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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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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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Cegan R, Vyskot B, Kejnovsky E, Kubat Z, Blavet H, Šafář J, Doležel J, Blavet N, Hobza R. Genomic diversity in two related plant species with and without sex chromosomes--Silene latifolia and S. vulgaris. PLoS One 2012; 7:e31898. [PMID: 22393373 PMCID: PMC3290532 DOI: 10.1371/journal.pone.0031898] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 01/16/2012] [Indexed: 01/25/2023] Open
Abstract
Background Genome size evolution is a complex process influenced by polyploidization, satellite DNA accumulation, and expansion of retroelements. How this process could be affected by different reproductive strategies is still poorly understood. Methodology/Principal Findings We analyzed differences in the number and distribution of major repetitive DNA elements in two closely related species, Silene latifolia and S. vulgaris. Both species are diploid and possess the same chromosome number (2n = 24), but differ in their genome size and mode of reproduction. The dioecious S. latifolia (1C = 2.70 pg DNA) possesses sex chromosomes and its genome is 2.5× larger than that of the gynodioecious S. vulgaris (1C = 1.13 pg DNA), which does not possess sex chromosomes. We discovered that the genome of S. latifolia is larger mainly due to the expansion of Ogre retrotransposons. Surprisingly, the centromeric STAR-C and TR1 tandem repeats were found to be more abundant in S. vulgaris, the species with the smaller genome. We further examined the distribution of major repetitive sequences in related species in the Caryophyllaceae family. The results of FISH (fluorescence in situ hybridization) on mitotic chromosomes with the Retand element indicate that large rearrangements occurred during the evolution of the Caryophyllaceae family. Conclusions/Significance Our data demonstrate that the evolution of genome size in the genus Silene is accompanied by the expansion of different repetitive elements with specific patterns in the dioecious species possessing the sex chromosomes.
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Affiliation(s)
- Radim Cegan
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno, Czech Republic
- Department of Plant Biology, Faculty of Agronomy, Mendel University in Brno, Brno, Czech Republic
| | - Boris Vyskot
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno, Czech Republic
| | - Eduard Kejnovsky
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno, Czech Republic
| | - Zdenek Kubat
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno, Czech Republic
| | - Hana Blavet
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno, Czech Republic
| | - Jan Šafář
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - Nicolas Blavet
- Institute of Integrative Biology, Plant Ecological Genetics, ETH Zurich, Zurich, Switzerland
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno, Czech Republic
- * E-mail:
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Marais GAB, Forrest A, Kamau E, Käfer J, Daubin V, Charlesworth D. Multiple nuclear gene phylogenetic analysis of the evolution of dioecy and sex chromosomes in the genus Silene. PLoS One 2011; 6:e21915. [PMID: 21853022 PMCID: PMC3154253 DOI: 10.1371/journal.pone.0021915] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 06/08/2011] [Indexed: 11/18/2022] Open
Abstract
In the plant genus Silene, separate sexes and sex chromosomes are believed to have evolved twice. Silene species that are wholly or largely hermaphroditic are assumed to represent the ancestral state from which dioecy evolved. This assumption is important for choice of outgroup species for inferring the genetic and chromosomal changes involved in the evolution of dioecy, but is mainly based on data from a single locus (ITS). To establish the order of events more clearly, and inform outgroup choice, we therefore carried out (i) multi-nuclear-gene phylogenetic analyses of 14 Silene species (including 7 hermaphrodite or gynodioecious species), representing species from both Silene clades with dioecious members, plus a more distantly related outgroup, and (ii) a BayesTraits character analysis of the evolution of dioecy. We confirm two origins of dioecy within this genus in agreement with recent work on comparing sex chromosomes from both clades with dioecious species. We conclude that sex chromosomes evolved after the origin of Silene and within a clade that includes only S. latifolia and its closest relatives. We estimate that sex chromosomes emerged soon after the split with the ancestor of S. viscosa, the probable closest non-dioecious S. latifolia relative among the species included in our study.
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Affiliation(s)
- Gabriel A B Marais
- Laboratoire de Biométrie et Biologie évolutive, UMR5558, Université Lyon 1, Centre National de la Recherche Scientifique, Villeurbanne, France.
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Blavet N, Charif D, Oger-Desfeux C, Marais GAB, Widmer A. Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database. BMC Genomics 2011; 12:376. [PMID: 21791039 PMCID: PMC3157477 DOI: 10.1186/1471-2164-12-376] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 07/26/2011] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The genus Silene is widely used as a model system for addressing ecological and evolutionary questions in plants, but advances in using the genus as a model system are impeded by the lack of available resources for studying its genome. Massively parallel sequencing cDNA has recently developed into an efficient method for characterizing the transcriptomes of non-model organisms, generating massive amounts of data that enable the study of multiple species in a comparative framework. The sequences generated provide an excellent resource for identifying expressed genes, characterizing functional variation and developing molecular markers, thereby laying the foundations for future studies on gene sequence and gene expression divergence. Here, we report the results of a comparative transcriptome sequencing study of eight individuals representing four Silene and one Dianthus species as outgroup. All sequences and annotations have been deposited in a newly developed and publicly available database called SiESTa, the Silene EST annotation database. RESULTS A total of 1,041,122 EST reads were generated in two runs on a Roche GS-FLX 454 pyrosequencing platform. EST reads were analyzed separately for all eight individuals sequenced and were assembled into contigs using TGICL. These were annotated with results from BLASTX searches and Gene Ontology (GO) terms, and thousands of single-nucleotide polymorphisms (SNPs) were characterized. Unassembled reads were kept as singletons and together with the contigs contributed to the unigenes characterized in each individual. The high quality of unigenes is evidenced by the proportion (49%) that have significant hits in similarity searches with the A. thaliana proteome. The SiESTa database is accessible at http://www.siesta.ethz.ch. CONCLUSION The sequence collections established in the present study provide an important genomic resource for four Silene and one Dianthus species and will help to further develop Silene as a plant model system. The genes characterized will be useful for future research not only in the species included in the present study, but also in related species for which no genomic resources are yet available. Our results demonstrate the efficiency of massively parallel transcriptome sequencing in a comparative framework as an approach for developing genomic resources in diverse groups of non-model organisms.
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Affiliation(s)
- Nicolas Blavet
- Institute of Integrative Biology (IBZ), ETH Zurich, Universitaetstrasse 16, Zürich, 8092, Switzerland
| | - Delphine Charif
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR 5558, Université Lyon 1, Villeurbanne, F-69622 cedex, France
| | - Christine Oger-Desfeux
- DTAMB/PRABI, IFR41, Université Lyon 1, Bâtiment Gregor Mendel, Villeurbanne, F-69622 cedex, France
| | - Gabriel AB Marais
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR 5558, Université Lyon 1, Villeurbanne, F-69622 cedex, France
| | - Alex Widmer
- Institute of Integrative Biology (IBZ), ETH Zurich, Universitaetstrasse 16, Zürich, 8092, Switzerland
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Oyama RK, Silber MV, Renner SS. A specific insertion of a solo-LTR characterizes the Y-chromosome of Bryonia dioica (Cucurbitaceae). BMC Res Notes 2010; 3:166. [PMID: 20546563 PMCID: PMC2898664 DOI: 10.1186/1756-0500-3-166] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 06/14/2010] [Indexed: 11/24/2022] Open
Abstract
Background Relatively few species of flowering plants are dioecious and even fewer are known to have sex chromosomes. Current theory posits that homomorphic sex chromosomes, such as found in Bryonia dioica (Cucurbitaceae), offer insight into the early stages in the evolution of sex chromosomes from autosomes. Little is known about these early steps, but an accumulation of transposable element sequences has been observed on the Y-chromosomes of some species with heteromorphic sex chromosomes. Recombination, by which transposable elements are removed, is suppressed on at least part of the emerging Y-chromosome, and this may explain the correlation between the emergence of sex chromosomes and transposable element enrichment. Findings We sequenced 2321 bp of the Y-chromosome in Bryonia dioica that flank a male-linked marker, BdY1, reported previously. Within this region, which should be suppressed for recombination, we observed a solo-LTR nested in a Copia-like transposable element. We also found other, presumably paralogous, solo-LTRs in a consensus sequence of the underlying Copia-like transposable element. Conclusions Given that solo-LTRs arise via recombination events, it is noteworthy that we find one in a genomic region where recombination should be suppressed. Although the solo-LTR could have arisen before recombination was suppressed, creating the male-linked marker BdY1, our previous study on B. dioica suggested that BdY1 may not lie in the recombination-suppressed region of the Y-chromosome in all populations. Presence of a solo-LTR near BdY1 therefore fits with the observed correlation between retrotransposon accumulation and the suppression of recombination early in the evolution of sex chromosomes. These findings further suggest that the homomorphic sex chromosomes of B. dioica, the first organism for which genetic XY sex-determination was inferred, are evolutionarily young and offer reference information for comparative studies of other plant sex chromosomes.
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Affiliation(s)
- Ryan K Oyama
- Systematic Botany & Mycology, Ludwig-Maximilians-Universität (LMU Munich), 80638 Munich, Germany.
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Gottlieb AM, Poggio L. Genomic screening in dioecious "yerba mate" tree (Ilex paraguariensis A. St. Hill., Aquifoliaceae) through representational difference analysis. Genetica 2010; 138:567-78. [PMID: 20221672 DOI: 10.1007/s10709-010-9449-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Accepted: 09/25/2009] [Indexed: 01/31/2023]
Abstract
The "yerba mate" tree, Ilex paraguariensis, is a functionally dioecious crop species with economic relevance in several South American countries. We report a genomic screening accomplished through representational difference analysis (RDA) in male and female I. paraguariensis trees. The aim of the present paper was to investigate the occurrence of sex-related genomic differences in order to develop an early gender detection molecular method that could help reducing energy inputs during the "yerba mate" processing and that could be suitable for breeding programs. An intra-experiment redundancy was detected via SSCP analysis and sequence characterization. Taking together both reciprocal RDA assays, fragments isolated can be discriminated into three main categories. The first category of fragments shows spurious affinities with available deposited sequences and could be considered as specific to I. paraguariensis. The second category comprises sequences identified as organellar or ribosomal plant DNA. Sequences grouped in the third category involve clones akin to conserved domains of retrotransposons (RNaseH, integrases and/or chromodomains) from at least two distinct lineages of Ty3/Gypsy retrotransposons and one from Ty1/Copia retroelements, which in addition are associated to sex determination regions of the Solanaceae, Caricaceae and Salicaceae. A contig sequence was assembled that codes for an integrase core domain and a chromodomain. The phylogenetic analysis of the so-called IPRE (for I. paraguariensis retroelement) integrase domain indicates that it belongs to the Del lineage of the Chromoviridae. This is the first report of mobile elements isolated and detected from the "yerba mate" tree. Although RDA derived fragments, so far tested, have been retrieved from both sexes with similar sequences, association to sex related regions cannot be completely discarded. Implications of present results are further discussed.
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Affiliation(s)
- Alexandra Marina Gottlieb
- Laboratorio de Citogenética y Evolución (LaCyE), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes y Costanera Norte s/n, 4to. Piso, Pabellón II, Ciudad Universitaria, C1428EHA, Ciudad Autónoma de Buenos Aires, Argentina.
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The role of repetitive DNA in structure and evolution of sex chromosomes in plants. Heredity (Edinb) 2009; 102:533-41. [PMID: 19277056 DOI: 10.1038/hdy.2009.17] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Eukaryotic genomes contain a large proportion of repetitive DNA sequences, mostly transposable elements (TEs) and tandem repeats. These repetitive sequences often colonize specific chromosomal (Y or W chromosomes, B chromosomes) or subchromosomal (telomeres, centromeres) niches. Sex chromosomes, especially non-recombining regions of the Y chromosome, are subject to different evolutionary forces compared with autosomes. In non-recombining regions of the Y chromosome repetitive DNA sequences are accumulated, representing a dominant and early process forming the Y chromosome, probably before genes start to degenerate. Here we review the occurrence and role of repetitive DNA in Y chromosome evolution in various species with a focus on dioecious plants. We also discuss the potential link between recombination and transposition in shaping genomes.
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Cermak T, Kubat Z, Hobza R, Koblizkova A, Widmer A, Macas J, Vyskot B, Kejnovsky E. Survey of repetitive sequences in Silene latifolia with respect to their distribution on sex chromosomes. Chromosome Res 2008; 16:961-76. [DOI: 10.1007/s10577-008-1254-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Revised: 07/10/2008] [Accepted: 07/10/2008] [Indexed: 10/21/2022]
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Marais GAB, Nicolas M, Bergero R, Chambrier P, Kejnovsky E, Monéger F, Hobza R, Widmer A, Charlesworth D. Evidence for degeneration of the Y chromosome in the dioecious plant Silene latifolia. Curr Biol 2008; 18:545-9. [PMID: 18394889 DOI: 10.1016/j.cub.2008.03.023] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Revised: 03/11/2008] [Accepted: 03/11/2008] [Indexed: 11/26/2022]
Abstract
The human Y--probably because of its nonrecombining nature--has lost 97% of its genes since X and Y chromosomes started to diverge [1, 2]. There are clear signs of degeneration in the Drosophila miranda neoY chromosome (an autosome fused to the Y chromosome), with neoY genes showing faster protein evolution [3-6], accumulation of unpreferred codons [6], more insertions of transposable elements [5, 7], and lower levels of expression [8] than neoX genes. In the many other taxa with sex chromosomes, Y degeneration has hardly been studied. In plants, many genes are expressed in pollen [9], and strong pollen selection may oppose the degeneration of plant Y chromosomes [10]. Silene latifolia is a dioecious plant with young heteromorphic sex chromosomes [11, 12]. Here we test whether the S. latifolia Y chromosome is undergoing genetic degeneration by analyzing seven sex-linked genes. S. latifolia Y-linked genes tend to evolve faster at the protein level than their X-linked homologs, and they have lower expression levels. Several Y gene introns have increased in length, with evidence for transposable-element accumulation. We detect signs of degeneration in most of the Y-linked gene sequences analyzed, similar to those of animal Y-linked and neo-Y chromosome genes.
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Affiliation(s)
- Gabriel A B Marais
- Université de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne Cedex, France.
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Jamilena M, Mariotti B, Manzano S. Plant sex chromosomes: molecular structure and function. Cytogenet Genome Res 2008; 120:255-64. [PMID: 18504355 DOI: 10.1159/000121075] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2007] [Indexed: 11/19/2022] Open
Abstract
Recent molecular and genomic studies carried out in a number of model dioecious plant species, including Asparagus officinalis, Carica papaya, Silene latifolia, Rumex acetosa and Marchantia polymorpha, have shed light on the molecular structure of both homomorphic and heteromorphic sex chromosomes, and also on the gene functions they have maintained since their evolution from a pair of autosomes. The molecular structure of sex chromosomes in species from different plant families represents the evolutionary pathway followed by sex chromosomes during their evolution. The degree of Y chromosome degeneration that accompanies the suppression of recombination between the Xs and Ys differs among species. The primitive Ys of A. officinalis and C. papaya have only diverged from their homomorphic Xs in a short male-specific and non-recombining region (MSY), while the heteromorphic Ys of S. latifolia, R. acetosa and M. polymorpha have diverged from their respective Xs. As in the Y chromosomes of mammals and Drosophila, the accumulation of repetitive DNA, including both transposable elements and satellite DNA, has played an important role in the divergence and size enlargement of plant Ys, and consequently in reducing gene density. Nevertheless, the degeneration process in plants does not appear to have reached the Y-linked genes. Although a low gene density has been found in the sequenced Y chromosome of M. polymorpha, most of its genes are essential and are expressed in the vegetative and reproductive organs in both male and females. Similarly, most of the Y-linked genes that have been isolated and characterized up to now in S. latifolia are housekeeping genes that have X-linked homologues, and are therefore expressed in both males and females. Only one of them seems to be degenerate with respect to its homologous region in the X. Sequence analysis of larger regions in the homomorphic X and Y chromosomes of papaya and asparagus, and also in the heteromorphic sex chromosomes of S. latifolia and R. acetosa, will reveal the degenerative changes that the Y-linked gene functions have experienced during sex chromosome evolution.
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Affiliation(s)
- M Jamilena
- Departamento de Biología Aplicada, Area de Genética, Escuela Politécnica Superior, Universidad de Almería, Almería, Spain.
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Kazama Y, Matsunaga S. The use of repetitive DNA in cytogenetic studies of plant sex chromosomes. Cytogenet Genome Res 2008; 120:247-54. [DOI: 10.1159/000121074] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2007] [Indexed: 11/19/2022] Open
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Mariotti B, Navajas-Pérez R, Lozano R, Parker JS, de la Herrán R, Rejón CR, Rejón MR, Garrido-Ramos M, Jamilena M. Cloning and characterization of dispersed repetitive DNA derived from microdissected sex chromosomes of Rumex acetosa. Genome 2006; 49:114-21. [PMID: 16498461 DOI: 10.1139/g05-089] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Rumex acetosa is characterized by a multiple chromosome system (2n = 12 + XX for females, and 2n = 12 + XY1Y2 for males), in which sex is determined by the ratio between the number of X chromosomes and autosome sets. For a better understanding of the molecular structure and evolution of plant sex chromosomes, we have generated a sex chromosome specific library of R. acetosa by microdissection. The screening of this library has allowed us to identify 5 repetitive DNA families that have been characterized in detail. One of these families, DOP-20, has shown no homology with other sequences in databases. Nevertheless, the putative proteins encoded by the other 4 families, DOP-8, DOP-47, DOP-60, and DOP-61, show homology with proteins from different plant retroelements, including poly proteins from Ty3-gypsy- and Ty1-copia-like long terminal repeat (LTR) retroelements, and reverse transcriptase from non-LTR retro elements. Results indicate that sequences from these 5 families are dispersed throughout the genome of both males and females, but no appreciable accumulation or differentiation of these types of sequences have been found in the Y chromosomes. These repetitive DNA sequences are more conserved in the genome of other dioecious species such as Rumex papillaris, Rumex intermedius, Rumex thyrsoides, Rumex hastatulus, and Rumex suffruticosus, than in the polygamous, gynodioecious, or hermaphrodite species Rumex induratus, Rumex lunaria, Rumex con glom er atus, Rumex crispus, and Rumex bucephalo phorus, which supports a single origin of dioecious species in this genus. The implication of these transposable elements in the origin and evolution of the heteromorphic sex chromosomes of R. acetosa is discussed.
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Affiliation(s)
- Beatrice Mariotti
- Departamento de Biología Aplicada, Escuela Politécnica Superior, Universidad de Almería, 04120 Almería, Spain
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Kejnovsky E, Kubat Z, Macas J, Hobza R, Mracek J, Vyskot B. Retand: a novel family of gypsy-like retrotransposons harboring an amplified tandem repeat. Mol Genet Genomics 2006; 276:254-63. [PMID: 16826419 DOI: 10.1007/s00438-006-0140-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2005] [Accepted: 06/02/2006] [Indexed: 12/13/2022]
Abstract
In this paper we describe a pair of novel Ty3/gypsy retrotransposons isolated from the dioecious plant Silene latifolia, consisting of a non-autonomous element Retand-1 (3.7 kb) and its autonomous partner Retand-2 (11.1 kb). These two elements have highly similar long terminal repeat (LTR) sequences but differ in the presence of the typical retroelement coding regions (gag-pol genes), most of which are missing in Retand-1. Moreover, Retand-2 contains two additional open reading frames in antisense orientation localized between the pol gene and right LTR. Retand transcripts were detected in all organs tested (leaves, flower buds and roots) which, together with the high sequence similarity of LTRs in individual elements, indicates their recent transpositional activity. The autonomous elements are similarly abundant (2,700 copies) as non-autonomous ones (2,100 copies) in S. latifolia genome. Retand elements are also present in other Silene species, mostly in subtelomeric heterochromatin regions of all chromosomes. The only exception is the subtelomere of the short arm of the Y chromosome in S. latifolia which is known to lack the terminal heterochromatin. An interesting feature of the Retand elements is the presence of a tandem repeat sequence, which is more amplified in the non-autonomous Retand-1.
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Affiliation(s)
- Eduard Kejnovsky
- Laboratory of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic.
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Natali L, Santini S, Giordani T, Minelli S, Maestrini P, Cionini PG, Cavallini A. Distribution of Ty3-gypsy- and Ty1-copia-like DNA sequences in the genus Helianthus and other Asteraceae. Genome 2006; 49:64-72. [PMID: 16462902 DOI: 10.1139/g05-058] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Two repeated DNA sequences, pHaS13 and pHaS211, which revealed similarity to the int gene of Ty3-gypsy retrotransposons and the RNAse-H gene of Ty1-copia retroelements, respectively, were surveyed in Asteraceae species and within the genus Helianthus. Southern analysis of the genome of selected Asteraceae that belong to different tribes showed that pHaS13- and pHaS211-related subfamilies of gypsy- and copia-like retroelements are highly redundant only in Helianthus and, to a lesser extent, in Tithonia, a Helianthus strict relative. However, under low stringency posthybridization washes, bands were observed in almost all the other Asteraceae tested when pHaS13 was used as a probe, and in several species when pHaS211 was hybridized. FISH analysis of pHaS13 or pHaS211 probes was performed in species in which labelling was observed in Southern hybridizations carried out under high stringency conditions (Helianthus annuus, Tithonia rotundifolia, Ageratum spp., Leontopodium spp., Senecio vulgaris for pHaS13, and H. annuus, Tithonia rotundifolia, and S. vulgaris for pHaS211). Scattered labelling was observed over all metaphase chromosomes, indicating a large dispersal of both Ty3-gypsy- and Ty1-copia-like retroelements. However, preferential localization of Ty3-gypsy-like sequences at centromeric chromosome regions was observed in all of the species studies but one, even in species in which pHaS13-related elements are poorly represented. Ty1-copia -like sequences showed preferential localization at the chromosome ends only in H. annuus. To study the evolution of gypsy- and copia-like retrotransposons in Helianthus, cladograms were built based on the Southern blot hybridization patterns of pHaS13 or pHaS211 sequences to DNA digests of several species of this genus. Both cladograms agree in splitting the genomes studied into annuals and perennials. Differences that occurred within the clades of perennial and annual species between gypsy- and copia-like retroelements indicated that these retrotransposons were differentially active during Helianthus speciation, suggesting that the evolution of the 2 retroelement families was, within limits, independent.Key words: Asteraceae, FISH, genome evolution, Helianthus, retrotransposons, Ty1-copia, Ty3-gypsy.
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Affiliation(s)
- L Natali
- Dipartimento de Biologia della Piante Agrarie, Sezione de Genetica, Pisa, Italy
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18
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Scotti I, Delph LF. SELECTIVE TRADE-OFFS AND SEX-CHROMOSOME EVOLUTION IN SILENE LATIFOLIA. Evolution 2006. [DOI: 10.1554/05-698.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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19
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Khadka DK, Nejidat A, Tal M, Golan-Goldhirsh A. Molecular characterization of a gender-linked DNA marker and a related gene in Mercurialis annua L. PLANTA 2005; 222:1063-70. [PMID: 16049676 DOI: 10.1007/s00425-005-0046-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2004] [Accepted: 04/15/2005] [Indexed: 05/03/2023]
Abstract
The dioecious Mercurialis annua L. was used as a model plant to study some aspects of the molecular basis of sex determination in plants. We report in this paper the characterization of a previously identified male specific DNA marker, OPB01-1562, from diploid dioecious M. annua. The marker co-segregated with male sex in the progeny of hormonally feminized males. Sequence analysis showed the presence of approximately 0.6 kb retrotransposon-like sequence at its 3' end. Homologous sequences were isolated from diploid female, hexaploid male and monoecious plants. These sequences contained RNaseH and integrase domains of reverse transcriptase and were most similar to pineapple retrotransposon dea1, hence were named M. annua retrotransposon-like sequences (MARL-1 to MARL-5). A 771 bp fragment isolated from a diploid female, named fem771, was homologous to the 5' end of OPB01-1562. Results from DNA blot hybridization suggested OPB01-1562 and fem771 to be from the same locus and MARL-1 from a different one. RNA blot hybridization with OPB01-1562 and MARL-1 detected an approximately 2.8 kb transcript which was expressed strongly in stems and flowers of females but not males. This transcript was named M. annua female expressed (Mafex). Sex linkage of OPB01-1562 and expression of Mafex detected by OPB01-1562 strongly suggested Mafex to be a candidate gene involved in sex determination in M. annua.
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Affiliation(s)
- Deepak Kumar Khadka
- Albert Katz Department of Dryland Biotechnologies Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, 84990 Israel
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20
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Sakamoto K, Abe T, Matsuyama T, Yoshida S, Ohmido N, Fukui K, Satoh S. RAPD markers encoding retrotransposable elements are linked to the male sex in Cannabis sativa L. Genome 2005; 48:931-6. [PMID: 16391699 DOI: 10.1139/g05-056] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Male-associated DNA sequences were analyzed in Cannabis sativa L. (hemp), a dioecious plant with heteromorphic sex chromosomes. DNA was isolated from male and female plants and subjected to random amplified polymorphic DNA analysis. Of 120 primers, 17 yielded 400 to 1500-bp fragments detectable in male, but not female, plants. These fragments were cloned and used as probes in gel-blot analysis of genomic DNA. When male and female DNA was hybridized with 2 of these male-specific fragments, MADC(male-associated DNA sequences in C. sativa)3 and MADC4, particularly intense bands specific to male plants were detected in addition to bands common to both sexes. The MADC3 and MADC4 sequences were shown to encode gag/pol polyproteins of copia-like retrotransposons. Fluorescence in situ hybridization with MADC3 and MADC4 as probes revealed a number of intense signals on the Y chromosome as well as dispersed signals on all chromosomes. The gel-blot analysis and fluorescence in situ hybridization results presented here support the hypothesis that accumulation of retrotransposable elements on the Y chromosome might be 1 cause of heteromorphism of sex chromosomes.Key words: Cannabis sativa, FISH, RAPD, retrotransposon, sex chromosome.
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Affiliation(s)
- Koichi Sakamoto
- Plant Function Laboratory, The Institute of Physical and Chemical Research, Saitama, Japan.
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21
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Meagher TR, Vassiliadis C. Phenotypic impacts of repetitive DNA in flowering plants. THE NEW PHYTOLOGIST 2005; 168:71-80. [PMID: 16159322 DOI: 10.1111/j.1469-8137.2005.01527.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The discovery that nuclear DNA content varies widely among species, and even within species, was unexpected because it was thought that the number of genes required for an organism should be common across taxa. We now know that the bulk of nuclear DNA content variation is caused by repetitive DNA sequences characterized according to the nature of repeat (tandem vs dispersed) or chromosomal location/mechanism of replication (pericentromeric, telomeric or subtelomeric, microsatellites, minisatellites, satellites, transposable elements, retroelements). Variation in repetitive DNA, manifested as variation in nuclear DNA content, has been shown to have broad ecological and life-history consequences. For example, large genome size appears to limit fitness in extreme environmental conditions. Within species, variation in DNA content has been coupled to growth and development, such as maturation time in crop species. In Silene latifolia, DNA content is negatively correlated with flower size, a character that, in turn, has well documented ecological significance. These intraspecific studies suggest a connection between repetitive DNA and quantitative genetic determination of continuous characters. Novel insights into mechanisms by which repetitive DNA influences phenotype will lead to models of evolutionary change that extend well beyond the conventional view of evolution by allelic substitution.
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Affiliation(s)
- Thomas R Meagher
- Centre for Evolution, Genes & Genomics, School of Biology, Sir Harold Mitchell Building, University of St Andrews, St Andrews, Fife KY16 9TH, UK.
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Meagher TR, Costich DE. 'Junk' DNA and long-term phenotypic evolution in Silene section Elisanthe (Caryophyllaceae). Proc Biol Sci 2005; 271 Suppl 6:S493-7. [PMID: 15801614 PMCID: PMC1810120 DOI: 10.1098/rsbl.2004.0211] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Nuclear DNA content variation over orders of magnitude across species has been attributed to 'junk' repetitive DNA with limited adaptive significance. By contrast, our previous work on Silene latifolia showed that DNA content is negatively correlated with flower size, a character of clear adaptive relevance. The present paper explores this relationship in a broader phylogenetic context to investigate the long-term evolutionary impacts of DNA content variation. The relationship between nuclear DNA content and phenotype variation was determined for four closely related species of Silene section Elisanthe (Caryophyllaceae). In addition to a consistent sexual dimorphism in DNA content across all of the species, we found DNA content variation among populations within, as well as among, species. We also found a general trend towards a negative correlation between DNA content and flower and leaf size over all four species, within males and females as well as overall. These results indicate that repetitive DNA may play a role in long-term phenotypic evolution.
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Matsunaga S, Lebel-Hardenack S, Kejnovsky E, Vyskot B, Grant SR, Kawano S. An anther- and petal-specific gene SlMF1 is a multicopy gene with homologous sequences on sex chromosomes. Genes Genet Syst 2005; 80:395-401. [PMID: 16501308 DOI: 10.1266/ggs.80.395] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A male flower-specific gene SlMF1 was isolated from male flower buds of the dioecious plant Silene latifolia. SlMF1 is expressed in all the floral meristems at the very early stage of development in both male and female flower buds. At the mature stage of development in male flower buds, SlMF1 transcripts were specifically accumulated in pollen mother cells, tapetal cells, and the developing tips of petals. Genomic Southern hybridization revealed that SlMF1 was a multicopy gene with a Y chromosome-linked homologous sequence. PCR analyses with flow-sorted chromosomes showed that SlMF1 was localized on both autosomes and the X chromosome.
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Affiliation(s)
- Sachihiro Matsunaga
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Yamadaoka, Suita, Japan.
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Characterization of two SEPALLATA MADS-box genes from the dioecious plant Silene latifolia. ACTA ACUST UNITED AC 2004. [DOI: 10.1007/s00497-004-0230-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Matsunaga S, Uchida W, Kawano S. Sex-Specific Cell Division during Development of Unisexual Flowers in the Dioecious Plant Silene latifolia. ACTA ACUST UNITED AC 2004; 45:795-802. [PMID: 15215515 DOI: 10.1093/pcp/pch081] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
We analyzed cell division patterns during the differentiation of unisexual flowers of the dioecious plant Silene latifolia using in situ hybridization with histone H4 and cyclin A1 genes. The gene expression patterns indicated that the activation of cell divisions in whorls 3 and 4 was reversed in young male and female flower buds. During maturation of flower buds, a remarkable reduction in cell division activity occurred in the male gynoecium primordium and female stamen primordia. Our analyses showed that differential activation and reduction of cell division strongly correlated with sex-specific promotion and cessation in the sex differentiation of unisexual flowers.
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Affiliation(s)
- Sachihiro Matsunaga
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba, 277-8562 Japan.
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26
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Lengerova M, Kejnovsky E, Hobza R, Macas J, Grant SR, Vyskot B. Multicolor FISH mapping of the dioecious model plant, Silene latifolia. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 108:1193-9. [PMID: 14727034 DOI: 10.1007/s00122-003-1568-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2003] [Accepted: 12/04/2003] [Indexed: 05/18/2023]
Abstract
Silene latifolia is a key plant model in the study of sex determination and sex chromosome evolution. Current studies have been based on genetic mapping of the sequences linked to sex chromosomes with analysis of their characters and relative positions on the X and Y chromosomes. Until recently, very few DNA sequences have been physically mapped to the sex chromosomes of S. latifolia. We have carried out multicolor fluorescent in situ hybridization (FISH) analysis of S. latifolia chromosomes based on the presence and intensity of FISH signals on individual chromosomes. We have generated new markers by constructing and screening a sample bacterial artificial chromosome (BAC) library for appropriate FISH probes. Five newly isolated BAC clones yielded discrete signals on the chromosomes: two were specific for one autosome pair and three hybridized preferentially to the sex chromosomes. We present the FISH hybridization patterns of these five BAC inserts together with previously described repetitive sequences (X-43.1, 25S rDNA and 5S rDNA) and use them to analyze the S. latifolia karyotype. The autosomes of S. latifolia are difficult to distinguish based on their relative arm lengths. Using one BAC insert and the three repetitive sequences, we have constructed a standard FISH karyotype that can be used to distinguish all autosome pairs. We also analyze the hybridization patterns of these sequences on the sex chromosomes and discuss the utility of the karyotype mapping strategy presented to study sex chromosome evolution and Y chromosome degeneration.
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Affiliation(s)
- M Lengerova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
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27
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Obara M, Matsunaga S, Nakao S, Kawano S. A plant Y chromosome-STS marker encoding a degenerate retrotransposon. Genes Genet Syst 2002; 77:393-8. [PMID: 12589074 DOI: 10.1266/ggs.77.393] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The dioecious plant Silene latifolia has both X and Y sex chromosomes. Male-specific random amplified polymorphic DNA (RAPD) fragments were analyzed to identify Y-chromosome-linked sequences. One of the RAPD fragments, MS4, was converted into a more reliable and reproducible sequence-tagged site (STS) marker. A set of MS4 STS primers was used to amplify two genomic DNA fragments (MS4a and MS4b) from a male plant and one (MS4a) from a female plant, which indicates that MS4b is located on the Y chromosome. Sequence analysis revealed that MS4a encoded a gag protein of a Ty3-gypsy-like retrotransposon. A 147-bp region from the middle of MS4a was deleted in MS4b. The MS4b sequence was not detected in the most closely related dioecious species, S. dioica. This suggests that a retrotransposon with the MS4b sequence has degenerated recently on the Y chromosome.
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Affiliation(s)
- Mari Obara
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
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