, and discuss the outcome in autopolyploids and allopolyploids. The most stable system possibly has an SLR on just one chromosome, with a strongly dominant genetic factor in the heterogametic sex (e.g., xxxY male in a tetraploid). If recombination occurs with its homolog, this will prevent Y chromosome degeneration. Polyploidy may also allow for reversibility of multiplied Z or X chromosomes into autosomes. Otherwise, low dosage of Y-linked SLRs compared to their multiple homologous x copies may cause loss of reliable sex-determination at higher ploidy levels. We discuss some questions that can be studied using genome sequencing, chromosome level-assemblies, gene expression studies and analysis of loci under selection.
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Affiliation(s)
- Li He
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants, University of Göttingen, Göttingen, Germany
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7
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Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. PLoS Genet 2022; 18:e1010226. [PMID: 35793353 PMCID: PMC9292114 DOI: 10.1371/journal.pgen.1010226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 07/18/2022] [Accepted: 04/29/2022] [Indexed: 11/19/2022] Open
Abstract
Polyploidization may precipitate dramatic changes to the genome, including chromosome rearrangements, gene loss, and changes in gene expression. In dioecious plants, the sex-determining mechanism may also be disrupted by polyploidization, with the potential evolution of hermaphroditism. However, while dioecy appears to have persisted through a ploidy transition in some species, it is unknown whether the newly formed polyploid maintained its sex-determining system uninterrupted, or whether dioecy re-evolved after a period of hermaphroditism. Here, we develop a bioinformatic pipeline using RNA-sequencing data from natural populations to demonstrate that the allopolyploid plant Mercurialis canariensis directly inherited its sex-determining region from one of its diploid progenitor species, M. annua, and likely remained dioecious through the transition. The sex-determining region of M. canariensis is smaller than that of its diploid progenitor, suggesting that the non-recombining region of M. annua expanded subsequent to the polyploid origin of M. canariensis. Homeologous pairs show partial sexual subfunctionalization. We discuss the possibility that gene duplicates created by polyploidization might contribute to resolving sexual antagonism.
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8
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Gerchen JF, Veltsos P, Pannell JR. Recurrent allopolyploidization, Y-chromosome introgression and the evolution of sexual systems in the plant genus Mercurialis. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210224. [PMID: 35306889 PMCID: PMC8935306 DOI: 10.1098/rstb.2021.0224] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The plant genus Mercurialis includes dioecious, monoecious and androdioecious species (where males coexist with hermaphrodites). Its diversification involved reticulate evolution via hybridization and polyploidization. The Y chromosome of the diploid species Mercurialis annua shows only mild signs of degeneration. We used sequence variation at a Y-linked locus in several species and at multiple autosomal and pseudoautosomal loci to investigate the origin and evolution of the Y chromosome across the genus. Our study provides evidence for further cases of allopolyploid speciation. It also reveals that all lineages with separate sexes (with one possible exception) share the same ancestral Y chromosome. Surprisingly, males in androdioecious populations of hexaploid M. annua carry a Y chromosome that is not derived from either of its two putative progenitor lineages but from a more distantly related perennial dioecious lineage via introgression. These results throw new light on the evolution of sexual systems and polyploidy in Mercurialis and secure it as a promising model for further study of plant sex chromosomes. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.
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Affiliation(s)
- J F Gerchen
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - P Veltsos
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - J R Pannell
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
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Masuda K, Ikeda Y, Matsuura T, Kawakatsu T, Tao R, Kubo Y, Ushijima K, Henry IM, Akagi T. Reinvention of hermaphroditism via activation of a RADIALIS-like gene in hexaploid persimmon. NATURE PLANTS 2022; 8:217-224. [PMID: 35301445 DOI: 10.1038/s41477-022-01107-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 02/10/2022] [Indexed: 05/29/2023]
Abstract
In flowering plants, different lineages have independently transitioned from the ancestral hermaphroditic state into and out of various sexual systems1. Polyploidizations are often associated with this plasticity in sexual systems2,3. Persimmons (the genus Diospyros) have evolved dioecy via lineage-specific palaeoploidizations. More recently, hexaploid D. kaki has established monoecy and also exhibits reversions from male to hermaphrodite flowers in response to natural environmental signals (natural hermaphroditism, NH), or to artificial cytokinin treatment (artificial hermaphroditism, AH). We sought to identify the molecular pathways underlying these polyploid-specific reversions to hermaphroditism. Co-expression network analyses identified regulatory pathways specific to NH or AH transitions. Surprisingly, the two pathways appeared to be antagonistic, with abscisic acid and cytokinin signalling for NH and AH, respectively. Among the genes common to both pathways leading to hermaphroditic flowers, we identified a small-Myb RADIALIS-like gene, named DkRAD, which is specifically activated in hexaploid D. kaki. Consistently, ectopic overexpression of DkRAD in two model plants resulted in hypergrowth of the gynoecium. These results suggest that production of hermaphrodite flowers via polyploidization depends on DkRAD activation, which is not associated with a loss-of-function within the existing sex determination pathway, but rather represents a new path to (or reinvention of) hermaphroditism.
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Affiliation(s)
- Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Yoko Ikeda
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Takakazu Matsuura
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Taiji Kawakatsu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yasutaka Kubo
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Koichiro Ushijima
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Isabelle M Henry
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA, USA
| | - Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
- JST-PRESTO, Saitama, Japan.
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Al‐Dossary O, Alsubaie B, Kharabian‐Masouleh A, Al‐Mssallem I, Furtado A, Henry RJ. The jojoba genome reveals wide divergence of the sex chromosomes in a dioecious plant. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1283-1294. [PMID: 34570389 PMCID: PMC9293028 DOI: 10.1111/tpj.15509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Most flowering plants are hermaphrodites, but around 6% of species are dioecious, having separate male and female plants. Sex chromosomes and some sex-specific genes have been reported in plants, but the genome sequences have not been compared. We now report the genome sequence of male and female jojoba (Simmondsia chinensis) plants, revealing a very large difference in the sex chromosomes. The male genome assembly was 832 Mb and the female 822 Mb. This was explained by the large size differences in the Y chromosome (37.6 Mb) compared with the X chromosome (26.9 Mb). Relative to the X chromosome, the Y chromosome had two large insertions each of more than 5 Mb containing more than 400 genes. Many of the genes in the chromosome-specific regions were novel. These male-specific regions included many flowering-related and stress response genes. Smaller insertions found only in the X chromosome totalled 877 kb. The wide divergence of the sex chromosomes suggests a long period of adaptation to diverging sex-specific roles. Male and female plants may have evolved to accommodate factors such as differing reproductive resource allocation requirements under the stress of the desert environment in which the plants are found. The sex-determining regions accumulate genes beneficial to each sex. This has required the evolution of many more novel sex-specific genes than has been reported for other organisms. This suggest that dioecious plants provide a novel source of genes for manipulation of reproductive performance and environmental adaptation in crops.
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Affiliation(s)
- Othman Al‐Dossary
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbane4072Australia
- College of Agriculture and Food SciencesKing Faisal UniversityAl Hofuf36362Saudi Arabia
| | - Bader Alsubaie
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbane4072Australia
- College of Agriculture and Food SciencesKing Faisal UniversityAl Hofuf36362Saudi Arabia
| | | | - Ibrahim Al‐Mssallem
- College of Agriculture and Food SciencesKing Faisal UniversityAl Hofuf36362Saudi Arabia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbane4072Australia
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbane4072Australia
- ARC Centre of Excellence for Plant Success in Nature and AgricultureUniversity of QueenslandBrisbane4072Australia
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11
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Genome size variation in Cactaceae and its relationship with invasiveness and seed traits. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02557-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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12
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Kučera J, Svitok M, Gbúrová Štubňová E, Mártonfiová L, Lafon Placette C, Slovák M. Eunuchs or Females? Causes and Consequences of Gynodioecy on Morphology, Ploidy, and Ecology of Stellaria graminea L. (Caryophyllaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:589093. [PMID: 33912199 PMCID: PMC8072285 DOI: 10.3389/fpls.2021.589093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Plant speciation results from intricate processes such as polyploidization, reproductive strategy shifts and adaptation. These evolutionary processes often co-occur, blurring their respective contributions and interactions in the speciation continuum. Here, relying on a large-scale study, we tested whether gynodioecy triggers the divergent evolution of flower morphology and genome between sexes, and contributes to the establishment of polyploids and colonization of ecological niches in Stellaria graminea. We found that gynodioecy in S. graminea leads to flower morphology divergence between females and hermaphrodites, likely due to sexual selection. Contrary to our expectations, gynodioecy occurs evenly in diploids and tetraploids, suggesting that this reproductive strategy was not involved in the establishment of polyploids. Both diploid and tetraploid females have a larger genome size than hermaphrodites, suggesting the presence of sex chromosomes. Finally, ecology differs between cytotypes and to a lesser extent between sexes, suggesting that the link between environment and presence of females is indirect and likely explained by other aspects of the species' life history. Our study shows that gynodioecy leads to the consistent evolution of sexual traits across a wide range of populations, cytotypes and environments within a given species, and this likely contributes to the phenotypic and genetic distinctiveness of the species from its sister clades.
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Affiliation(s)
- Jaromír Kučera
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Marek Svitok
- Faculty of Ecology and Environmental Sciences, Technical University in Zvolen, Zvolen, Slovakia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia
| | - Eliška Gbúrová Štubňová
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
- Slovak National Museum, Natural History Museum, Bratislava, Slovakia
| | | | | | - Marek Slovák
- Plant Science and Biodiversity Centre, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Botany, Charles University, Prague, Czechia
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Carey S, Yu Q, Harkess A. The Diversity of Plant Sex Chromosomes Highlighted through Advances in Genome Sequencing. Genes (Basel) 2021; 12:381. [PMID: 33800038 PMCID: PMC8000587 DOI: 10.3390/genes12030381] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 01/21/2023] Open
Abstract
For centuries, scientists have been intrigued by the origin of dioecy in plants, characterizing sex-specific development, uncovering cytological differences between the sexes, and developing theoretical models. Through the invention and continued improvements in genomic technologies, we have truly begun to unlock the genetic basis of dioecy in many species. Here we broadly review the advances in research on dioecy and sex chromosomes. We start by first discussing the early works that built the foundation for current studies and the advances in genome sequencing that have facilitated more-recent findings. We next discuss the analyses of sex chromosomes and sex-determination genes uncovered by genome sequencing. We synthesize these results to find some patterns are emerging, such as the role of duplications, the involvement of hormones in sex-determination, and support for the two-locus model for the origin of dioecy. Though across systems, there are also many novel insights into how sex chromosomes evolve, including different sex-determining genes and routes to suppressed recombination. We propose the future of research in plant sex chromosomes should involve interdisciplinary approaches, combining cutting-edge technologies with the classics to unravel the patterns that can be found across the hundreds of independent origins.
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Affiliation(s)
- Sarah Carey
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA;
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Qingyi Yu
- Texas A&M AgriLife Research, Texas A&M University System, Dallas, TX 75252, USA
| | - Alex Harkess
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA;
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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14
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Bondada R, Somasundaram S, Marimuthu MP, Badarudeen MA, Puthiyaveedu VK, Maruthachalam R. Natural epialleles of Arabidopsis SUPERMAN display superwoman phenotypes. Commun Biol 2020; 3:772. [PMID: 33319840 PMCID: PMC7738503 DOI: 10.1038/s42003-020-01525-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 11/25/2020] [Indexed: 01/07/2023] Open
Abstract
Epimutations are heritable changes in gene function due to loss or gain of DNA cytosine methylation or chromatin modifications without changes in the DNA sequence. Only a few natural epimutations displaying discernible phenotypes are documented in plants. Here, we report natural epimutations in the cadastral gene, SUPERMAN(SUP), showing striking phenotypes despite normal transcription, discovered in a natural tetraploid, and subsequently in eleven diploid Arabidopsis genetic accessions. This natural lois lane(lol) epialleles behave as recessive mendelian alleles displaying a spectrum of silent to strong superwoman phenotypes affecting only the carpel whorl, in contrast to semi-dominant superman or supersex features manifested by induced epialleles which affect both stamen and carpel whorls. Despite its unknown origin, natural lol epialleles are subjected to the same epigenetic regulation as induced clk epialleles. The existence of superwoman epialleles in diverse wild populations is interpreted in the light of the evolution of unisexuality in plants. Ramesh Bondada et al. report natural epimutations in the Arabidopsis SUPERMAN gene from tetraploid and diploid accessions. The existence of these epialleles in diverse wild populations have the potential to shed light on the evolution of unisexuality in plants.
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Affiliation(s)
- Ramesh Bondada
- School of Biology, Indian Institute of Science Education and Research (IISER)-Thiruvananthapuram, Vithura, Kerala, 695551, India
| | - Saravanakumar Somasundaram
- School of Biology, Indian Institute of Science Education and Research (IISER)-Thiruvananthapuram, Vithura, Kerala, 695551, India
| | | | - Mohammed Afsal Badarudeen
- School of Biology, Indian Institute of Science Education and Research (IISER)-Thiruvananthapuram, Vithura, Kerala, 695551, India
| | - Vaishak Kanjirakol Puthiyaveedu
- School of Biology, Indian Institute of Science Education and Research (IISER)-Thiruvananthapuram, Vithura, Kerala, 695551, India
| | - Ravi Maruthachalam
- School of Biology, Indian Institute of Science Education and Research (IISER)-Thiruvananthapuram, Vithura, Kerala, 695551, India.
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15
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Li W, Wu H, Li X, Chen Y, Yin T. Fine mapping of the sex locus in Salix triandra confirms a consistent sex determination mechanism in genus Salix. HORTICULTURE RESEARCH 2020; 7:64. [PMID: 32377355 PMCID: PMC7193568 DOI: 10.1038/s41438-020-0289-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 02/27/2020] [Accepted: 03/02/2020] [Indexed: 05/19/2023]
Abstract
Salix triandra belongs to section Amygdalinae in genus Salix, which is in a different section from the willow species in which sex determination has been well studied. Studying sex determination in distantly related willow species will help to clarify whether the sexes of different willows arise through a common sex determination system. For this purpose, we generated an intraspecific full-sib F1 population for S. triandra and constructed high-density genetic linkage maps for the crossing parents using restriction site-associated DNA sequencing and following a two-way pseudo-testcross strategy. With the established maps, the sex locus was positioned in linkage group XV only in the maternal map, and no sex linkage was detected in the paternal map. Consistent with previous findings in other willow species, our study showed that chromosome XV was the incipient sex chromosome and that females were the heterogametic sex in S. triandra. Therefore, sex in this willow species is also determined through a ZW sex determination system. We further performed fine mapping in the vicinity of the sex locus with SSR markers. By comparing the physical and genetic distances for the target interval encompassing the sex determination gene confined by SSRs, severe recombination repression was revealed in the sex determination region in the female map. The recombination rate in the confined interval encompassing the sex locus was approximately eight-fold lower than the genome-wide average. This study provides critical information relevant to sex determination in S. triandra.
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Affiliation(s)
- Wei Li
- The Key Lab of Cultivar Innovation and Germplasm Improvement of Salicaceae, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Huaitong Wu
- The Key Lab of Cultivar Innovation and Germplasm Improvement of Salicaceae, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Xiaoping Li
- The Key Lab of Cultivar Innovation and Germplasm Improvement of Salicaceae, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Yingnan Chen
- The Key Lab of Cultivar Innovation and Germplasm Improvement of Salicaceae, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
| | - Tongming Yin
- The Key Lab of Cultivar Innovation and Germplasm Improvement of Salicaceae, College of Forestry, Nanjing Forestry University, Nanjing, 210037 China
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16
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Gunn BF, Murphy DJ, Walsh NG, Conran JG, Pires JC, Macfarlane TD, Birch JL. Evolution of Lomandroideae: Multiple origins of polyploidy and biome occupancy in Australia. Mol Phylogenet Evol 2020; 149:106836. [PMID: 32304826 DOI: 10.1016/j.ympev.2020.106836] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 02/03/2023]
Abstract
Asparagaceae: Lomandroideae are a species-rich and economically important subfamily in the monocot order Asparagales, with a center of diversity in Australia. Lomandroideae are ecologically diverse, occupying mesic and arid biomes in Australia and possessing an array of key traits, including sexual dimorphism, storage organs and polyploidy that are potentially adaptive for survival in seasonally arid and fire-dependent habitats. The Lomandroideae phylogeny was reconstructed using maximum likelihood and Bayesian inference criteria, based on plastome data from genome-skimming to infer relationships. A fossil-calibrated chronogram provided a temporal framework for understanding trait transitions. Ancestral state reconstructions and phylogenetic comparative trait correlation analyses provided insights into the evolutionary and ecological drivers associated with Lomandroideae diversification. Lomandroideae diverged from the other Asparagaceae ca. 56.61 million years ago (95% highest posterior density values 70.31-45.34 million years) and the major lineages diversified since the Oligocene. The most recent common ancestor of the clade likely occupied the mesic biome, was hermaphroditic and geophytic. Biome occupancy transitions were correlated with polyploidy and the presence of storage roots. Polyploidy potentially serves as an "enabler" trait, generating novel phenotypes, which may confer tolerance to climatic ranges and soil conditions putatively required for expansion into and occupation of new arid biomes. Storage roots, as a key factor driving biome transitions, may have been associated with fire rather than with aridification events in the Australian flora. This study contributes significantly to our understanding of biome evolution by identifying polyploidy and storage organs as key factors associated with transitions in biome occupancy in this lineage.
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Affiliation(s)
- Bee F Gunn
- Royal Botanic Gardens Victoria, Birdwood Ave., Melbourne, VIC 3004, Australia.
| | - Daniel J Murphy
- Royal Botanic Gardens Victoria, Birdwood Ave., Melbourne, VIC 3004, Australia.
| | - Neville G Walsh
- Royal Botanic Gardens Victoria, Birdwood Ave., Melbourne, VIC 3004, Australia.
| | - John G Conran
- The University of Adelaide, School of Biological Sciences, Adelaide, SA 5005, Australia.
| | - J Chris Pires
- University of Missouri, Div. of Biological Sciences, 105 Tucker Hall, Columbia, MO 65211-7400, USA.
| | - Terry D Macfarlane
- Dept. of Biodiversity, Conservation and Attractions, 17 Dick Perry Ave., Technology Park, Western Precinct, Kensington, WA 6983, Australia.
| | - Joanne L Birch
- The University of Melbourne, School of BioSciences, Parkville, VIC 3010, Australia.
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17
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Guerrero PC, Majure LC, Cornejo-Romero A, Hernández-Hernández T. Phylogenetic Relationships and Evolutionary Trends in the Cactus Family. J Hered 2020; 110:4-21. [PMID: 30476167 DOI: 10.1093/jhered/esy064] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/21/2018] [Indexed: 12/29/2022] Open
Abstract
Members of the cactus family are keystone species of arid and semiarid biomes in the Americas, as they provide shelter and resources to support other members of ecosystems. Extraordinary examples are the several species of flies of the genus Drosophila that lay eggs and feed in their rotting stems, which provide a model system for studying evolutionary processes. Although there is significant progress in understanding the evolution of Drosophila species, there are gaps in our knowledge about the cactus lineages hosting them. Here, we review the current knowledge about the evolution of Cactaceae, focusing on phylogenetic relationships and trends revealed by the study of DNA sequence data. During the last several decades, the availability of molecular phylogenies has considerably increased our understanding of the relationships, biogeography, and evolution of traits in the family. Remarkably, although succulent cacti have very low growth rates and long generation times, they underwent some of the fastest diversifications observed in the plant kingdom, possibly fostered by strong ecological interactions. We have a better understanding of the reproductive biology, population structure and speciation mechanisms in different clades. The recent publication of complete genomes for some species has revealed the importance of phenomena such as incomplete lineage sorting. Hybridization and polyploidization are common in the family, and have been studied using a variety of phylogenetic methods. We discuss potential future avenues for research in Cactaceae, emphasizing the need of a concerted effort among scientists in the Americas, together with the analyses of data from novel sequencing techniques.
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Affiliation(s)
- Pablo C Guerrero
- Departamento de Botánica, Universidad de Concepción, Chile, Concepción, Chile
| | - Lucas C Majure
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ.,Florida Museum of Natural History, University of Florida, Gainesville, FL
| | - Amelia Cornejo-Romero
- Departamento de Botánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
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18
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Sabatti M, Gaudet M, Müller NA, Kersten B, Gaudiano C, Scarascia Mugnozza G, Fladung M, Beritognolo I. Long-term study of a subdioecious Populus ×canescens family reveals sex lability of females and reproduction behaviour of cosexual plants. PLANT REPRODUCTION 2020; 33:1-17. [PMID: 31650409 DOI: 10.1007/s00497-019-00378-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
Cosexual Populus ×canescens plants are inconstant females with life course plasticity of sex phenotype and can reproduce by selfing. Populus species are dioecious, but deviations from dioecy are reported in some cases. The objectives of this study were to investigate the phenotypic expression and the inheritance of subdioecy in a Populus ×canescens pedigree. The F1 progeny was monitored for sex during 14 years. Thirty per cent of individuals expressed deviations from dioecy and long-term plasticity of sex. Some plants started flowering as male, then became cosexual, and finally turned female. Two cosexual individuals were self-pollinated and generated a selfed progeny markedly impaired by inbreeding depression, but able to reproduce by outcrossing. Sex segregation of the F1 progeny statistically fitted the expected ratio 1:2:1 (female:male:cosexual). By analysis of DNA markers, the cosexual individuals were genetically clustered with the females. The segregation ratio and the genetic profile indicated that cosexual plants were female with altered sex phenotype. Linkage analysis identified a putative sex-determining region with suppressed recombination on chromosome 19 of the male Populus tremula parent. The male sex trait was linked to the pericentromeric region of the P. tremula chromosome 19, whereas the cosexual trait was linked to chromosome 19 of the female Populus alba parent. A genetic model is proposed to explain inheritance and phenotypic expression of sex.
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Affiliation(s)
- Maurizio Sabatti
- Department for Innovation in Biological, Agro-food and Forest systems (DIBAF), University of Tuscia, Viterbo, Italy.
| | - Muriel Gaudet
- Institute of Research on Terrestrial Ecosystems (IRET), National Research Council (CNR), Porano, TR, Italy
| | - Niels A Müller
- Thünen-Institute of Forest Genetics, Sieker Landstr.2, 22927, Grosshansdorf, Germany
| | - Birgit Kersten
- Thünen-Institute of Forest Genetics, Sieker Landstr.2, 22927, Grosshansdorf, Germany
| | - Cosimo Gaudiano
- Department for Innovation in Biological, Agro-food and Forest systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Giuseppe Scarascia Mugnozza
- Department for Innovation in Biological, Agro-food and Forest systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Matthias Fladung
- Thünen-Institute of Forest Genetics, Sieker Landstr.2, 22927, Grosshansdorf, Germany
| | - Isacco Beritognolo
- Institute of Research on Terrestrial Ecosystems (IRET), National Research Council (CNR), Porano, TR, Italy
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19
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Wang LL, Zhang ZQ, Yang YP, Duan YW. The coexistence of hermaphroditic and dioecious plants is associated with polyploidy and gender dimorphism in Dasiphora fruticosa. PLANT DIVERSITY 2019; 41:323-329. [PMID: 31934677 PMCID: PMC6951273 DOI: 10.1016/j.pld.2019.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/06/2019] [Accepted: 06/10/2019] [Indexed: 06/10/2023]
Abstract
Dasiphora fruticosa comprises male, female and hermaphrodite plants, which are distributed sympatrically in some populations on the Qinghai-Tibet Plateau. To explore what governs the coexistence of these three sexual phenotypes, we investigated the DNA contents, pollen and ovule production, pollen deposition, and performed hand-pollination in both hermaphroditic and dioecious individuals of D. fruticosa. Flow cytometry confirmed that the DNA content of males and females were almost twice as much as that of the hermaphrodites. Male and female flowers produced more pollen grains and ovules than hermaphroditic flowers. Hand-pollinated treatments showed that unisexual flowers were sterile in one sexual function and bisexual flowers were fertile for both functions, but no sterile seeds were produced between unisexual and bisexual flowers. Our findings imply that polyploidy is related to gender dimorphism, and both are likely to play a strong role in the coexistence of two cryptic biological species of D. fruticosa (low ploidy hermaphroditic species and high ploidy dioecious species) in the Qinghai-Tibet Plateau.
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Affiliation(s)
- Lin-Lin Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Germplasm Bank of Wild Species, Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi-Qiang Zhang
- Laboratory of Ecology and Evolutionary Biology, Yunnan University, Kunming, Yunnan, 650091, China
| | - Yong-Ping Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Germplasm Bank of Wild Species, Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Yuan-Wen Duan
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Germplasm Bank of Wild Species, Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
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20
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Tennessen JA, Wei N, Straub SCK, Govindarajulu R, Liston A, Ashman TL. Repeated translocation of a gene cassette drives sex-chromosome turnover in strawberries. PLoS Biol 2018; 16:e2006062. [PMID: 30148831 PMCID: PMC6128632 DOI: 10.1371/journal.pbio.2006062] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 09/07/2018] [Accepted: 08/09/2018] [Indexed: 11/30/2022] Open
Abstract
Turnovers of sex-determining systems represent important diversifying forces across eukaryotes. Shifts in sex chromosomes—but conservation of the master sex-determining genes—characterize distantly related animal lineages. Yet in plants, in which separate sexes have evolved repeatedly and sex chromosomes are typically homomorphic, we do not know whether such translocations drive sex-chromosome turnovers within closely related taxonomic groups. This phenomenon can only be demonstrated by identifying sex-associated nucleotide sequences, still largely unknown in plants. The wild North American octoploid strawberries (Fragaria) exhibit separate sexes (dioecy) with homomorphic, female heterogametic (ZW) inheritance, yet sex maps to three different chromosomes in different taxa. To characterize these turnovers, we identified sequences unique to females and assembled their reads into contigs. For most octoploid Fragaria taxa, a short (13 kb) sequence was observed in all females and never in males, implicating it as the sex-determining region (SDR). This female-specific “SDR cassette” contains both a gene with a known role in fruit and pollen production and a novel retrogene absent on Z and autosomal chromosomes. Phylogenetic comparison of SDR cassettes revealed three clades and a history of repeated translocation. Remarkably, the translocations can be ordered temporally due to the capture of adjacent sequence with each successive move. The accumulation of the “souvenir” sequence—and the resultant expansion of the hemizygous SDR over time—could have been adaptive by locking genes into linkage with sex. Terminal inverted repeats at the insertion borders suggest a means of movement. To our knowledge, this is the first plant SDR shown to be translocated, and it suggests a new mechanism (“move-lock-grow”) for expansion and diversification of incipient sex chromosomes. Sex chromosomes frequently restructure themselves during organismal evolution, often becoming highly differentiated. This dynamic process is poorly understood for most taxa, especially during the early stages typical of many dioecious flowering plants. We show that in wild strawberries, a female-specific region of DNA is associated with sex and has repeatedly changed its genomic location, each time increasing the size of the hemizygous female-specific sequence on the W sex chromosome. This observation shows, for the first time to our knowledge, that plant sex regions can “jump” and suggests that this phenomenon may be adaptive by gathering and locking new genes into linkage with sex. This conserved and presumed causal sex-determining sequence, which varies in both genomic location and degree of differentiation, will facilitate future studies to understand how sex chromosomes first begin to differentiate.
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Affiliation(s)
- Jacob A. Tennessen
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, United States of America
| | - Na Wei
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Shannon C. K. Straub
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Rajanikanth Govindarajulu
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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21
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Zhou R, Macaya-Sanz D, Rodgers-Melnick E, Carlson CH, Gouker FE, Evans LM, Schmutz J, Jenkins JW, Yan J, Tuskan GA, Smart LB, DiFazio SP. Characterization of a large sex determination region in Salix purpurea L. (Salicaceae). Mol Genet Genomics 2018; 293:1437-1452. [PMID: 30022352 DOI: 10.1007/s00438-018-1473-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/09/2018] [Indexed: 12/30/2022]
Abstract
Dioecy has evolved numerous times in plants, but heteromorphic sex chromosomes are apparently rare. Sex determination has been studied in multiple Salix and Populus (Salicaceae) species, and P. trichocarpa has an XY sex determination system on chromosome 19, while S. suchowensis and S. viminalis have a ZW system on chromosome 15. Here we use whole genome sequencing coupled with quantitative trait locus mapping and a genome-wide association study to characterize the genomic composition of the non-recombining portion of the sex determination region. We demonstrate that Salix purpurea also has a ZW system on chromosome 15. The sex determination region has reduced recombination, high structural polymorphism, an abundance of transposable elements, and contains genes that are involved in sex expression in other plants. We also show that chromosome 19 contains sex-associated markers in this S. purpurea assembly, along with other autosomes. This raises the intriguing possibility of a translocation of the sex determination region within the Salicaceae lineage, suggesting a common evolutionary origin of the Populus and Salix sex determination loci.
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Affiliation(s)
- Ran Zhou
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506-6057, USA
| | - David Macaya-Sanz
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506-6057, USA
| | - Eli Rodgers-Melnick
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506-6057, USA
| | - Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - Fred E Gouker
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - Luke M Evans
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506-6057, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA.,Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Jerry W Jenkins
- HudsonAlpha Institute of Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Juying Yan
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Gerald A Tuskan
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.,Biosciences Division, Oak Ridge National Lab, Oak Ridge, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506-6057, USA.
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22
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Henry IM, Akagi T, Tao R, Comai L. One Hundred Ways to Invent the Sexes: Theoretical and Observed Paths to Dioecy in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:553-575. [PMID: 29719167 DOI: 10.1146/annurev-arplant-042817-040615] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Dioecy, the presence of male and female flowers on separate individuals, is both widespread and uncommon within flowering plants, with only a few percent of dioecious species spread across most major phylogenetic taxa. It is therefore safe to assume that dioecy evolved independently in these different groups, which allows us to ask questions regarding the molecular and developmental mechanisms underlying these independent transitions to dioecy. We start this review by examining the problem from the standpoint of a genetic engineer trying to develop dioecy, discuss various potential solutions, and compare them to models proposed in the past and based on genetic and evolutionary considerations. Next, we present recent information regarding candidate sex determinants in three species, acquired using newly established genomic approaches. Although such specific information is still scarce, it is slowly becoming apparent that various genes or pathways can be altered to evolve dioecy.
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Affiliation(s)
- Isabelle M Henry
- Department of Plant Biology, University of California, Davis, California 95616, USA; ,
- Genome Center, University of California, Davis, California 95616, USA
| | - Takashi Akagi
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan; ,
| | - Ryutaro Tao
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan; ,
| | - Luca Comai
- Department of Plant Biology, University of California, Davis, California 95616, USA; ,
- Genome Center, University of California, Davis, California 95616, USA
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23
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Wei N, Govindarajulu R, Tennessen JA, Liston A, Ashman TL. Genetic Mapping and Phylogenetic Analysis Reveal Intraspecific Variation in Sex Chromosomes of the Virginian Strawberry. J Hered 2018; 108:731-739. [PMID: 29036451 DOI: 10.1093/jhered/esx077] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 09/20/2017] [Indexed: 11/12/2022] Open
Abstract
With their extraordinary diversity in sexual systems, flowering plants offer unparalleled opportunities to understand sex determination and to reveal generalities in the evolution of sex chromosomes. Comparative genetic mapping of related taxa with good phylogenetic resolution can delineate the extent of sex chromosome diversity within plant groups, and lead the way to understanding the evolutionary drivers of such diversity. The North American octoploid wild strawberries provide such an opportunity. We performed linkage mapping using targeted sequence capture for the subdioecious western Fragaria virginiana ssp. platypetala and compared the location of its sex-determining region (SDR) to those of 2 other (sub)dioecious species, the eastern subspecies, F. virginiana ssp. virginiana (whose SDR is at 0-5.5 Mb on chromosome VI of the B2 subgenome), and the sister species F. chiloensis (whose SDR is at 37 Mb on chromosome VI of the Av subgenome). Male sterility was dominant in F. virginiana ssp. platypetala and mapped to a chromosome also in homeologous group VI. Likewise, one major quantitative trait locus (QTL) for female fertility overlapped the male sterility region. However, the SDR mapped to yet another subgenome (B1), and to a different location (13 Mb), but similar to the location inferred in one population of the naturally occurring hybrid between F. chiloensis and F. virginiana (F. ×ananassa ssp. cuneifolia). Phylogenetic analysis of chromosomes across the octoploid taxa showed consistent subgenomic composition reflecting shared evolutionary history but also reinforced within-species variation in the SDR-carrying chromosome, suggesting either repeated evolution, or recent turnovers in SDR.
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Affiliation(s)
- Na Wei
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Rajanikanth Govindarajulu
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260.,Department of Biology, West Virginia University, Morgantown, WV 26505
| | - Jacob A Tennessen
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
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24
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No difference in plasticity between different ploidy levels in the Mediterranean herb Mercurialis annua. Sci Rep 2017; 7:9484. [PMID: 28842565 PMCID: PMC5572718 DOI: 10.1038/s41598-017-07877-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/04/2017] [Indexed: 11/08/2022] Open
Abstract
Increased phenotypic plasticity for a number of plant traits has been suggested as a possible reason for the success and spread of polyploids. One such trait is a plant's sex allocation (or gender), which influences its reproductive success directly as a function of the potentially heterogeneous mating prospects in the population. However, it is unknown how polyploidy per se might affect plasticity in a plant's sex allocation. Although there have been numerous comparisons between diploid and (usually) tetraploid taxa, we know very little about how elevated ploidy above the diploid level might affect plasticity. Here, we ask whether different ploidy levels > 2x express different plasticity in the ruderal plant Mercurialis annua. We grew tetraploid and hexaploid hermaphrodites under different levels of nutrient availability and compared their reaction norms for growth (above-ground biomass, SLA) and reproductive traits (reproductive effort, phenotypic gender). Overall, we found that an increase in ploidy level from 4x to 6x in M. annua is associated with an increase in the relative biomass allocated to seeds, measured as female reproductive effort. However, our study provides no support for the idea that increasing ploidy level increases the ability to express different phenotypes in response to changes in the environment.
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25
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Alix K, Gérard PR, Schwarzacher T, Heslop-Harrison JS(P. Polyploidy and interspecific hybridization: partners for adaptation, speciation and evolution in plants. ANNALS OF BOTANY 2017; 120:183-194. [PMID: 28854567 PMCID: PMC5737848 DOI: 10.1093/aob/mcx079] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 05/31/2017] [Indexed: 05/15/2023]
Abstract
BACKGROUND Polyploidy or whole-genome duplication is now recognized as being present in almost all lineages of higher plants, with multiple rounds of polyploidy occurring in most extant species. The ancient evolutionary events have been identified through genome sequence analysis, while recent hybridization events are found in about half of the world's crops and wild species. Building from this new paradigm for understanding plant evolution, the papers in this Special Issue address questions about polyploidy in ecology, adaptation, reproduction and speciation of wild and cultivated plants from diverse ecosystems. Other papers, including this review, consider genomic aspects of polyploidy. APPROACHES Discovery of the evolutionary consequences of new, evolutionarily recent and ancient polyploidy requires a range of approaches. Large-scale studies of both single species and whole ecosystems, with hundreds to tens of thousands of individuals, sometimes involving 'garden' or transplant experiments, are important for studying adaptation. Molecular studies of genomes are needed to measure diversity in genotypes, showing ancestors, the nature and number of polyploidy and backcross events that have occurred, and allowing analysis of gene expression and transposable element activation. Speciation events and the impact of reticulate evolution require comprehensive phylogenetic analyses and can be assisted by resynthesis of hybrids. In this Special Issue, we include studies ranging in scope from experimental and genomic, through ecological to more theoretical. CONCLUSIONS The success of polyploidy, displacing the diploid ancestors of almost all plants, is well illustrated by the huge angiosperm diversity that is assumed to originate from recurrent polyploidization events. Strikingly, polyploidization often occurred prior to or simultaneously with major evolutionary transitions and adaptive radiation of species, supporting the concept that polyploidy plays a predominant role in bursts of adaptive speciation. Polyploidy results in immediate genetic redundancy and represents, with the emergence of new gene functions, an important source of novelty. Along with recombination, gene mutation, transposon activity and chromosomal rearrangement, polyploidy and whole-genome duplication act as drivers of evolution and divergence in plant behaviour and gene function, enabling diversification, speciation and hence plant evolution.
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Affiliation(s)
- Karine Alix
- GQE – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
- For correspondence. E-mail
| | - Pierre R. Gérard
- GQE – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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26
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Segraves KA. The effects of genome duplications in a community context. THE NEW PHYTOLOGIST 2017; 215:57-69. [PMID: 28418074 DOI: 10.1111/nph.14564] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/16/2017] [Indexed: 06/07/2023]
Abstract
Contents 57 I. 57 II. 59 III. 59 IV. 63 V. 64 VI. 64 VII. 66 66 References 66 SUMMARY: Whole-genome duplication (WGD), or polyploidy, has important effects on the genotype and phenotype of plants, potentially altering ecological interactions with other organisms. Even though the connections between polyploidy and species interactions have been recognized for some time, we are only just beginning to test whether WGD affects community context. Here I review the sparse information on polyploidy and community context and then present a set of hypotheses for future work. Thus far, community-level studies of polyploids suggest an array of outcomes, from no changes in community context to shifts in the abundance and composition of interacting species. I propose a number of mechanisms for how WGD could alter community context and how the emergence of polyploids in populations could also alter the community context of parental diploids and other plant species. Resolving how and when these changes are expected to occur will require a deeper understanding of the connections among WGD, phenotypic changes, and the direct and indirect effects of species interactions.
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Affiliation(s)
- Kari A Segraves
- Department of Biology, Syracuse University, Syracuse, NY, 13244, USA
- Archbold Biological Station, Venus, FL, 33960, USA
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27
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Zenil‐Ferguson R, Ponciano JM, Burleigh JG. Testing the association of phenotypes with polyploidy: An example using herbaceous and woody eudicots. Evolution 2017; 71:1138-1148. [DOI: 10.1111/evo.13226] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 02/17/2017] [Indexed: 01/08/2023]
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28
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Käfer J, Marais GAB, Pannell JR. On the rarity of dioecy in flowering plants. Mol Ecol 2017; 26:1225-1241. [PMID: 28101895 DOI: 10.1111/mec.14020] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 12/27/2016] [Accepted: 12/28/2016] [Indexed: 01/21/2023]
Abstract
Dioecy, the coexistence of separate male and female individuals in a population, is a rare but phylogenetically widespread sexual system in flowering plants. While research has concentrated on why and how dioecy evolves from hermaphroditism, the question of why dioecy is rare, despite repeated transitions to it, has received much less attention. Previous phylogenetic and theoretical studies have suggested that dioecy might be an evolutionary dead end. However, recent research indicates that the phylogenetic support for this hypothesis is attributable to a methodological bias and that there is no evidence for reduced diversification in dioecious angiosperms. The relative rarity of dioecy thus remains a puzzle. Here, we review evidence for the hypothesis that dioecy might be rare not because it is an evolutionary dead end, but rather because it easily reverts to hermaphroditism. We review what is known about transitions between hermaphroditism and dioecy, and conclude that there is an important need to consider more widely the possibility of transitions away from dioecy, both from an empirical and a theoretical point of view, and by combining tools from molecular evolution and insights from ecology.
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Affiliation(s)
- Jos Käfer
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR 5558, Université Lyon 1, Bât. Grégor Mendel 43, bd du 11 novembre 1918, 69622, Villeurbanne cedex, France
| | - Gabriel A B Marais
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR 5558, Université Lyon 1, Bât. Grégor Mendel 43, bd du 11 novembre 1918, 69622, Villeurbanne cedex, France
| | - John R Pannell
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
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29
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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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30
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Šmarda P, Veselý P, Šmerda J, Bureš P, Knápek O, Chytrá M. Polyploidy in a 'living fossil' Ginkgo biloba. THE NEW PHYTOLOGIST 2016; 212:11-4. [PMID: 27265838 DOI: 10.1111/nph.14062] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Affiliation(s)
- Petr Šmarda
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Pavel Veselý
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Jakub Šmerda
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Petr Bureš
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Ondřej Knápek
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
| | - Magdaléna Chytrá
- Botanical Garden of the Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
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31
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Retrotransposon Proliferation Coincident with the Evolution of Dioecy in Asparagus. G3-GENES GENOMES GENETICS 2016; 6:2679-85. [PMID: 27342737 PMCID: PMC5015926 DOI: 10.1534/g3.116.030239] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Current phylogenetic sampling reveals that dioecy and an XY sex chromosome pair evolved once, or possibly twice, in the genus Asparagus. Although there appear to be some lineage-specific polyploidization events, the base chromosome number of 2n = 2× = 20 is relatively conserved across the Asparagus genus. Regardless, dioecious species tend to have larger genomes than hermaphroditic species. Here, we test whether this genome size expansion in dioecious species is related to a polyploidization and subsequent chromosome fusion, or to retrotransposon proliferation in dioecious species. We first estimate genome sizes, or use published values, for four hermaphrodites and four dioecious species distributed across the phylogeny, and show that dioecious species typically have larger genomes than hermaphroditic species. Utilizing a phylogenomic approach, we find no evidence for ancient polyploidization contributing to increased genome sizes of sampled dioecious species. We do find support for an ancient whole genome duplication (WGD) event predating the diversification of the Asparagus genus. Repetitive DNA content of the four hermaphroditic and four dioecious species was characterized based on randomly sampled whole genome shotgun sequencing, and common elements were annotated. Across our broad phylogenetic sampling, Ty-1 Copia retroelements, in particular, have undergone a marked proliferation in dioecious species. In the absence of a detectable WGD event, retrotransposon proliferation is the most likely explanation for the precipitous increase in genome size in dioecious Asparagus species.
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Tennessen JA, Govindarajulu R, Liston A, Ashman T. Homomorphic ZW chromosomes in a wild strawberry show distinctive recombination heterogeneity but a small sex-determining region. THE NEW PHYTOLOGIST 2016; 211:1412-23. [PMID: 27102236 PMCID: PMC5074332 DOI: 10.1111/nph.13983] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 03/21/2016] [Indexed: 05/10/2023]
Abstract
Recombination in ancient, heteromorphic sex chromosomes is typically suppressed at the sex-determining region (SDR) and proportionally elevated in the pseudoautosomal region (PAR). However, little is known about recombination dynamics of young, homomorphic plant sex chromosomes. We examine male and female function in crosses and unrelated samples of the dioecious octoploid strawberry Fragaria chiloensis in order to map the small and recently evolved SDR controlling both traits and to examine recombination patterns on the incipient ZW chromosome. The SDR of this ZW system is located within a 280 kb window, in which the maternal recombination rate is lower than the paternal one. In contrast to the SDR, the maternal PAR recombination rate is much higher than the rates of the paternal PAR or autosomes, culminating in an elevated chromosome-wide rate. W-specific divergence is elevated within the SDR and a single polymorphism is observed in high species-wide linkage disequilibrium with sex. Selection for recombination suppression within the small SDR may be weak, but fluctuating sex ratios could favor elevated recombination in the PAR to remove deleterious mutations on the W. The recombination dynamics of this nascent sex chromosome with a modestly diverged SDR may be typical of other dioecious plants.
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Affiliation(s)
- Jacob A. Tennessen
- Department of Integrative BiologyOregon State UniversityCorvallisOR97331USA
| | | | - Aaron Liston
- Department of Botany and Plant PathologyOregon State UniversityCorvallisOR97331USA
| | - Tia‐Lynn Ashman
- Department of Biological SciencesUniversity of PittsburghPittsburghPA15260‐3929USA
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33
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Barker MS, Husband BC, Pires JC. Spreading Winge and flying high: The evolutionary importance of polyploidy after a century of study. AMERICAN JOURNAL OF BOTANY 2016; 103:1139-45. [PMID: 27480249 DOI: 10.3732/ajb.1600272] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 07/20/2016] [Indexed: 05/10/2023]
Affiliation(s)
- Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 USA
| | - Brian C Husband
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1 Canada
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 USA
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34
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Glick L, Sabath N, Ashman TL, Goldberg E, Mayrose I. Polyploidy and sexual system in angiosperms: Is there an association? AMERICAN JOURNAL OF BOTANY 2016; 103:1223-1235. [PMID: 27352832 DOI: 10.3732/ajb.1500424] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 04/19/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Flowering plants display a variety of sexual systems, ranging from complete cosexuality (hermaphroditism) to separate-sexed individuals (dioecy). While dioecy is relatively rare, it has evolved many times and is present in many plant families. Transitions in sexual systems are hypothesized to be affected by large genomic events such as whole-genome duplication, or polyploidy, and several models have been proposed to explain the observed patterns of association. METHODS In this study, we assessed the association between ploidy and sexual system (separate or combined sexes). To this end, we assembled a database of ploidy levels and sexual systems for ∼1000 species, spanning 18 genera and 15 families. We applied several phylogenetic comparative approaches, including Pagel's coevolutionary framework and sister clade analyses, for detecting correlations between ploidy level and sexual system. KEY RESULTS Our results indicate a broad association between polyploidy and sexual system dimorphism, with low evolutionary stability of the diploid-dioecious condition observed in several clades. A detailed examination of the clades exhibiting this correlation reveals that it is underlain by various patterns of transition rate asymmetry. CONCLUSIONS We conclude that the long-hypothesized connection between ploidy and sexual system holds in some clades, although it may well be affected by factors that differ from clade to clade. Our results further demonstrate that to better understand the evolutionary processes involved, more sophisticated methods and extensive and detailed data sets are required for both broad and focused inquiry.
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Affiliation(s)
- Lior Glick
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Niv Sabath
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Tia-Lynn Ashman
- Department of Biological Sciences University of Pittsburgh, Pittsburgh, Pennsylvania 15260 USA
| | - Emma Goldberg
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota 55108-6097 USA
| | - Itay Mayrose
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
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35
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Yakimowski SB, Barrett SCH. The role of hybridization in the evolution of sexual system diversity in a clonal, aquatic plant. Evolution 2016; 70:1200-11. [PMID: 27150128 DOI: 10.1111/evo.12941] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/21/2016] [Accepted: 04/26/2016] [Indexed: 01/25/2023]
Abstract
The stable coexistence within populations of females, males, and hermaphrodites (subdioecy) is enigmatic because theoretical models indicate that maintenance of this sexual system involves highly restricted conditions. Subdioecy is more commonly interpreted as a transitory stage along the gynodioecious pathway from hermaphroditism to dioecy. The widespread, North American, aquatic plant Sagittaria latifolia is largely composed of monoecious or dioecious populations; however, subdioecious populations with high frequencies of hermaphrodites (mean frequency = 0.50) characterize the northern range boundary of dioecy in eastern North America. We investigated two hypotheses for the origin of subdioecy in this region. Using polymorphic microsatellite loci, we evaluated whether subdioecy arises through selection on standing genetic variation for male sex inconstancy in dioecious populations, or results from hybridization between monoecious and dioecious populations. We found evidence for both pathways to subdioecy, although hybridization was the more common mechanism, with genetic evidence of admixture in nine of 14 subdioecious populations examined. Hybridization has also played a role in the origin of androdioecious populations in S. latifolia, a mechanism not often considered in the evolution of this rare sexual system. Our study demonstrates how hybridization has the potential to play a role in the diversification of plant sexual systems.
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Affiliation(s)
- Sarah B Yakimowski
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B2, Canada. .,Current Address: Department of Biology, Queen's University, 116 Barrie Street, Kingston, Ontario, K7L 3N6, Canada.
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B2, Canada
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36
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Sabath N, Goldberg EE, Glick L, Einhorn M, Ashman TL, Ming R, Otto SP, Vamosi JC, Mayrose I. Dioecy does not consistently accelerate or slow lineage diversification across multiple genera of angiosperms. THE NEW PHYTOLOGIST 2016; 209:1290-1300. [PMID: 26467174 DOI: 10.1111/nph.13696] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 08/25/2015] [Indexed: 06/05/2023]
Abstract
Dioecy, the sexual system in which male and female organs are found in separate individuals, allows greater specialization for sex-specific functions and can be advantageous under various ecological and environmental conditions. However, dioecy is rare among flowering plants. Previous studies identified contradictory trends regarding the relative diversification rates of dioecious lineages vs their nondioecious counterparts, depending on the methods and data used. We gathered detailed species-level data for dozens of genera that contain both dioecious and nondioecious species. We then applied a probabilistic approach that accounts for differential speciation, extinction, and transition rates between states to examine whether there is an association between dioecy and lineage diversification. We found a bimodal distribution, whereby dioecious lineages exhibited higher diversification in certain genera but lower diversification in others. Additional analyses did not uncover an ecological or life history trait that could explain a context-dependent effect of dioecy on diversification. Furthermore, in-depth simulations of neutral characters demonstrated that such bimodality is also found when simulating neutral characters across the observed trees. Our analyses suggest that - at least for these genera with the currently available data - dioecy neither consistently places a strong brake on diversification nor is a strong driver.
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Affiliation(s)
- Niv Sabath
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Emma E Goldberg
- Department of Ecology, Evolution & Behavior, University of Minnesota, St Paul, MN, 55108-6097, USA
| | - Lior Glick
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Moshe Einhorn
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Haixia Institute for Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sarah P Otto
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6J 3S7, Canada
| | - Jana C Vamosi
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Itay Mayrose
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
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37
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Miller JS, Kamath A, Husband BC, Levin RA. Correlated polymorphism in cytotype and sexual system within a monophyletic species, Lycium californicum. ANNALS OF BOTANY 2016; 117:307-17. [PMID: 26546375 PMCID: PMC4724043 DOI: 10.1093/aob/mcv167] [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: 06/02/2015] [Revised: 07/30/2015] [Accepted: 09/18/2015] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS Polyploidy has important effects on reproductive systems in plants and has been implicated in the evolution of dimorphic sexual systems. In particular, higher ploidy is associated with gender dimorphism across Lycium species (Solanaceae) and across populations within the species Lycium californicum. Previous research on the association of cytotype and sexual system within L. californicum sampled a limited portion of the species range, and did not investigate evolutionary transitions between sexual systems. Lycium californicum occurs in arid regions on offshore islands and mainland regions in the south-western United States and Mexico, motivating a more comprehensive analysis of intraspecific variation in sexual system and cytotype across the full range of this species. METHODS Sexual system (dimorphic vs. cosexual) was determined for 34 populations across the geographical range of L. californicum using field observations of pollen production, and was confirmed using morphological measurements and among-plant correlations of primary sexual traits. Ploidy was inferred using flow cytometry in 28 populations. DNA sequence data from four plastid and two nuclear regions were used to reconstruct relationships among populations and to map transitions in sexual system and ploidy. KEY RESULTS Lycium californicum is monophyletic, ancestrally diploid and cosexual, and the association of gender dimorphism and polyploidy appears to have two evolutionary origins in this species. Compared with cosexual populations, dimorphic populations had bimodal anther size distributions, negative correlations between male and female floral traits, and larger coefficients of variation for primary sexual traits. Flow cytometry confirmed tetraploidy in dimorphic populations, whereas cosexual populations were diploid. CONCLUSIONS Tetraploidy and gender dimorphism are perfectly correlated in L. californicum, and the distribution of tetraploid-dimorphic populations is restricted to populations in Arizona and the Baja California peninsula. The analysis suggests that tetraploidy and dimorphism likely established in Baja California and may have evolved multiple times.
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Affiliation(s)
- Jill S Miller
- Department of Biology, Amherst College, Amherst, MA 01002 USA,
| | - Ambika Kamath
- Department of Biology, Amherst College, Amherst, MA 01002 USA, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA and
| | - Brian C Husband
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1 Canada
| | - Rachel A Levin
- Department of Biology, Amherst College, Amherst, MA 01002 USA
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Yagi K, Pawełkowicz M, Osipowski P, Siedlecka E, Przybecki Z, Tagashira N, Hoshi Y, Malepszy S, Pląder W. Molecular Cytogenetic Analysis of Cucumis Wild Species Distributed in Southern Africa: Physical Mapping of 5S and 45S rDNA with DAPI. Cytogenet Genome Res 2015; 146:80-7. [PMID: 26112877 DOI: 10.1159/000433572] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2015] [Indexed: 11/19/2022] Open
Abstract
Wild Cucumis species have been divided into Australian/Asian and African groups using morphological and phylogenetic characteristics, and new species have been described recently. No molecular cytogenetic information is available for most of these species. The crossability between 5 southern African Cucumis species (C. africanus, C. anguria, C. myriocarpus, C. zeyheri, and C. heptadactylus) has been reported; however, the evolutionary relationship among them is still unclear. Here, a molecular cytogenetic analysis using FISH with 5S and 45 S ribosomal DNA (rDNA) was used to investigate these Cucumis species based on sets of rDNA-bearing chromosomes (rch) types I, II and III. The molecular cytogenetic and phylogenetic results suggested that at least 2 steps of chromosomal rearrangements may have occurred during the evolution of tetraploid C. heptadactylus. In step 1, an additional 45 S rDNA site was observed in the chromosome (type III). In particular, C. myriocarpus had a variety of rch sets. Our results suggest that chromosomal rearrangements may have occurred in the 45 S rDNA sites. We propose that polyploid evolution occurred in step 2. This study provides insights into the chromosomal characteristics of African Cucumis species and contributes to the understanding of chromosomal evolution in this genus.
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Affiliation(s)
- Kouhei Yagi
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences-SGGW, Warsaw, Poland
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Perley DS, Jesson LK. Hybridization is associated with changes in sexual system in the bryophyte genus Atrichum. AMERICAN JOURNAL OF BOTANY 2015; 102:555-565. [PMID: 25878089 DOI: 10.3732/ajb.1400494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 03/07/2015] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY Over 50% of bryophytes have separate sexes, and numerous transitions have occurred between combined and separate sexes. Polyploidy and hybridization is one proximate mechanism hypothesized to cause evolutionary transitions to hermaphroditism in bryophytes because sex is expressed at the haploid stage and in nonpolyploid dioecious species males have a single V chromosome and females a U. Hermaphroditism can arise if gametophytes of allopolyploids have both U and V chromosomes. We examined the association between polyploidy and hermaphroditism in the bryophyte genus Atrichum, which has species where gametophytes can be haploid, diploid, or triploid, and some species have hermaphroditic individuals. METHODS We generated phylogenies of Atrichum from sequences of three plastid regions (rbcL, rps4, and trnL-trnF) and the second intron for the nuclear gene Leafy/Floricaula to further understand the relationships among haploid, diploid, and triploid species, and those with combined or separate sexes. KEY RESULTS The existence of multiple sequences of Leafy/Floricaula in diploid and triploid, but not haploid, individuals is consistent with independent allopolyploid origins of the diploid and triploid species. Allopolyploidy was associated with a likely gain in hermaphroditism in triploid Atrichum undulatum and possibly diploid A. altecristatum, but not in the allopolyploid A. crispulum (diploid at the gametophyte level). CONCLUSIONS These results highlight a role for hybridization and polyploidy in sexual system evolution, but the presence of diploid (allopolyploid) dioecious species suggest that other factors may influence the maintenance of sexual systems after an evolutionary transition.
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Affiliation(s)
- Danielle S Perley
- Department of Biology, University of New Brunswick, 10 Bailey Dr, Fredericton, Canada E3B5A3
| | - Linley K Jesson
- Department of Biology, University of New Brunswick, 10 Bailey Dr, Fredericton, Canada E3B5A3 Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany
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Blank CM, Levin RA, Miller JS. Intraspecific variation in gender strategies in Lycium (Solanaceae): associations with ploidy and changes in floral form following the evolution of gender dimorphism. AMERICAN JOURNAL OF BOTANY 2014; 101:2160-2168. [PMID: 25480712 DOI: 10.3732/ajb.1400356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
UNLABELLED • PREMISE OF THE STUDY An association between polyploidy and gender dimorphism has been noted in several plant lineages. Whereas the majority of Lycium species are diploid and have hermaphroditic flowers in cosexual populations, gender dimorphism (gynodioecy, dioecy) has been shown to be uniformly associated with polyploidy in previous studies. Preliminary field observations suggested that some populations of Lycium carolinianum were dimorphic, providing a test of this association.• METHODS We assessed sexual systems and cytotype variation (to infer ploidy) across 17 populations of L. carolinianum. Comparison of flowers in cosexual and dimorphic populations were used to infer changes in reproductive morphology associated with the evolution of gynodioecy.• KEY RESULTS The majority of populations were cosexual in gender expression, but dimorphism was present in the Yucatán and in some populations in Hawaii. Populations varied in ploidy and were either diploid or tetraploid. Floral sexual dimorphism was present in all gynodioecious populations, though the magnitude differed and was cryptic in some cases. Our results are consistent with the hypothesis that following the evolution of gynodioecy, flowers on hermaphrodites increased in size.• CONCLUSIONS Dimorphic sexual systems have likely evolved convergently in L. carolinianum. In contrast to previous studies, dimorphism is not perfectly associated with polyploidy. Although our sample from the Yucatán was both tetraploid and dimorphic, all populations in Hawaii were diploid regardless of sexual system. Ongoing phylogeographic and mating system studies will contribute to our understanding of reproductive evolution in this widespread, polymorphic species.
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Affiliation(s)
- Caitlin M Blank
- Department of Biology, Amherst College, Amherst, Massachusetts 01002 USA
| | - Rachel A Levin
- Department of Biology, Amherst College, Amherst, Massachusetts 01002 USA
| | - Jill S Miller
- Department of Biology, Amherst College, Amherst, Massachusetts 01002 USA
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Liston A, Cronn R, Ashman TL. Fragaria: a genus with deep historical roots and ripe for evolutionary and ecological insights. AMERICAN JOURNAL OF BOTANY 2014; 101:1686-99. [PMID: 25326614 DOI: 10.3732/ajb.1400140] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The cultivated strawberry, Fragaria ×ananassa, is one of the youngest domesticated plants. Its 18th century origin via hybridization in Europe between the North American F. virginiana and the South American F. chiloensis was documented by the botanist Antoine Nicolas Duchesne. His 1766 "Natural History of Strawberries" is an extraordinary work that integrates fundamental discoveries on the biology, ecology, and phylogeny of Fragaria with applied information on cultivation and ethnobotanical uses, serving as an inspiration for current research in the genus. Fragaria species exhibit the full range of sexual systems in the gynodioecy pathway from hermaphroditism to dioecy (and back again), as well as variation in self-compatibility, and evidence of sex chromosomes with female heterogamety. The genus is also characterized by interspecific hybridization and polyploidy, with a natural range of ploidy levels from diploids to decaploids. This biological diversity, combined with the availability of genomic resources and the ease of growing and experimenting with the plants, makes Fragaria a very attractive system for ecological and evolutionary genomics. The goal of this review is to introduce Fragaria as a model genus and to provide a roadmap for future integrative research. These research directions will deepen our understanding of the ecological and evolutionary context that shaped the ancestors of the cultivated strawberry, not only providing information that can be applied to efforts to shape the future of this important fruit crop but also our understanding of key transitions in plant evolution.
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Affiliation(s)
- Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 USA
| | - Richard Cronn
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, Oregon 97331 USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260 USA
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Renner SS. The relative and absolute frequencies of angiosperm sexual systems: dioecy, monoecy, gynodioecy, and an updated online database. AMERICAN JOURNAL OF BOTANY 2014; 101:1588-96. [PMID: 25326608 DOI: 10.3732/ajb.1400196] [Citation(s) in RCA: 323] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
UNLABELLED • PREMISE OF THE STUDY Separating sexual function between different individuals carries risks, especially for sedentary organisms. Nevertheless, many land plants have unisexual gametophytes or sporophytes. This study brings together data and theoretical insights from research over the past 20 yr on the occurrence and frequency of plant sexual systems, focusing on the flowering plants.• METHODS A list of genera with dioecious species, along with other information, is made available (http://www.umsl.edu/∼renners/). Frequencies of other sexual systems are tabulated, and data on the genetic regulation, ecological context, and theoretical benefits of dioecy reviewed.• KEY RESULTS There are 15600 dioecious angiosperms in 987 genera and 175 families, or 5-6% of the total species (7% of genera, 43% of families), with somewhere between 871 to 5000 independent origins of dioecy. Some 43% of all dioecious angiosperms are in just 34 entirely dioecious clades, arguing against a consistent negative influence of dioecy on diversification. About 31.6% of the dioecious species are wind-pollinated, compared with 5.5-6.4% of nondioecious angiosperms. Also, 1.4% of all angiosperm genera contain dioecious and monoecious species, while 0.4% contain dioecious and gynodioecious species. All remaining angiosperm sexual systems are rare. Chromosomal sex determination is known from 40 species; environmentally modulated sex allocation is common. Few phylogenetic studies have focused on the evolution of dioecy.• CONCLUSIONS The current focus is on the genetic mechanisms underlying unisexual flowers and individuals. Mixed strategies of sexual and vegetative dispersal, together with plants' sedentary life style, may often favor polygamous systems in which sexually inconstant individuals can persist. Nevertheless, there are huge entirely dioecious clades of tropical woody plants.
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Affiliation(s)
- Susanne S Renner
- Systematic Botany and Mycology, University of Munich, 80638 Munich, Germany
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