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Zhang GJ, Jia KL, Wang J, Gao WJ, Li SF. Genome-wide analysis of transposable elements and satellite DNA in Humulus scandens, a dioecious plant with XX/XY 1Y 2 chromosomes. FRONTIERS IN PLANT SCIENCE 2023; 14:1230250. [PMID: 37908838 PMCID: PMC10614002 DOI: 10.3389/fpls.2023.1230250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 10/04/2023] [Indexed: 11/02/2023]
Abstract
Transposable elements (TEs) and satellite DNAs, two major categories of repetitive sequences, are expected to accumulate in non-recombining genome regions, including sex-linked regions, and contribute to sex chromosome evolution. The dioecious plant, Humulus scandens, can be used for studying the evolution of the XX/XY1Y2 sex chromosomes. In this study, we thoroughly examined the repetitive components of male and female H. scandens using next-generation sequencing data followed by bioinformatics analysis and florescence in situ hybridization (FISH). The H. scandens genome has a high overall repetitive sequence composition, 68.30% in the female and 66.78% in the male genome, with abundant long terminal repeat (LTR) retrotransposons (RTs), including more Ty3/Gypsy than Ty1/Copia elements, particularly two Ty3/Gypsy lineages, Tekay and Retand. Most LTR-RT lineages were found dispersed across the chromosomes, though CRM and Athila elements were predominately found within the centromeres and the pericentromeric regions. The Athila elements also showed clearly higher FISH signal intensities in the Y1 and Y2 chromosomes than in the X or autosomes. Three novel satellite DNAs were specifically distributed in the centromeric and/or telomeric regions, with markedly different distributions on the X, Y1, and Y2 chromosomes. Combined with FISH using satellite DNAs to stain chromosomes during meiotic diakinesis, we determined the synapsis pattern and distinguish pseudoautosomal regions (PARs). The results indicate that the XY1Y2 sex chromosomes of H. scandens might have originated from a centric fission event. This study improves our understanding of the repetitive sequence organization of H. scandens genome and provides a basis for further analysis of their chromosome evolution process.
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Affiliation(s)
- Guo-Jun Zhang
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Ke-Li Jia
- College of Life Sciences, Henan Normal University, Xinxiang, China
- SanQuan Medical College, Xinxiang Medical University, Xinxiang, China
| | - Jin Wang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang, China
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Razumova OV, Divashuk MG, Alexandrov OS, Karlov GI. GISH painting of the Y chromosomes suggests advanced phases of sex chromosome evolution in three dioecious Cannabaceae species (Humulus lupulus, H. japonicus, and Cannabis sativa). PROTOPLASMA 2023; 260:249-256. [PMID: 35595927 DOI: 10.1007/s00709-022-01774-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
In plants, dioecy is relatively rare, and it involves sex chromosome systems that often developed independently over time. These characteristics make dioecious plants an attractive model to study sex chromosome evolution. To clarify the patterns of plant sex chromosome evolution, studies should be performed on a wide range of dioecious species. It is interesting to study the sex chromosomes in related species that evolved during a long period of independent sex chromosome evolution. The Cannabaceae family includes three dioecious species with heteromorphic sex chromosomes. Cannabis sativa and Humulus lupulus use the XX/XY chromosome system, whereas Humulus japonicus contains multiple sex chromosomes (XX/XY1Y2). To better understand sex chromosome evolution and the level of genomic divergence of these three related species, we undertook self-GISH and comparative GISH analyses. The self-GISH allowed visualization of the Y chromosomes of C. sativa, H. lupulus, and H. japonicus. The self-GISH signal was distributed along the entire Y chromosome, excluding the pseudo-autosomal region (PAR). Our results indicate that the male-specific region of the Y chromosome (MSY) spans the overwhelming majority of the Y chromosomes of all three species studied. The self-GISH results reveal the accumulation of repetitive DNA sequences in the Y chromosomes of all three species studied. This sequences presented in autosomes and/or chromosome X at a lower copy number than in Y. In comparative GISH experiments where the probe DNA of one species was applied to another species, a weak signal was exclusively detected on 45S rDNA sites, indicating a high level of genomic differentiation of the species used in this study. We demonstrate small PAR size and opposing large MSY and its positions on Y chromosomes. We also found that these genomes are highly differentiated. Furthermore, the data obtained in this study indicate a long period of independent and advanced sex chromosome evolution. Our study provides a valuable basis for future genomic studies of sex and suggests that the Cannabaceae family offers a promising model to study sex chromosome evolution.
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Affiliation(s)
- Olga V Razumova
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, Moscow, 127550, Russia
| | - Mikhail G Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, Moscow, 127550, Russia
| | - Oleg S Alexandrov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, Moscow, 127550, Russia
| | - Gennady I Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, Moscow, 127550, Russia.
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Mora-Calderón J, Scott-Moraga K, Bolaños-Villegas P. Analysis of Meiosis in Nonmodel Tropical Plants: The Case of Carica papaya Linn. Methods Mol Biol 2020; 2061:131-139. [PMID: 31583657 DOI: 10.1007/978-1-4939-9818-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
To develop plants that are more tolerant to drought, marginal soil fertility, and diseases and that satisfy demands for high yield, new cultivars of the tropical fruit papaya (Carica papaya L.) are needed. Nonetheless, in many cases, these traits are available in only wild relatives found throughout Latin America. Understanding meiotic progression may facilitate the introgression of desirable traits into commercial cultivars that maintain high fertility. In this protocol, we describe a practical and simple method to effectively isolate male meiocytes in order to document the behavior of papaya meiotic chromosomes.
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Affiliation(s)
- José Mora-Calderón
- Laboratory of Cell and Molecular Biology, Fabio Baudrit Agricultural Research Station, University of Costa Rica, Alajuela, Costa Rica
| | - Kalani Scott-Moraga
- Laboratory of Cell and Molecular Biology, Fabio Baudrit Agricultural Research Station, University of Costa Rica, Alajuela, Costa Rica
| | - Pablo Bolaños-Villegas
- Laboratory of Cell and Molecular Biology, Fabio Baudrit Agricultural Research Station, University of Costa Rica, Alajuela, Costa Rica.
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Li SF, Guo YJ, Li JR, Zhang DX, Wang BX, Li N, Deng CL, Gao WJ. The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach ( Spinacia oleracea L.). Mob DNA 2019; 10:3. [PMID: 30675191 PMCID: PMC6337768 DOI: 10.1186/s13100-019-0147-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/07/2019] [Indexed: 11/10/2022] Open
Abstract
Background Repetitive sequences, including transposable elements (TEs) and satellite DNAs, occupy a considerable portion of plant genomes. Analysis of the repeat fraction benefits the understanding of genome structure and evolution. Spinach (Spinacia oleracea L.), an important vegetable crop, is also a model dioecious plant species for studying sex determination and sex chromosome evolution. However, the repetitive sequences of the spinach genome have not been fully investigated. Results We extensively analyzed the repetitive components of draft spinach genome, especially TEs and satellites, by different strategies. A total of 16,002 full-length TEs were identified. Among the most abundant long terminal repeat (LTR) retrotransposons (REs), Copia elements were overrepresented compared with Gypsy ones. Angela was the most dominating Copia lineage; Ogre/Tat was the most abundant Gypsy lineage. The mean insertion age of LTR-REs was 1.42 million years; approximately 83.7% of these elements were retrotransposed during the last two million years. RepeatMasker totally masked about 64.05% of the spinach genome, with LTR-REs, non-LTR-REs, and DNA transposons occupying 49.2, 2.4, and 5.6%, respectively. Fluorescence in situ hybridization (FISH) analysis showed that most LTR-REs dispersed all over the chromosomes, by contrast, elements of CRM lineage were distributed at the centromeric region of all chromosomes. In addition, Ogre/Tat lineage mainly accumulated on sex chromosomes, and satellites Spsat2 and Spsat3 were exclusively located at the telomeric region of the short arm of sex chromosomes. Conclusions We reliably annotated the TE fraction of the draft genome of spinach. FISH analysis indicates that Ogre/Tat lineage and the sex chromosome-specific satellites DNAs might participate in sex chromosome formation and evolution. Based on FISH signals of microsatellites, together with 45S rDNA, a fine karyotype of spinach was established. This study improves our knowledge of repetitive sequence organization in spinach genome and aids in accurate spinach karyotype construction. Electronic supplementary material The online version of this article (10.1186/s13100-019-0147-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shu-Fen Li
- 1College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Yu-Jiao Guo
- 1College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Jia-Rong Li
- 1College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Dong-Xu Zhang
- 2College of Life Science, Shanxi Datong University, Datong, 037009 China
| | - Bing-Xiao Wang
- 1College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Ning Li
- 1College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Chuan-Liang Deng
- 1College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Wu-Jun Gao
- 1College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
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Puterova J, Kubat Z, Kejnovsky E, Jesionek W, Cizkova J, Vyskot B, Hobza R. The slowdown of Y chromosome expansion in dioecious Silene latifolia due to DNA loss and male-specific silencing of retrotransposons. BMC Genomics 2018; 19:153. [PMID: 29458354 PMCID: PMC5819184 DOI: 10.1186/s12864-018-4547-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/13/2018] [Indexed: 11/10/2022] Open
Abstract
Background The rise and fall of the Y chromosome was demonstrated in animals but plants often possess the large evolutionarily young Y chromosome that is thought has expanded recently. Break-even points dividing expansion and shrinkage phase of plant Y chromosome evolution are still to be determined. To assess the size dynamics of the Y chromosome, we studied intraspecific genome size variation and genome composition of male and female individuals in a dioecious plant Silene latifolia, a well-established model for sex-chromosomes evolution. Results Our genome size data are the first to demonstrate that regardless of intraspecific genome size variation, Y chromosome has retained its size in S. latifolia. Bioinformatics study of genome composition showed that constancy of Y chromosome size was caused by Y chromosome DNA loss and the female-specific proliferation of recently active dominant retrotransposons. We show that several families of retrotransposons have contributed to genome size variation but not to Y chromosome size change. Conclusions Our results suggest that the large Y chromosome of S. latifolia has slowed down or stopped its expansion. Female-specific proliferation of retrotransposons, enlarging the genome with exception of the Y chromosome, was probably caused by silencing of highly active retrotransposons in males and represents an adaptive mechanism to suppress degenerative processes in the haploid stage. Sex specific silencing of transposons might be widespread in plants but hidden in traditional hermaphroditic model plants. Electronic supplementary material The online version of this article (10.1186/s12864-018-4547-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Janka Puterova
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 612 00, Brno, Czech Republic.,Department of Information Systems, Faculty of Information Technology, Brno University of Technology, 61200, Brno, Czech Republic
| | - Zdenek Kubat
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 612 00, Brno, Czech Republic.
| | - Eduard Kejnovsky
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 612 00, Brno, Czech Republic
| | - Wojciech Jesionek
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 612 00, Brno, Czech Republic
| | - Jana Cizkova
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Czech Academy of Sciences, 783 71, Olomouc - Holice, Czech Republic
| | - Boris Vyskot
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 612 00, Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 612 00, Brno, Czech Republic. .,Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Czech Academy of Sciences, 783 71, Olomouc - Holice, Czech Republic.
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Chromosome Evolution in Connection with Repetitive Sequences and Epigenetics in Plants. Genes (Basel) 2017; 8:genes8100290. [PMID: 29064432 PMCID: PMC5664140 DOI: 10.3390/genes8100290] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 10/16/2017] [Accepted: 10/18/2017] [Indexed: 01/18/2023] Open
Abstract
Chromosome evolution is a fundamental aspect of evolutionary biology. The evolution of chromosome size, structure and shape, number, and the change in DNA composition suggest the high plasticity of nuclear genomes at the chromosomal level. Repetitive DNA sequences, which represent a conspicuous fraction of every eukaryotic genome, particularly in plants, are found to be tightly linked with plant chromosome evolution. Different classes of repetitive sequences have distinct distribution patterns on the chromosomes. Mounting evidence shows that repetitive sequences may play multiple generative roles in shaping the chromosome karyotypes in plants. Furthermore, recent development in our understanding of the repetitive sequences and plant chromosome evolution has elucidated the involvement of a spectrum of epigenetic modification. In this review, we focused on the recent evidence relating to the distribution pattern of repetitive sequences in plant chromosomes and highlighted their potential relevance to chromosome evolution in plants. We also discussed the possible connections between evolution and epigenetic alterations in chromosome structure and repatterning, such as heterochromatin formation, centromere function, and epigenetic-associated transposable element inactivation.
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7
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VanBuren R, Wai CM, Zhang J, Han J, Arro J, Lin Z, Liao Z, Yu Q, Wang ML, Zee F, Moore RC, Charlesworth D, Ming R. Extremely low nucleotide diversity in the X-linked region of papaya caused by a strong selective sweep. Genome Biol 2016; 17:230. [PMID: 27890017 PMCID: PMC5125041 DOI: 10.1186/s13059-016-1095-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 10/31/2016] [Indexed: 11/10/2022] Open
Abstract
Background The papaya Y-linked region showed clear population structure, resulting in the detection of the ancestral male population that domesticated hermaphrodite papayas were selected from. The same populations were used to study nucleotide diversity and population structure in the X-linked region. Results Diversity is very low for all genes in the X-linked region in the wild dioecious population, with nucleotide diversity πsyn = 0.00017, tenfold lower than the autosomal region (πsyn = 0.0017) and 12-fold lower than the Y-linked region (πsyn = 0.0021). Analysis of the X-linked sequences shows an undivided population, suggesting a geographically wide diversity-reducing event, whereas two subpopulations were observed in the autosomes separating gynodioecy and dioecy and three subpopulations in the Y-linked region separating three male populations. The extremely low diversity in the papaya X-linked region was probably caused by a recent, strong selective sweep before domestication, involving either the spread of a recessive mutation in an X-linked gene that is beneficial to males or a partially dominant mutation that benefitted females or both sexes. Nucleotide diversity in the domesticated X samples is about half that in the wild Xs, probably due to the bottleneck when hermaphrodites were selected during domestication. Conclusions The extreme low nucleotide diversity in the papaya X-linked region is much greater than observed in humans, great apes, and the neo-X chromosome of Drosophila miranda, which show the expected pattern of Y-linked genes < X-linked genes < autosomal genes; papaya shows an unprecedented pattern of X-linked genes < autosomal genes < Y-linked genes. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1095-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Robert VanBuren
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ching Man Wai
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jisen Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jennifer Han
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jie Arro
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Zhicong Lin
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Zhenyang Liao
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Qingyi Yu
- Texas A&M AgriLife Research, Department of Plant Pathology & Microbiology, Texas A&M University System, Dallas, TX, 75252, USA
| | - Ming-Li Wang
- Hawaii Agriculture Research Center, Kunia, HI, 96759, USA
| | - Francis Zee
- USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, HI, 96720, USA
| | - Richard C Moore
- Department of Botany, Miami University, Oxford, OH, 45056, USA
| | - Deborah Charlesworth
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, UK
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China. .,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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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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Li SF, Zhang GJ, Zhang XJ, Yuan JH, Deng CL, Gu LF, Gao WJ. DPTEdb, an integrative database of transposable elements in dioecious plants. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw078. [PMID: 27173524 PMCID: PMC4865326 DOI: 10.1093/database/baw078] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 04/22/2016] [Indexed: 02/02/2023]
Abstract
Dioecious plants usually harbor ‘young’ sex chromosomes, providing an opportunity to study the early stages of sex chromosome evolution. Transposable elements (TEs) are mobile DNA elements frequently found in plants and are suggested to play important roles in plant sex chromosome evolution. The genomes of several dioecious plants have been sequenced, offering an opportunity to annotate and mine the TE data. However, comprehensive and unified annotation of TEs in these dioecious plants is still lacking. In this study, we constructed a dioecious plant transposable element database (DPTEdb). DPTEdb is a specific, comprehensive and unified relational database and web interface. We used a combination of de novo, structure-based and homology-based approaches to identify TEs from the genome assemblies of previously published data, as well as our own. The database currently integrates eight dioecious plant species and a total of 31 340 TEs along with classification information. DPTEdb provides user-friendly web interfaces to browse, search and download the TE sequences in the database. Users can also use tools, including BLAST, GetORF, HMMER, Cut sequence and JBrowse, to analyze TE data. Given the role of TEs in plant sex chromosome evolution, the database will contribute to the investigation of TEs in structural, functional and evolutionary dynamics of the genome of dioecious plants. In addition, the database will supplement the research of sex diversification and sex chromosome evolution of dioecious plants. Database URL: http://genedenovoweb.ticp.net:81/DPTEdb/index.php
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Affiliation(s)
- Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Guo-Jun Zhang
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China
| | - Xue-Jin Zhang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Jin-Hong Yuan
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Lian-Feng Gu
- Basic Forestry and Proteomics Center, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
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10
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Li SF, Zhang GJ, Yuan JH, Deng CL, Gao WJ. Repetitive sequences and epigenetic modification: inseparable partners play important roles in the evolution of plant sex chromosomes. PLANTA 2016; 243:1083-95. [PMID: 26919983 DOI: 10.1007/s00425-016-2485-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 02/07/2016] [Indexed: 05/03/2023]
Abstract
The present review discusses the roles of repetitive sequences played in plant sex chromosome evolution, and highlights epigenetic modification as potential mechanism of repetitive sequences involved in sex chromosome evolution. Sex determination in plants is mostly based on sex chromosomes. Classic theory proposes that sex chromosomes evolve from a specific pair of autosomes with emergence of a sex-determining gene(s). Subsequently, the newly formed sex chromosomes stop recombination in a small region around the sex-determining locus, and over time, the non-recombining region expands to almost all parts of the sex chromosomes. Accumulation of repetitive sequences, mostly transposable elements and tandem repeats, is a conspicuous feature of the non-recombining region of the Y chromosome, even in primitive one. Repetitive sequences may play multiple roles in sex chromosome evolution, such as triggering heterochromatization and causing recombination suppression, leading to structural and morphological differentiation of sex chromosomes, and promoting Y chromosome degeneration and X chromosome dosage compensation. In this article, we review the current status of this field, and based on preliminary evidence, we posit that repetitive sequences are involved in sex chromosome evolution probably via epigenetic modification, such as DNA and histone methylation, with small interfering RNAs as the mediator.
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Affiliation(s)
- Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Guo-Jun Zhang
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003, China
| | - Jin-Hong Yuan
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
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Abstract
Dioecy (separate male and female individuals) ensures outcrossing and is more prevalent in animals than in plants. Although it is common in bryophytes and gymnosperms, only 5% of angiosperms are dioecious. In dioecious higher plants, flowers borne on male and female individuals are, respectively deficient in functional gynoecium and androecium. Dioecy is inherited via three sex chromosome systems: XX/XY, XX/X0 and WZ/ZZ, such that XX or WZ is female and XY, X0 or ZZ are males. The XX/XY system generates the rarer XX/X0 and WZ/ZZ systems. An autosome pair begets XY chromosomes. A recessive loss-of-androecium mutation (ana) creates X chromosome and a dominant gynoecium-suppressing (GYS) mutation creates Y chromosome. The ana/ANA and gys/GYS loci are in the sex-determining region (SDR) of the XY pair. Accumulation of inversions, deleterious mutations and repeat elements, especially transposons, in the SDR of Y suppresses recombination between X and Y in SDR, making Y labile and increasingly degenerate and heteromorphic from X. Continued recombination between X and Y in their pseudoautosomal region located at the ends of chromosomal arms allows survival of the degenerated Y and of the species. Dioecy is presumably a component of the evolutionary cycle for the origin of new species. Inbred hermaphrodite species assume dioecy. Later they suffer degenerate-Y-led population regression. Cross-hybridization between such extinguishing species and heterologous species, followed by genome duplication of segregants from hybrids, give rise to new species.
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Lappin FM, Medert CM, Hawkins KK, Mardonovich S, Wu M, Moore RC. A polymorphic pseudoautosomal boundary in the Carica papaya sex chromosomes. Mol Genet Genomics 2015; 290:1511-22. [DOI: 10.1007/s00438-015-1000-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 01/23/2015] [Indexed: 12/14/2022]
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