1
|
Liu C, Fu S, Yi C, Liu Y, Huang Y, Guo X, Zhang K, Liu Q, Birchler JA, Han F. Unveiling the distinctive traits of functional rye centromeres: minisatellites, retrotransposons, and R-loop formation. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2524-0. [PMID: 38805064 DOI: 10.1007/s11427-023-2524-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 05/29/2024]
Abstract
Centromeres play a vital role in cellular division by facilitating kinetochore assembly and spindle attachments. Despite their conserved functionality, centromeric DNA sequences exhibit rapid evolution, presenting diverse sizes and compositions across species. The functional significance of rye centromeric DNA sequences, particularly in centromere identity, remains unclear. In this study, we comprehensively characterized the sequence composition and organization of rye centromeres. Our findings revealed that these centromeres are primarily composed of long terminal repeat retrotransposons (LTR-RTs) and interspersed minisatellites. We systematically classified LTR-RTs into five categories, highlighting the prevalence of younger CRS1, CRS2, and CRS3 of CRSs (centromeric retrotransposons of Secale cereale) were primarily located in the core centromeres and exhibited a higher association with CENH3 nucleosomes. The minisatellites, mainly derived from retrotransposons, along with CRSs, played a pivotal role in establishing functional centromeres in rye. Additionally, we observed the formation of R-loops at specific regions of CRS1, CRS2, and CRS3, with both rye pericentromeres and centromeres exhibiting enrichment in R-loops. Notably, these R-loops selectively formed at binding regions of the CENH3 nucleosome in rye centromeres, suggesting a potential role in mediating the precise loading of CENH3 to centromeres and contributing to centromere specification. Our work provides insights into the DNA sequence composition, distribution, and potential function of R-loops in rye centromeres. This knowledge contributes valuable information to understanding the genetics and epigenetics of rye centromeres, offering implications for the development of synthetic centromeres in future plant modifications and beyond.
Collapse
Affiliation(s)
- Chang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shulan Fu
- Key Laboratory for Plant Genetics and Breeding, Sichuan Agricultural University, Chengdu, 611130, China
| | - Congyang Yi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuhong Huang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianrui Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kaibiao Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qian Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - James A Birchler
- Division of Biological Science, University of Missouri, Columbia, 65211-7400, USA
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
2
|
Borgognone A, Castanera R, Morselli M, López-Varas L, Rubbi L, Pisabarro AG, Pellegrini M, Ramírez L. Transposon-associated epigenetic silencing during Pleurotus ostreatus life cycle. DNA Res 2019; 25:451-464. [PMID: 29893819 PMCID: PMC6191308 DOI: 10.1093/dnares/dsy016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 05/15/2018] [Indexed: 12/14/2022] Open
Abstract
Transposable elements constitute an important fraction of eukaryotic genomes. Given their mutagenic potential, host-genomes have evolved epigenetic defense mechanisms to limit their expansion. In fungi, epigenetic modifications have been widely studied in ascomycetes, although we lack a global picture of the epigenetic landscape in basidiomycetes. In this study, we analysed the genome-wide epigenetic and transcriptional patterns of the white-rot basidiomycete Pleurotus ostreatus throughout its life cycle. Our results performed by using high-throughput sequencing analyses revealed that strain-specific DNA methylation profiles are primarily involved in the repression of transposon activity and suggest that 21 nt small RNAs play a key role in transposon silencing. Furthermore, we provide evidence that transposon-associated DNA methylation, but not sRNA production, is directly involved in the silencing of genes surrounded by transposons. Remarkably, we found that nucleus-specific methylation levels varied in dikaryotic strains sharing identical genetic complement but different subculture conditions. Finally, we identified key genes activated in the fruiting process through the comparative analysis of transcriptomes. This study provides an integrated picture of epigenetic defense mechanisms leading to the transcriptional silencing of transposons and surrounding genes in basidiomycetes. Moreover, our findings suggest that transcriptional but not methylation reprogramming triggers fruitbody development in P. ostreatus.
Collapse
Affiliation(s)
- Alessandra Borgognone
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Navarre, Spain
| | - Raúl Castanera
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Navarre, Spain
| | - Marco Morselli
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, USA.,Institute for Genomics and Proteomics, UCLA-U.S. Department of Energy (DOE), University of California, Los Angeles, USA
| | - Leticia López-Varas
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Navarre, Spain
| | - Liudmilla Rubbi
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, USA
| | - Antonio G Pisabarro
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Navarre, Spain
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, USA.,Institute for Genomics and Proteomics, UCLA-U.S. Department of Energy (DOE), University of California, Los Angeles, USA
| | - Lucía Ramírez
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, Pamplona, Navarre, Spain
| |
Collapse
|
3
|
Neumann P, Novák P, Hoštáková N, Macas J. Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification. Mob DNA 2019; 10:1. [PMID: 30622655 PMCID: PMC6317226 DOI: 10.1186/s13100-018-0144-1] [Citation(s) in RCA: 187] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/20/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Plant LTR-retrotransposons are classified into two superfamilies, Ty1/copia and Ty3/gypsy. They are further divided into an enormous number of families which are, due to the high diversity of their nucleotide sequences, usually specific to a single or a group of closely related species. Previous attempts to group these families into broader categories reflecting their phylogenetic relationships were limited either to analyzing a narrow range of plant species or to analyzing a small numbers of elements. Furthermore, there is no reference database that allows for similarity based classification of LTR-retrotransposons. RESULTS We have assembled a database of retrotransposon encoded polyprotein domains sequences extracted from 5410 Ty1/copia elements and 8453 Ty3/gypsy elements sampled from 80 species representing major groups of green plants (Viridiplantae). Phylogenetic analysis of the three most conserved polyprotein domains (RT, RH and INT) led to dividing Ty1/copia and Ty3/gypsy retrotransposons into 16 and 14 lineages respectively. We also characterized various features of LTR-retrotransposon sequences including additional polyprotein domains, extra open reading frames and primer binding sites, and found that the occurrence and/or type of these features correlates with phylogenies inferred from the three protein domains. CONCLUSIONS We have established an improved classification system applicable to LTR-retrotransposons from a wide range of plant species. This system reflects phylogenetic relationships as well as distinct sequence and structural features of the elements. A comprehensive database of retrotransposon protein domains (REXdb) that reflects this classification provides a reference for efficient and unified annotation of LTR-retrotransposons in plant genomes. Access to REXdb related tools is implemented in the RepeatExplorer web server (https://repeatexplorer-elixir.cerit-sc.cz/) or using a standalone version of REXdb that can be downloaded seaparately from RepeatExplorer web page (http://repeatexplorer.org/).
Collapse
Affiliation(s)
- Pavel Neumann
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, 37005 České Budějovice, Czech Republic
| | - Petr Novák
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, 37005 České Budějovice, Czech Republic
| | - Nina Hoštáková
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, 37005 České Budějovice, Czech Republic
| | - Jiří Macas
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, 37005 České Budějovice, Czech Republic
| |
Collapse
|
4
|
Carpentier MC, Manfroi E, Wei FJ, Wu HP, Lasserre E, Llauro C, Debladis E, Akakpo R, Hsing YI, Panaud O. Retrotranspositional landscape of Asian rice revealed by 3000 genomes. Nat Commun 2019; 10:24. [PMID: 30604755 PMCID: PMC6318337 DOI: 10.1038/s41467-018-07974-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 12/05/2018] [Indexed: 12/21/2022] Open
Abstract
The recent release of genomic sequences for 3000 rice varieties provides access to the genetic diversity at species level for this crop. We take advantage of this resource to unravel some features of the retrotranspositional landscape of rice. We develop software TRACKPOSON specifically for the detection of transposable elements insertion polymorphisms (TIPs) from large datasets. We apply this tool to 32 families of retrotransposons and identify more than 50,000 TIPs in the 3000 rice genomes. Most polymorphisms are found at very low frequency, suggesting that they may have occurred recently in agro. A genome-wide association study shows that these activations in rice may be triggered by external stimuli, rather than by the alteration of genetic factors involved in transposable element silencing pathways. Finally, the TIPs dataset is used to trace the origin of rice domestication. Our results suggest that rice originated from three distinct domestication events.
Collapse
Affiliation(s)
- Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Ernandes Manfroi
- Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 90040-060, Brazil
| | - Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, 115, Taipei, Taiwan
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, 305-8687, Ibaraki, Japan
| | - Hshin-Ping Wu
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, 115, Taipei, Taiwan
| | - Eric Lasserre
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Christel Llauro
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Emilie Debladis
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Roland Akakpo
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, 115, Taipei, Taiwan
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France.
- Institut Universitaire de France, 1 rue Descartes, 75231, Paris Cedex 05, France.
| |
Collapse
|
5
|
Ji JL, Yang LM, Fang ZY, Zhuang M, Zhang YY, Lv HH, Liu YM, Li ZS. Recessive male sterility in cabbage (Brassica oleracea var. capitata) caused by loss of function of BoCYP704B1 due to the insertion of a LTR-retrotransposon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1441-1451. [PMID: 28405714 DOI: 10.1007/s00122-017-2899-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 03/27/2017] [Indexed: 06/07/2023]
Abstract
The LTR-retrotransposon insertion in BoCYP704B1 is proved to be the primary cause of the male sterility in cabbage. Effective allele-specific markers were developed for marker-assisted selection of male sterile gene. 83121A is a spontaneous male sterile mutant identified from cabbage. Genetic analysis indicated that male sterility is controlled by a single recessive gene. Pollen wall formation in the 83121A mutant was severely defective, with a lack of sporopollenin or exine. To understand the mechanisms of male sterility in 83121A, transcription analysis using RNA-Seq was carried out in the buds of the male sterile line 83121A and the male fertile line 83121B, which are near-isogenic lines differing only in the fertility trait. Via expression analysis of differentially expressed genes involved in pollen exine development before the bicellular pollen stage, BoCYP704B1 was identified as a candidate gene, which was approximately downregulated 30-fold in 83121A. BoCYP704B1 is a member of the evolutionarily conserved CYP704B family, which is essential for sporopollenin formation. The BoCYP704B1 transcript is specifically detected in the developing anthers of wild-type cabbage. Further sequence analysis revealed that a 5424-bp long terminal repeat-retrotransposon (LTR-RT) was inserted into the first exon of BoCYP704B1 in 83121A, which is not found in wild-type plants. The insertion of LTR-RT not only reduced the expression of BoCYP704B1 but also altered structure of protein encoded by BoCYP704B1. Moreover, linkage analysis showed that the homozygotic mutational BoCYP704B1 always cosegregated with male sterility. These data suggest that the LTR-RT insertion in BoCYP704B1 hinders sporopollenin formation in 83121A leading to male sterility. The allele-specific markers developed in this study were effective for marker-assisted selection of the male sterile gene.
Collapse
Affiliation(s)
- Jia-Lei Ji
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Li-Mei Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
| | - Zhi-Yuan Fang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Mu Zhuang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Yang-Yong Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Hong-Hao Lv
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Yu-Mei Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Zhan-Sheng Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| |
Collapse
|
6
|
Payen T, Murat C, Martin F. Reconstructing the evolutionary history of gypsy retrotransposons in the Périgord black truffle (Tuber melanosporum Vittad.). MYCORRHIZA 2016; 26:553-563. [PMID: 27025914 DOI: 10.1007/s00572-016-0692-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 03/21/2016] [Indexed: 06/05/2023]
Abstract
Truffles are ascomycete fungi belonging to genus Tuber, and they form ectomycorrhizal associations with trees and shrubs. Transposable elements constitute more than 50 % of the black Périgord truffle (Tuber melanosporum) genome, which are mainly class 1 gypsy retrotransposons, but their impact on its genome is unknown. The aims of this study are to investigate the diversity of gypsy retrotransposons in this species and their evolutionary history by analysing the reference genome and six resequenced genomes of different geographic accessions. Using the reverse transcriptase sequences, six different gypsy retrotransposon clades were identified. Tmt1 and Tmt6 are the most abundant transposable elements, representing 14 and 13 % of the T. melanosporum genome, respectively. Tmt6 showed a major burst of proliferation between 1 and 4 million years ago, but evidence of more recent transposition was observed. Except for Tmt2, the other clades tend to aggregate, and their mode of transposition excluded the master copy model. This suggests that each new copy has the same probability of transposing as other copies. This study provides a better view of the diversity and dynamic nature of gypsy retrotransposons in T. melanosporum. Even if the major gypsy retrotransposon bursts are old, some elements seem to have transposed recently, suggesting that they may continue to model the truffle genomes.
Collapse
Affiliation(s)
- Thibaut Payen
- UMR1136, "Interactions Arbres/Micro-organismes", INRA, Université de Lorraine, Laboratoire d'Excellence ARBRE, F-54280, Champenoux, France
| | - Claude Murat
- UMR1136, "Interactions Arbres/Micro-organismes", INRA, Université de Lorraine, Laboratoire d'Excellence ARBRE, F-54280, Champenoux, France.
| | - Francis Martin
- UMR1136, "Interactions Arbres/Micro-organismes", INRA, Université de Lorraine, Laboratoire d'Excellence ARBRE, F-54280, Champenoux, France
| |
Collapse
|
7
|
Wegrzyn JL, Liechty JD, Stevens KA, Wu LS, Loopstra CA, Vasquez-Gross HA, Dougherty WM, Lin BY, Zieve JJ, Martínez-García PJ, Holt C, Yandell M, Zimin AV, Yorke JA, Crepeau MW, Puiu D, Salzberg SL, de Jong PJ, Mockaitis K, Main D, Langley CH, Neale DB. Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics 2014; 196:891-909. [PMID: 24653211 PMCID: PMC3948814 DOI: 10.1534/genetics.113.159996] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 12/13/2013] [Indexed: 01/08/2023] Open
Abstract
The largest genus in the conifer family Pinaceae is Pinus, with over 100 species. The size and complexity of their genomes (∼20-40 Gb, 2n = 24) have delayed the arrival of a well-annotated reference sequence. In this study, we present the annotation of the first whole-genome shotgun assembly of loblolly pine (Pinus taeda L.), which comprises 20.1 Gb of sequence. The MAKER-P annotation pipeline combined evidence-based alignments and ab initio predictions to generate 50,172 gene models, of which 15,653 are classified as high confidence. Clustering these gene models with 13 other plant species resulted in 20,646 gene families, of which 1554 are predicted to be unique to conifers. Among the conifer gene families, 159 are composed exclusively of loblolly pine members. The gene models for loblolly pine have the highest median and mean intron lengths of 24 fully sequenced plant genomes. Conifer genomes are full of repetitive DNA, with the most significant contributions from long-terminal-repeat retrotransposons. In depth analysis of the tandem and interspersed repetitive content yielded a combined estimate of 82%.
Collapse
Affiliation(s)
- Jill L. Wegrzyn
- Department of Plant Sciences, University of California, Davis, California 95616
| | - John D. Liechty
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Kristian A. Stevens
- Department of Evolution and Ecology, University of California, Davis, California 95616
| | - Le-Shin Wu
- National Center for Genome Analysis Support, Indiana University, Bloomington, Indiana 47405
| | - Carol A. Loopstra
- Department of Ecosystem Science and Management, Texas A&M University, College Station, Texas 77843
| | | | - William M. Dougherty
- Department of Evolution and Ecology, University of California, Davis, California 95616
| | - Brian Y. Lin
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Jacob J. Zieve
- Department of Plant Sciences, University of California, Davis, California 95616
| | | | - Carson Holt
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112
| | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112
| | - Aleksey V. Zimin
- Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742
| | - James A. Yorke
- Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742
- Departments of Mathematics and Physics, University of Maryland, College Park, Maryland 20742
| | - Marc W. Crepeau
- Department of Evolution and Ecology, University of California, Davis, California 95616
| | - Daniela Puiu
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University, Baltimore, Maryland 21205
| | - Steven L. Salzberg
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University, Baltimore, Maryland 21205
| | - Pieter J. de Jong
- Children’s Hospital Oakland Research Institute, Oakland, California 94609
| | | | - Doreen Main
- Department of Horticulture, Washington State University, Pullman, Washington 99163
| | - Charles H. Langley
- Department of Evolution and Ecology, University of California, Davis, California 95616
| | - David B. Neale
- Department of Plant Sciences, University of California, Davis, California 95616
| |
Collapse
|
8
|
Gao D, Abernathy B, Rohksar D, Schmutz J, Jackson SA. Annotation and sequence diversity of transposable elements in common bean (Phaseolus vulgaris). FRONTIERS IN PLANT SCIENCE 2014; 5:339. [PMID: 25071814 PMCID: PMC4093653 DOI: 10.3389/fpls.2014.00339] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 06/25/2014] [Indexed: 05/21/2023]
Abstract
Common bean (Phaseolus vulgaris) is an important legume crop grown and consumed worldwide. With the availability of the common bean genome sequence, the next challenge is to annotate the genome and characterize functional DNA elements. Transposable elements (TEs) are the most abundant component of plant genomes and can dramatically affect genome evolution and genetic variation. Thus, it is pivotal to identify TEs in the common bean genome. In this study, we performed a genome-wide transposon annotation in common bean using a combination of homology and sequence structure-based methods. We developed a 2.12-Mb transposon database which includes 791 representative transposon sequences and is available upon request or from www.phytozome.org. Of note, nearly all transposons in the database are previously unrecognized TEs. More than 5,000 transposon-related expressed sequence tags (ESTs) were detected which indicates that some transposons may be transcriptionally active. Two Ty1-copia retrotransposon families were found to encode the envelope-like protein which has rarely been identified in plant genomes. Also, we identified an extra open reading frame (ORF) termed ORF2 from 15 Ty3-gypsy families that was located between the ORF encoding the retrotransposase and the 3'LTR. The ORF2 was in opposite transcriptional orientation to retrotransposase. Sequence homology searches and phylogenetic analysis suggested that the ORF2 may have an ancient origin, but its function is not clear. These transposon data provide a useful resource for understanding the genome organization and evolution and may be used to identify active TEs for developing transposon-tagging system in common bean and other related genomes.
Collapse
Affiliation(s)
- Dongying Gao
- Center for Applied Genetic Technologies, University of GeorgiaAthens, GA, USA
| | - Brian Abernathy
- Center for Applied Genetic Technologies, University of GeorgiaAthens, GA, USA
| | - Daniel Rohksar
- US Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
| | - Jeremy Schmutz
- US Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
- HudsonAlpha Institute of BiotechnologyHuntsville, AL, USA
| | - Scott A. Jackson
- Center for Applied Genetic Technologies, University of GeorgiaAthens, GA, USA
- *Correspondence: Scott A. Jackson, Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA e-mail:
| |
Collapse
|
9
|
Wegrzyn JL, Lin BY, Zieve JJ, Dougherty WM, Martínez-García PJ, Koriabine M, Holtz-Morris A, deJong P, Crepeau M, Langley CH, Puiu D, Salzberg SL, Neale DB, Stevens KA. Insights into the loblolly pine genome: characterization of BAC and fosmid sequences. PLoS One 2013; 8:e72439. [PMID: 24023741 PMCID: PMC3762812 DOI: 10.1371/journal.pone.0072439] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 07/10/2013] [Indexed: 12/22/2022] Open
Abstract
Despite their prevalence and importance, the genome sequences of loblolly pine, Norway spruce, and white spruce, three ecologically and economically important conifer species, are just becoming available to the research community. Following the completion of these large assemblies, annotation efforts will be undertaken to characterize the reference sequences. Accurate annotation of these ancient genomes would be aided by a comprehensive repeat library; however, few studies have generated enough sequence to fully evaluate and catalog their non-genic content. In this paper, two sets of loblolly pine genomic sequence, 103 previously assembled BACs and 90,954 newly sequenced and assembled fosmid scaffolds, were analyzed. Together, this sequence represents 280 Mbp (roughly 1% of the loblolly pine genome) and one of the most comprehensive studies of repetitive elements and genes in a gymnosperm species. A combination of homology and de novo methodologies were applied to identify both conserved and novel repeats. Similarity analysis estimated a repetitive content of 27% that included both full and partial elements. When combined with the de novo investigation, the estimate increased to almost 86%. Over 60% of the repetitive sequence consists of full or partial LTR (long terminal repeat) retrotransposons. Through de novo approaches, 6,270 novel, full-length transposable element families and 9,415 sub-families were identified. Among those 6,270 families, 82% were annotated as single-copy. Several of the novel, high-copy families are described here, with the largest, PtPiedmont, comprising 133 full-length copies. In addition to repeats, analysis of the coding region reported 23 full-length eukaryotic orthologous proteins (KOGS) and another 29 novel or orthologous genes. These discoveries, along with other genomic resources, will be used to annotate conifer genomes and address long-standing questions about gymnosperm evolution.
Collapse
Affiliation(s)
- Jill L. Wegrzyn
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
- * E-mail: (JLW); (KAS)
| | - Brian Y. Lin
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Jacob J. Zieve
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - William M. Dougherty
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
| | - Pedro J. Martínez-García
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Maxim Koriabine
- Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Ann Holtz-Morris
- Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Pieter deJong
- Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Marc Crepeau
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
| | - Charles H. Langley
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
| | - Daniela Puiu
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Steven L. Salzberg
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - David B. Neale
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Kristian A. Stevens
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
- * E-mail: (JLW); (KAS)
| |
Collapse
|
10
|
Qi LL, Wu JJ, Friebe B, Qian C, Gu YQ, Fu DL, Gill BS. Sequence organization and evolutionary dynamics of Brachypodium-specific centromere retrotransposons. Chromosome Res 2013; 21:507-21. [PMID: 23955173 DOI: 10.1007/s10577-013-9378-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 07/30/2013] [Accepted: 07/30/2013] [Indexed: 12/18/2022]
Abstract
Brachypodium distachyon is a wild annual grass belonging to the Pooideae, more closely related to wheat, barley, and forage grasses than rice and maize. As an experimental model, the completed genome sequence of B. distachyon provides a unique opportunity to study centromere evolution during the speciation of grasses. Centromeric satellite sequences have been identified in B. distachyon, but little is known about centromeric retrotransposons in this species. In the present study, bacterial artificial chromosome (BAC)-fluorescence in situ hybridization was conducted in maize, rice, barley, wheat, and rye using B. distachyon (Bd) centromere-specific BAC clones. Eight Bd centromeric BAC clones gave no detectable fluorescence in situ hybridization (FISH) signals on the chromosomes of rice and maize, and three of them also did not yield any FISH signals in barley, wheat, and rye. In addition, four of five Triticeae centromeric BAC clones did not hybridize to the B. distachyon centromeres, implying certain unique features of Brachypodium centromeres. Analysis of Brachypodium centromeric BAC sequences identified a long terminal repeat (LTR)-centromere retrotransposon of B. distachyon (CRBd1). This element was found in high copy number accounting for 1.6 % of the B. distachyon genome, and is enriched in Brachypodium centromeric regions. CRBd1 accumulated in active centromeres, but was lost from inactive ones. The LTR of CRBd1 appears to be specific to B. distachyon centromeres. These results reveal different evolutionary events of this retrotransposon family across grass species.
Collapse
Affiliation(s)
- L L Qi
- Northern Crop Science Laboratory, USDA-ARS, 1605 Albrecht Blvd N, Fargo, ND 58102-2765, USA.
| | | | | | | | | | | | | |
Collapse
|
11
|
Čížková J, Hřibová E, Humplíková L, Christelová P, Suchánková P, Doležel J. Molecular analysis and genomic organization of major DNA satellites in banana (Musa spp.). PLoS One 2013; 8:e54808. [PMID: 23372772 PMCID: PMC3553004 DOI: 10.1371/journal.pone.0054808] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 12/17/2012] [Indexed: 02/03/2023] Open
Abstract
Satellite DNA sequences consist of tandemly arranged repetitive units up to thousands nucleotides long in head-to-tail orientation. The evolutionary processes by which satellites arise and evolve include unequal crossing over, gene conversion, transposition and extra chromosomal circular DNA formation. Large blocks of satellite DNA are often observed in heterochromatic regions of chromosomes and are a typical component of centromeric and telomeric regions. Satellite-rich loci may show specific banding patterns and facilitate chromosome identification and analysis of structural chromosome changes. Unlike many other genomes, nuclear genomes of banana (Musa spp.) are poor in satellite DNA and the information on this class of DNA remains limited. The banana cultivars are seed sterile clones originating mostly from natural intra-specific crosses within M. acuminata (A genome) and inter-specific crosses between M. acuminata and M. balbisiana (B genome). Previous studies revealed the closely related nature of the A and B genomes, including similarities in repetitive DNA. In this study we focused on two main banana DNA satellites, which were previously identified in silico. Their genomic organization and molecular diversity was analyzed in a set of nineteen Musa accessions, including representatives of A, B and S (M. schizocarpa) genomes and their inter-specific hybrids. The two DNA satellites showed a high level of sequence conservation within, and a high homology between Musa species. FISH with probes for the satellite DNA sequences, rRNA genes and a single-copy BAC clone 2G17 resulted in characteristic chromosome banding patterns in M. acuminata and M. balbisiana which may aid in determining genomic constitution in interspecific hybrids. In addition to improving the knowledge on Musa satellite DNA, our study increases the number of cytogenetic markers and the number of individual chromosomes, which can be identified in Musa.
Collapse
Affiliation(s)
- Jana Čížková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Eva Hřibová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Lenka Humplíková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Pavla Christelová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Pavla Suchánková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| |
Collapse
|
12
|
Moritoh S, Eun CH, Ono A, Asao H, Okano Y, Yamaguchi K, Shimatani Z, Koizumi A, Terada R. Targeted disruption of an orthologue of DOMAINS REARRANGED METHYLASE 2, OsDRM2, impairs the growth of rice plants by abnormal DNA methylation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 71:85-98. [PMID: 22380881 DOI: 10.1111/j.1365-313x.2012.04974.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Recent methylome analyses of the entire Arabidopsis thaliana genome using various mutants have provided detailed information about the DNA methylation pattern and its function. However, information about DNA methylation in other plants is limited, partly because of the lack of mutants. To study DNA methylation in rice (Oryza sativa) we applied homologous recombination-mediated gene targeting to generate targeted disruptants of OsDRM2, a rice orthologue of DOMAINS REARRANGED METHYLASE 1 and 2 (DRM1/2), which encode DNA methyltransferases responsible for de novo and non-CG methylation in Arabidopsis. Whereas Arabidopsis drm1 drm2 double mutants showed no morphological alterations, targeted disruptants of rice OsDRM2 displayed pleiotropic developmental phenotypes in both vegetative and reproductive stages, including growth defects, semi-dwarfed stature, reductions in tiller number, delayed heading or no heading, abnormal panicle and spikelet morphology, and complete sterility. In these osdrm2 disruptants, a 13.9% decrease in 5-methylcytosine was observed by HPLC analysis. The CG and non-CG methylation levels were reduced in RIRE7/CRR1 retrotransposons, and in 5S rDNA repeats. Associated transcriptional activation was detected in RIRE7/CRR1. Furthermore, de novo methylation by an RNA-directed DNA methylation (RdDM) process involving transgene-derived exogenous small interfering RNA (siRNA) was deficient in osdrm2-disrupted cells. Impaired growth and abnormal DNA methylation of osdrm2 disruptants were restored by the complementation of wild-type OsDRM2 cDNA. Our results suggest that OsDRM2 is responsible for de novo, CG and non-CG methylation in rice genomic sequences, and that DNA methylation regulated by OsDRM2 is essential for proper rice development in both vegetative and reproductive stages.
Collapse
Affiliation(s)
- Satoru Moritoh
- National Institute for Basic Biology, Okazaki 444-8585, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Staginnus C, Desel C, Schmidt T, Kahl G. Assembling a puzzle of dispersed retrotransposable sequences in the genome of chickpea (Cicer arietinum L.). Genome 2011; 53:1090-102. [PMID: 21164541 DOI: 10.1139/g10-093] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Several repetitive elements are known to be present in the genome of chickpea (Cicer arietinum L.) including satellite DNA and En/Spm transposons as well as two dispersed, highly repetitive elements, CaRep1 and CaRep2. PCR was used to prove that CaRep1, CaRep2, and previously isolated CaRep3 of C. arietinum represent different segments of a highly repetitive Ty3-gypsy-like retrotransposon (Metaviridae) designated CaRep that makes up large parts of the intercalary heterochromatin. The full sequence of this element including the LTRs and untranslated internal regions was isolated by selective amplification. The restriction pattern of CaRep was different within the annual species of the genus Cicer, suggesting its rearrangement during the evolution of the genus during the last 100 000 years. In addition to CaRep, another LTR and a non-LTR retrotransposon family were isolated, and their restriction patterns and physical localization in the chickpea genome were characterized. The LINE-like element CaLin is only of comparatively low abundance and reveals a considerable heterogeneity. The Ty1-copia-like element (Pseudoviridae) CaTy is located in the distal parts of the intercalary heterochromatin and adjacent euchromatic regions, but it is absent from the centromeric regions. These results together with earlier findings allow to depict the distribution of retroelements on chickpea chromosomes, which extensively resembles the retroelement landscape of the genome of the model legume Medicago truncatula Gaertn.
Collapse
Affiliation(s)
- C Staginnus
- Molecular BioSciences, Biocentre, University of Frankfurt am Main, Max-von-Laue-Straße 9, D-60438 Frankfurt am Main, Germany.
| | | | | | | |
Collapse
|
14
|
Plant centromeric retrotransposons: a structural and cytogenetic perspective. Mob DNA 2011; 2:4. [PMID: 21371312 PMCID: PMC3059260 DOI: 10.1186/1759-8753-2-4] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 03/03/2011] [Indexed: 12/12/2022] Open
Abstract
Background The centromeric and pericentromeric regions of plant chromosomes are colonized by Ty3/gypsy retrotransposons, which, on the basis of their reverse transcriptase sequences, form the chromovirus CRM clade. Despite their potential importance for centromere evolution and function, they have remained poorly characterized. In this work, we aimed to carry out a comprehensive survey of CRM clade elements with an emphasis on their diversity, structure, chromosomal distribution and transcriptional activity. Results We have surveyed a set of 190 CRM elements belonging to 81 different retrotransposon families, derived from 33 host species and falling into 12 plant families. The sequences at the C-terminus of their integrases were unexpectedly heterogeneous, despite the understanding that they are responsible for targeting to the centromere. This variation allowed the division of the CRM clade into the three groups A, B and C, and the members of each differed considerably with respect to their chromosomal distribution. The differences in chromosomal distribution coincided with variation in the integrase C-terminus sequences possessing a putative targeting domain (PTD). A majority of the group A elements possess the CR motif and are concentrated in the centromeric region, while members of group C have the type II chromodomain and are dispersed throughout the genome. Although representatives of the group B lack a PTD of any type, they appeared to be localized preferentially in the centromeres of tested species. All tested elements were found to be transcriptionally active. Conclusions Comprehensive analysis of the CRM clade elements showed that genuinely centromeric retrotransposons represent only a fraction of the CRM clade (group A). These centromeric retrotransposons represent an active component of centromeres of a wide range of angiosperm species, implying that they play an important role in plant centromere evolution. In addition, their transcriptional activity is consistent with the notion that the transcription of centromeric retrotransposons has a role in normal centromere function.
Collapse
|
15
|
Ohmido N, Ishimaru A, Kato S, Sato S, Tabata S, Fukui K. Integration of cytogenetic and genetic linkage maps of Lotus japonicus, a model plant for legumes. Chromosome Res 2010; 18:287-99. [PMID: 20076998 DOI: 10.1007/s10577-009-9103-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Revised: 11/05/2009] [Accepted: 11/25/2009] [Indexed: 01/26/2023]
|
16
|
Ohmido N, Fukui K, Kinoshita T. Recent advances in rice genome and chromosome structure research by fluorescence in situ hybridization (FISH). PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2010; 86:103-16. [PMID: 20154468 PMCID: PMC3417561 DOI: 10.2183/pjab.86.103] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Accepted: 01/04/2010] [Indexed: 05/28/2023]
Abstract
Fluorescence in situ hybridization (FISH) is an effective method for the physical mapping of genes and repetitive DNA sequences on chromosomes. Physical mapping of unique nucleotide sequences on specific rice chromosome regions was performed using a combination of chromosome identification and highly sensitive FISH. Increases in the detection sensitivity of smaller DNA sequences and improvements in spatial resolution have ushered in a new phase in FISH technology. Thus, it is now possible to perform in situ hybridization on somatic chromosomes, pachytene chromosomes, and even on extended DNA fibers (EDFs). Pachytene-FISH allows the integration of genetic linkage maps and quantitative chromosome maps. Visualization methods using FISH can reveal the spatial organization of the centromere, heterochromatin/euchromatin, and the terminal structures of rice chromosomes. Furthermore, EDF-FISH and the DNA combing technique can resolve a spatial distance of 1 kb between adjacent DNA sequences, and the detection of even a 300-bp target is now feasible. The copy numbers of various repetitive sequences and the sizes of various DNA molecules were quantitatively measured using the molecular combing technique. This review describes the significance of these advances in molecular cytology in rice and discusses future applications in plant studies using visualization techniques.
Collapse
Affiliation(s)
- Nobuko Ohmido
- Graduate School of Human Development and Environment, Kobe University, Kobe, Japan.
| | | | | |
Collapse
|
17
|
Gao D, Gill N, Kim HR, Walling JG, Zhang W, Fan C, Yu Y, Ma J, SanMiguel P, Jiang N, Cheng Z, Wing RA, Jiang J, Jackson SA. A lineage-specific centromere retrotransposon in Oryza brachyantha. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 60:820-831. [PMID: 19702667 DOI: 10.1111/j.1365-313x.2009.04005.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Most eukaryotic centromeres contain large quantities of repetitive DNA, such as satellite repeats and retrotransposons. Unlike most transposons in plant genomes, the centromeric retrotransposon (CR) family is conserved over long evolutionary periods among a majority of the grass species. CR elements are highly concentrated in centromeres, and are likely to play a role in centromere function. In order to study centromere evolution in the Oryza (rice) genus, we sequenced the orthologous region to centromere 8 of Oryza sativa from a related species, Oryza brachyantha. We found that O. brachyantha does not have the canonical CRR (CR of rice) found in the centromeres of all other Oryza species. Instead, a new Ty3-gypsy (Metaviridae) retroelement (FRetro3) was found to colonize the centromeres of this species. This retroelement is found in high copy numbers in the O. brachyantha genome, but not in other Oryza genomes, and based on the dating of long terminal repeats (LTRs) of FRetro3 it was amplified in the genome in the last few million years. Interestingly, there is a high level of removal of FRetro3 based on solo-LTRs to full-length elements, and this rapid turnover may have played a role in the replacement of the canonical CRR with the new element by active deletion. Comparison with previously described ChIP cloning data revealed that FRetro3 is found in CENH3-associated chromatin sequences. Thus, within a single lineage of the Oryza genus, the canonical component of grass centromeres has been replaced with a new retrotransposon that has all the hallmarks of a centromeric retroelement.
Collapse
Affiliation(s)
- Dongying Gao
- Molecular and Evolutionary Genetics, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Nested Ty3-gypsy retrotransposons of a single Beta procumbens centromere contain a putative chromodomain. Chromosome Res 2009; 17:379-96. [PMID: 19322668 DOI: 10.1007/s10577-009-9029-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2008] [Revised: 01/12/2009] [Accepted: 01/12/2009] [Indexed: 12/18/2022]
Abstract
LTR retrotransposons belong to a major group of DNA sequences that are often localized in plant centromeres. Using BAC inserts originating from the centromere of a monosomic wild beet (Beta procumbens) chromosome fragment in Beta vulgaris, two complete LTR retrotransposons were identified. Both elements, designated Beetle1 and Beetle2, possess a coding region with genes in the order characteristic for Ty3-gypsy retrotransposons. Beetle1 and Beetle2 have a chromodomain in the C-terminus of the integrase gene and are highly similar to the centromeric retrotransposons (CRs) of rice, maize, and barley. Both retroelements were localized in the centromeric region of B. procumbens chromosomes by fluorescence in-situ hybridization. They can therefore be classified as centromere-specific chromoviruses. PCR analysis using RNA as template indicated that Beetle1 and Beetle2 are transcriptionally active. On the basis of the sequence diversity between the LTR sequences, it was estimated that Beetle1 and Beetle2 transposed within the last 60,000 years and 130,000 years, respectively. The centromeric localization of Beetle1 and Beetle2 and their transcriptional activity combined with high sequence conservation within each family play an important structural role in the centromeres of B. procumbens chromosomes.
Collapse
|
19
|
Fukai E, Dobrowolska AD, Madsen LH, Madsen EB, Umehara Y, Kouchi H, Hirochika H, Stougaard J. Transposition of a 600 thousand-year-old LTR retrotransposon in the model legume Lotus japonicus. PLANT MOLECULAR BIOLOGY 2008; 68:653-63. [PMID: 18802778 DOI: 10.1007/s11103-008-9397-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Accepted: 09/01/2008] [Indexed: 05/08/2023]
Abstract
We have identified a new Ty3-gypsy retrotransposon family named LORE2 (Lotus retrotransposon 2) and documented its activity in the model legume Lotus japonicus. Three new LORE2 insertions were found in symbiotic mutant alleles isolated from a plant population, established by tissue culture mediated transformation of the L. japonicus Gifu accession. Low transcriptional and transpositional activities of LORE2 in cultured cells suggested that the LORE2 transpositions identified in the three symbiotic mutants occurred in intact plants, not in callus. Tracing of the transpositional events identified two active LORE2 members in Gifu. One of them named LORE2A possesses a deletion in its coding region and polymorphisms between intraelemental LTRs. LORE2A is thus an aged element, estimated as 600 thousand years old. Our findings indicate that plant genomes carry more cryptic LTR retrotransposons, i.e., aged yet active, than estimated before, and that these cryptic elements may have contributed to plant genome dynamics, for example, the burst of transpositions reported in several plant species.
Collapse
Affiliation(s)
- Eigo Fukai
- National Institute of Agrobiological Science, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
20
|
Tsuchimoto S, Hirao Y, Ohtsubo E, Ohtsubo H. New SINE families from rice, OsSN, with poly(A) at the 3' ends. Genes Genet Syst 2008; 83:227-36. [PMID: 18670134 DOI: 10.1266/ggs.83.227] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A database search of the sequences flanking a member of rice retrotransposon RIRE7 revealed that a 298-bp sequence in the region downstream of the member is a repetitive sequence interspersed in the genome of Oryza sativa cv. Nipponbare. Most of the repetitive sequences were flanked by a direct repeat of a target-site sequence, about 14 bp in length. The consensus sequence, 293 bp in length, had no regions encoding any proteins but had sequence motifs of an internal promoter of RNA polymerase III. These indicate that the sequence is a retroposon SINE, designated OsSN1 (Oryza sativa SINE1). OsSN1 is a new rice SINE, because it has no homology with any of the three p-SINE families previously identified from rice, and because it has a stretch of A at the 3' end, unlike p-SINE and any other Gramineae SINEs which have a stretch of T at the 3' end. The Nipponbare genome was found to have many members related to OsSN1, forming two additional new SINE families (designated OsSN2 and OsSN3). OsSN2 and OsSN3 are highly homologous to the 3' and 5' regions of OsSN1, respectively. This suggests that OsSN1 has a mosaic structure, which is generated by sequence exchange (or shuffling) between ancestral OsSN2 and OsSN3. Despite the absence of homology in the 3' regions between OsSN1 (or OsSN2) and OsSN3, a sequence, 5'-TTCTC-3', is commonly present in the region preceding the A stretch at the 3' end. This sequence together with the A stretch and a stem-loop structure found in the region near the A stretch are assumed to be important for retroposition. OsSN members were present in strains of Oryza species, as were p-SINE members. Some of the members showed insertion polymorphism at the respective loci among the rice strains. p-SINE had such polymorphic members, which are useful for classification and phylogenetic analysis of various strains of Oryza species. The polymorphic members of OsSN were more frequently found than those of p-SINE, and therefore, such members are likely to be useful for extensive taxonomic and phylogenetic studies on various rice strains.
Collapse
Affiliation(s)
- Suguru Tsuchimoto
- Institute of Molecular and Cellular Biosciences, the University of Tokyo, Tokyo, Japan.
| | | | | | | |
Collapse
|
21
|
Takata M, Kiyohara A, Takasu A, Kishima Y, Ohtsubo H, Sano Y. Rice transposable elements are characterized by various methylation environments in the genome. BMC Genomics 2007; 8:469. [PMID: 18093338 PMCID: PMC2222647 DOI: 10.1186/1471-2164-8-469] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2007] [Accepted: 12/20/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent studies using high-throughput methods have revealed that transposable elements (TEs) are a comprehensive target for DNA methylation. However, the relationship between TEs and their genomic environment regarding methylation still remains unclear. The rice genome contains representatives of all known TE families with different characteristics of chromosomal distribution, structure, transposition, size, and copy number. Here we studied the DNA methylation state around 12 TEs in nine genomic DNAs from cultivated rice strains and their closely related wild strains. RESULTS We employed a transposon display (TD) method to analyze the methylation environments in the genomes. The 12 TE families, consisting of four class I elements, seven class II elements, and one element of a different class, were differentially distributed in the rice chromosomes: some elements were concentrated in the centromeric or pericentromeric regions, but others were located in euchromatic regions. The TD analyses revealed that the TE families were embedded in flanking sequences with different methylation degrees. Each TE had flanking sequences with similar degrees of methylation among the nine rice strains. The class I elements tended to be present in highly methylated regions, while those of the class II elements showed widely varying degrees of methylation. In some TE families, the degrees of methylation were markedly lower than the average methylation state of the genome. In two families, dramatic changes of the methylation state occurred depending on the distance from the TE. CONCLUSION Our results demonstrate that the TE families in the rice genomes can be characterized by the methylation states of their surroundings. The copy number and degree of conservation of the TE family are not likely to be correlated with the degree of methylation. We discuss possible relationships between the methylation state of TEs and their surroundings. This is the first report demonstrating that TEs in the genome are associated with a particular methylation environment that is a feature of a given TE.
Collapse
Affiliation(s)
- Miwako Takata
- Laboratory of Plant Breeding, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.
| | | | | | | | | | | |
Collapse
|
22
|
Chaparro C, Guyot R, Zuccolo A, Piégu B, Panaud O. RetrOryza: a database of the rice LTR-retrotransposons. Nucleic Acids Res 2006; 35:D66-70. [PMID: 17071960 PMCID: PMC1635335 DOI: 10.1093/nar/gkl780] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Long terminal repeat (LTR)-retrotransposons comprise a significant portion of the rice genome. Their complete characterization is thus necessary if the sequenced genome is to be annotated correctly. In addition, because LTR-retrotransposons can influence the expression of neighboring genes, the complete identification of these elements in the rice genome is essential in order to study their putative functional interactions with the plant genes. The aims of the database are to (i) Assemble a comprehensive dataset of LTR-retrotransposons that includes not only abundant elements, but also low copy number elements. (ii) Provide an interface to efficiently access the resources stored in the database. This interface should also allow the community to annotate these elements. (iii) Provide a means for identifying LTR-retrotransposons inserted near genes. Here we present the results, where 242 complete LTR-retrotransposons have been structurally and functionally annotated. A web interface to the database has been made available (http://www.retroryza.org/), through which the user can annotate a sequence or search for LTR-retrotransposons in the neighborhood of a gene of interest.
Collapse
Affiliation(s)
| | | | - Andrea Zuccolo
- Department of Plant Sciences, Arizona Genomics Institute, University of ArizonaTucson, AZ 85721, USA
| | | | - Olivier Panaud
- To whom correspondence should be addressed. Tel: +33 468 661773; Fax: +33 468 668499;
| |
Collapse
|
23
|
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.
Collapse
Affiliation(s)
- Beatrice Mariotti
- Departamento de Biología Aplicada, Escuela Politécnica Superior, Universidad de Almería, 04120 Almería, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Bao W, Zhang W, Yang Q, Zhang Y, Han B, Gu M, Xue Y, Cheng Z. Diversity of centromeric repeats in two closely related wild rice species, Oryza officinalis and Oryza rhizomatis. Mol Genet Genomics 2006; 275:421-30. [PMID: 16463049 DOI: 10.1007/s00438-006-0103-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2005] [Accepted: 01/12/2006] [Indexed: 11/26/2022]
Abstract
Oryza officinalis (CC, 2n = 24) and Oryza rhizomatis (CC, 2n = 24) belong to the Oryza genus, which contains more than 20 identified wild rice species. Although much has been known about the molecular composition and organization of centromeres in Oryza sativa, relatively little is known of its wild relatives. In the present study, we isolated and characterized a 126-bp centromeric satellite (CentO-C) from three bacterial artificial chromosomes of O. officinalis. In addition to CentO-C, low abundance of CentO satellites is also present in O. officinalis. In order to determine the chromosomal locations and distributions of CentO-C (126-bp), CentO (155 bp) and TrsC (366 bp) satellite within O. officinalis, fluorescence in situ hybridization examination was done on pachytene or metaphase I chromosomes. We found that only ten centromeres (excluding centromere 7 and 2) contain CentO-C arrays in O. officinalis, while centromere 7 comprises CentO satellites, and centromere 2 is devoid of any detectable satellites. For TrsC satellites, it was detected at multiple subtelomeric regions in O. officinalis, however, in O. rhizomatis, TrsC sequences were detected both in the four centromeric regions (CEN 3, 4, 10, 11) and the multiple subtelomeric regions. Therefore, these data reveal the evolutionary diversification pattern of centromere DNA within/or between close related species, and could provide an insight into the dynamic evolutionary processes of rice centromere.
Collapse
Affiliation(s)
- Weidong Bao
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Vitte C, Panaud O. LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model. Cytogenet Genome Res 2005; 110:91-107. [PMID: 16093661 DOI: 10.1159/000084941] [Citation(s) in RCA: 180] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2003] [Accepted: 04/14/2004] [Indexed: 12/11/2022] Open
Abstract
Long Terminal Repeat (LTR) retrotransposons are ubiquitous components of plant genomes. Because of their copy-and-paste mode of transposition, these elements tend to increase their copy number while they are active. In addition, it is now well established that the differences in genome size observed in the plant kingdom are accompanied by variations in LTR retrotransposon content, suggesting that LTR retrotransposons might be important players in the evolution of plant genome size, along with polyploidy. The recent availability of large genomic sequences for many crop species has made it possible to examine in detail how LTR retrotransposons actually drive genomic changes in plants. In the present paper, we provide a review of the recent publications that have contributed to the knowledge of plant LTR retrotransposons, as structural components of the genomes, as well as from an evolutionary genomic perspective. These studies have shown that plant genomes undergo genome size increases through bursts of retrotransposition, while there is a counteracting process that tends to eliminate the transposed copies from the genomes. This process involves recombination mechanisms that occur either between the LTRs of the elements, leading to the formation of solo-LTRs, or between direct repeats anywhere in the sequence of the element, leading to internal deletions. All these studies have led to the emergence of a new model for plant genome evolution that takes into account both genome size increases (through retrotransposition) and decreases (through solo-LTR and deletion formation). In the conclusion, we discuss this new model and present the future prospects in the study of plant genome evolution in relation to the activity of transposable elements.
Collapse
Affiliation(s)
- C Vitte
- Laboratoire Ecologie, Systématique et Evolution, Université Paris-Sud, Orsay, France
| | | |
Collapse
|
26
|
Sharma S, Raina SN. Organization and evolution of highly repeated satellite DNA sequences in plant chromosomes. Cytogenet Genome Res 2005; 109:15-26. [PMID: 15753554 DOI: 10.1159/000082377] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2004] [Accepted: 04/14/2004] [Indexed: 11/19/2022] Open
Abstract
A major component of the plant nuclear genome is constituted by different classes of repetitive DNA sequences. The structural, functional and evolutionary aspects of the satellite repetitive DNA families, and their organization in the chromosomes is reviewed. The tandem satellite DNA sequences exhibit characteristic chromosomal locations, usually at subtelomeric and centromeric regions. The repetitive DNA family(ies) may be widely distributed in a taxonomic family or a genus, or may be specific for a species, genome or even a chromosome. They may acquire large-scale variations in their sequence and copy number over an evolutionary time-scale. These features have formed the basis of extensive utilization of repetitive sequences for taxonomic and phylogenetic studies. Hybrid polyploids have especially proven to be excellent models for studying the evolution of repetitive DNA sequences. Recent studies explicitly show that some repetitive DNA families localized at the telomeres and centromeres have acquired important structural and functional significance. The repetitive elements are under different evolutionary constraints as compared to the genes. Satellite DNA families are thought to arise de novo as a consequence of molecular mechanisms such as unequal crossing over, rolling circle amplification, replication slippage and mutation that constitute "molecular drive".
Collapse
Affiliation(s)
- S Sharma
- Laboratory of Cellular and Molecular Cytogenetics, Department of Botany, University of Delhi, Delhi, India.
| | | |
Collapse
|
27
|
Fischer C, Bouneau L, Coutanceau JP, Weissenbach J, Ozouf-Costaz C, Volff JN. Diversity and clustered distribution of retrotransposable elements in the compact genome of the pufferfish Tetraodon nigroviridis. Cytogenet Genome Res 2005; 110:522-36. [PMID: 16093705 DOI: 10.1159/000084985] [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] [Received: 02/05/2004] [Accepted: 03/25/2004] [Indexed: 12/15/2022] Open
Abstract
We report the characterization and chromosomal distribution of retroelements in the compact genome of the pufferfish Tetraodon nigroviridis. We have reconstructed partial/complete retroelement sequences, established their phylogenetic relationship to other known eukaryotic retrotransposons, and performed double-color FISH analyses to gain new insights into their patterns of chromosomal distribution. We could identify 43 different reverse transcriptase retrotransposons belonging to the three major known subclasses (14 non-LTR retrotransposons from seven clades, 25 LTR retrotransposons representing the five major known groups, and four Penelope-like elements), and well as two SINEs (non-autonomous retroelements). Such a diversity of retrotransposable elements, which seems to be relatively common in fish but not in mammals, is astonishing in such a compact genome. The total number of retroelements was approximately 3000, roughly representing only 2.6% of the genome of T. nigroviridis. This is much less than in other vertebrate genomes, reflecting the compact nature of the genome of this pufferfish. Major differences in copy number were observed between different clades, indicating differential success in invading and persisting in the genome. Some retroelements displayed evidence of recent activity. Finally, FISH analysis showed that retrotransposable elements preferentially accumulate in specific heterochromatic regions of the genome of T. nigroviridis, revealing a degree of genomic compartmentalization not observed in the human genome.
Collapse
Affiliation(s)
- C Fischer
- Genoscope/Centre National de Séquençage, CNRS-UMR 8030, Evry, France.
| | | | | | | | | | | |
Collapse
|
28
|
Gorinsek B, Gubensek F, Kordis D. Phylogenomic analysis of chromoviruses. Cytogenet Genome Res 2005; 110:543-52. [PMID: 16093707 DOI: 10.1159/000084987] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2003] [Accepted: 03/08/2004] [Indexed: 11/19/2022] Open
Abstract
Genome sequences of model organisms provide a unique opportunity to obtain insight into the complete diversity of any transposable element (TE) group. A limited number of chromoviruses, the chromodomain containing genus of Metaviridae, is known from plant, fungal and vertebrate genomes. By searching diverse eukaryotic genome databases, we have found a surprisingly large number of new, structurally intact and highly conserved chromoviral elements, greatly exceeding the number of previously known chromoviruses. In this study, we examined the diversity, origin and evolution of chromoviruses in Eukaryota. Chromoviral diversity in plants, fungi and vertebrates, as shown by phylogenetic analyses, was found to be much greater than previously expected. A novel centromere-specific chromoviral lineage was found to be widespread and highly conserved in all seed plants. The age of chromoviruses has been significantly extended by finding their representatives in the most basal plant lineages (green and red algae), in Heterokonta (oomycetes) and in Cercozoa (plasmodiophorids). The evolutionary origin of chromoviruses has been found to be no earlier than in Cercozoa, since none can be found in the basal eukaryotic lineages, despite the extensive genome data. The evolutionary dynamics of chromoviruses can be explained by a strict vertical transmission in plants and fungi, while in Metazoa it is more complex. The currently available genome data clearly show that chromoviruses are the most widespread and one of the oldest Metaviridae clade.
Collapse
Affiliation(s)
- B Gorinsek
- Department of Biochemistry and Molecular Biology, Jozef Stefan Institute, Ljubljana, Slovenia
| | | | | |
Collapse
|
29
|
Kordis D. A genomic perspective on the chromodomain-containing retrotransposons: Chromoviruses. Gene 2005; 347:161-73. [PMID: 15777633 DOI: 10.1016/j.gene.2004.12.017] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2004] [Revised: 12/01/2004] [Accepted: 12/07/2004] [Indexed: 12/31/2022]
Abstract
Chromoviruses, chromodomain-containing retrotransposons, are the only Metaviridae (Ty3/gypsy group of retrotransposons) clade with a Eukaryota-wide distribution. They have a common evolutionary origin and are the most prolific and diverse Metaviridae clade. The fusion of a retrotransposon and a chromodomain, was most probably responsible for their extreme evolutionary success in Eukaryota. Analysis of the massive amount of genome sequence data for different eukaryotic lineages has provided an in depth insight into the diversity, evolution, neofunctionalization, high rate of genomic turnover and origin of chromoviruses in Eukaryota. This review attempts to summarise the unique aspects of chromoviruses from a genomic perspective.
Collapse
Affiliation(s)
- Dusan Kordis
- Department of Biochemistry and Molecular Biology, Jozef Stefan Institute, Jamova 39, 1001 Ljubljana, Slovenia.
| |
Collapse
|
30
|
Pereira V. Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome. Genome Biol 2004; 5:R79. [PMID: 15461797 PMCID: PMC545599 DOI: 10.1186/gb-2004-5-10-r79] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2004] [Revised: 08/03/2004] [Accepted: 08/17/2004] [Indexed: 11/18/2022] Open
Abstract
An analysis of the distribution and age of LTR retrotransposons in the Arabidopsis genome revealed that Pseudoviridae insert randomly along the chromosome and have been recently active whereas Metaviridae were more active in the past and preferentially target heterochromatin. Background Genome evolution and size variation in multicellular organisms are profoundly influenced by the activity of retrotransposons. In higher eukaryotes with compact genomes retrotransposons are found in lower copy numbers than in larger genomes, which could be due to either suppression of transposition or to elimination of insertions, and are non-randomly distributed along the chromosomes. The evolutionary mechanisms constraining retrotransposon copy number and chromosomal distribution are still poorly understood. Results I investigated the evolutionary dynamics of long terminal repeat (LTR)-retrotransposons in the compact Arabidopsis thaliana genome, using an automated method for obtaining genome-wide, age and physical distribution profiles for different groups of elements, and then comparing the distributions of young and old insertions. Elements of the Pseudoviridae family insert randomly along the chromosomes and have been recently active, but insertions tend to be lost from euchromatic regions where they are less likely to fix, with a half-life estimated at approximately 470,000 years. In contrast, members of the Metaviridae (particularly Athila) preferentially target heterochromatin, and were more active in the past. Conclusion Diverse evolutionary mechanisms have constrained both the copy number and chromosomal distribution of retrotransposons within a single genome. In A. thaliana, their non-random genomic distribution is due to both selection against insertions in euchromatin and preferential targeting of heterochromatin. Constant turnover of euchromatic insertions and a decline in activity for the elements that target heterochromatin have both limited the contribution of retrotransposon DNA to genome size expansion in A. thaliana.
Collapse
Affiliation(s)
- Vini Pereira
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, UK.
| |
Collapse
|
31
|
Abstract
The diversity, origin, and evolution of chromoviruses in Eukaryota were examined using the massive amount of genome sequence data for different eukaryotic lineages. A surprisingly large number of novel full-length chromoviral elements were found, greatly exceeding the number of the known chromoviruses. These new elements are mostly structurally intact and highly conserved. Chromoviruses in the key Amniota lineage, the reptiles, have been analyzed by PCR to explain their evolutionary dynamics in amniotes. Phylogenetic analyses provide evidence for a novel centromere-specific chromoviral clade that is widespread and highly conserved in all seed plants. Chromoviral diversity in plants, fungi, and vertebrates, as shown by phylogenetic analyses, was found to be much greater than previously expected. The age of plant chromoviruses has been significantly extended by finding their representatives in the most basal plant lineages, the green and the red algae. The evolutionary origin of chromoviruses has been found to be no earlier than in Cercozoa. The evolutionary history and dynamics of chromoviruses can be explained simply by strict vertical transmission in plants, followed by more complex evolution in fungi and in Metazoa. The currently available data clearly show that chromoviruses indeed represent the oldest and the most widespread clade of Metaviridae.
Collapse
Affiliation(s)
- Benjamin Gorinsek
- Department of Biochemistry and Molecular Biology, Jozef Stefan Institute, Ljubljana, Slovenia
| | | | | |
Collapse
|
32
|
Zhang Y, Huang Y, Zhang L, Li Y, Lu T, Lu Y, Feng Q, Zhao Q, Cheng Z, Xue Y, Wing RA, Han B. Structural features of the rice chromosome 4 centromere. Nucleic Acids Res 2004; 32:2023-30. [PMID: 15064362 PMCID: PMC390372 DOI: 10.1093/nar/gkh521] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A complete sequence of a chromosome centromere is necessary for fully understanding centromere function. We reported the sequence structures of the first complete rice chromosome centromere through sequencing a large insert bacterial artificial chromosome clone-based contig, which covered the rice chromosome 4 centromere. Complete sequencing of the 124-kb rice chromosome 4 centromere revealed that it consisted of 18 tracts of 379 tandemly arrayed repeats known as CentO and a total of 19 centromeric retroelements (CRs) but no unique sequences were detected. Four tracts, composed of 65 CentO repeats, were located in the opposite orientation, and 18 CentO tracts were flanked by 19 retroelements. The CRs were classified into four types, and the type I retroelements appeared to be more specific to rice centromeres. The preferential insert of the CRs among CentO repeats indicated that the centromere-specific retroelements may contribute to centromere expansion during evolution. The presence of three intact retrotransposons in the centromere suggests that they may be responsible for functional centromere initiation through a transcription-mediated mechanism.
Collapse
Affiliation(s)
- Yu Zhang
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Akiyama Y, Conner JA, Goel S, Morishige DT, Mullet JE, Hanna WW, Ozias-Akins P. High-resolution physical mapping in Pennisetum squamulatum reveals extensive chromosomal heteromorphism of the genomic region associated with apomixis. PLANT PHYSIOLOGY 2004; 134:1733-41. [PMID: 15064383 PMCID: PMC419846 DOI: 10.1104/pp.103.033969] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2003] [Revised: 01/07/2004] [Accepted: 01/07/2004] [Indexed: 05/18/2023]
Abstract
Gametophytic apomixis is asexual reproduction as a consequence of parthenogenetic development of a chromosomally unreduced egg. The trait leads to the production of embryos with a maternal genotype, i.e. progeny are clones of the maternal plant. The application of the trait in agriculture could be a tremendous tool for crop improvement through conventional and nonconventional breeding methods. Unfortunately, there are no major crops that reproduce by apomixis, and interspecific hybridization with wild relatives has not yet resulted in commercially viable germplasm. Pennisetum squamulatum is an aposporous apomict from which the gene(s) for apomixis has been transferred to sexual pearl millet by backcrossing. Twelve molecular markers that are linked with apomixis coexist in a tight linkage block called the apospory-specific genomic region (ASGR), and several of these markers have been shown to be hemizygous in the polyploid genome of P. squamulatum. High resolution genetic mapping of these markers has not been possible because of low recombination in this region of the genome. We now show the physical arrangement of bacterial artificial chromosomes containing apomixis-linked molecular markers by high resolution fluorescence in situ hybridization on pachytene chromosomes. The size of the ASGR, currently defined as the entire hemizygous region that hybridizes with apomixis-linked bacterial artificial chromosomes, was estimated on pachytene and mitotic chromosomes to be approximately 50 Mbp (a quarter of the chromosome). The ASGR includes highly repetitive sequences from an Opie-2-like retrotransposon family that are particularly abundant in this region of the genome.
Collapse
Affiliation(s)
- Yukio Akiyama
- Department of Horticulture, University of Georgia, Tifton, Georgia 31793-0748, USA
| | | | | | | | | | | | | |
Collapse
|
34
|
Dechyeva D, Gindullis F, Schmidt T. Divergence of satellite DNA and interspersion of dispersed repeats in the genome of the wild beet Beta procumbens. Chromosome Res 2003; 11:3-21. [PMID: 12675302 DOI: 10.1023/a:1022005514470] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Several repetitive sequences of the genome of Beta procumbens Chr. Sm., a wild beet species of the section Procumbentes of the genus Beta have been isolated. According to their genomic organization, the repeats were assigned to satellite DNA and families of dispersed DNA sequences. The tandem repeats are 229-246 bp long and belong to an AluI restriction satellite designated pAp11. Monomers of this satellite DNA form subfamilies which can be distinguished by the divergence or methylation of an internal restriction site. The satellite is amplified in the section Procumbentes, but is also found in species of the section Beta including cultivated beet (Beta vulgaris). The existence of the pAp11 satellite in distantly related species suggests that the AluI sequence family is an ancient component of Beta genomes and the ancestor of the diverged satellite subfamily pEV4 in B. vulgaris. Comparative fluorescent in-situ hybridization revealed remarkable differences in the chromosomal position between B. procumbens and B. vulgaris, indicating that the pAp11 and pEV4 satellites were most likely involved in the expansion or rearrangement of the intercalary B. vulgaris heterochromatin. Furthermore, we describe the molecular structure, and genomic and chromosomal organization of two repetitive DNA families which were designated pAp4 and pAp22 and are 1354 and 582 bp long, respectively. The families consist of sequence elements which are widely dispersed along B. procumbens chromosomes with local clustering and exclusion from distal euchromatic regions. FISH on meiotic chromosomes showed that both dispersed repeats are colocalized in some chromosomal regions. The interspersion of repeats of the pAp4 and pAp22 family was studied by PCR and enabled the determination of repeat flanking sequences. Sequence analysis revealed that pAp22 is either derived from or part of a long terminal repeat (LTR) of an Athila-like retrotransposon. Southern analysis and FISH with pAp4 and pAp22 showed that both dispersed repeats are species-specific and can be used as DNA probes to discriminate parental genomes in interspecific hybrids. This was tested in the sugar beet hybrid PRO1 which contains a small B. procumbens chromosome fragment.
Collapse
Affiliation(s)
- Daryna Dechyeva
- Plant Molecular Cytogenetics Group, Institute of Crop Science and Plant Breeding, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24118 Kiel, Germany
| | | | | |
Collapse
|
35
|
Matsunaga S, Yagisawa F, Yamamoto M, Uchida W, Nakao S, Kawano S. LTR retrotransposons in the dioecious plant Silene latifolia. Genome 2002; 45:745-51. [PMID: 12175078 DOI: 10.1139/g02-026] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Conserved domains of two types of LTR retrotransposons, Tyl-copia- and Ty3-gypsy-like retrotransposons, were isolated from the dioecious plant Silene latifolia, whose sex is determined by X and Y chromosomes. Southern hybridization analyses using these retrotransposons as probes resulted in identical patterns from male and female genomes. Fluorescence in situ hybridization indicated that these retrotransposons do not accumulate specifically in the sex chromosomes. These results suggest that recombination between the sex chromosomes of S. latifolia has not been severely reduced. Conserved reverse transcriptase regions of Ty1-copia-like retrotransposons were isolated from 13 different Silene species and classified into two major families. Their categorization suggests that parallel divergence of the Ty1-copia-like retrotransposons occurred during the differentiation of Silene species. Most functional retrotransposons from three dioecious species, S. latifolia, S. dioica, and S. diclinis, fell into two clusters. The evolutionary dynamics of retrotransposons implies that, in the genus Silene, dioecious species evolved recently from gynodioecious species.
Collapse
Affiliation(s)
- Sachihiro Matsunaga
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan.
| | | | | | | | | | | |
Collapse
|
36
|
Hudakova S, Michalek W, Presting GG, ten Hoopen R, dos Santos K, Jasencakova Z, Schubert I. Sequence organization of barley centromeres. Nucleic Acids Res 2001; 29:5029-35. [PMID: 11812833 PMCID: PMC97617 DOI: 10.1093/nar/29.24.5029] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
By sequencing, fingerprinting and in situ hybridization of a centromere-specific large insert clone (BAC 7), the sequence organization of centromeric DNA of barley could be elucidated. Within 23 kb, three copies of the Ty3/gypsy-like retroelement cereba were present. Two elements of approximately 7 kb, arranged in tandem, include long terminal repeats (LTRs) (approximately 1 kb) similar to the rice centromeric retrotransposon RIRE 7 and to the cereal centromeric sequence family, the primer binding site, the complete polygene flanked by untranslated regions, as well as a polypurine tract 5' of the downstream LTR. The high density (approximately 200 elements/centromere) and completeness of cereba elements and the absence of internally deleted elements and solo LTRs from the BAC 7 insert represent unique features of the barley centromeres as compared to those of other cereals. Obviously, the conserved cereba elements together with barley-specific G+C-rich satellite sequences constitute the major components of centromeric DNA in this species.
Collapse
Affiliation(s)
- S Hudakova
- Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany
| | | | | | | | | | | | | |
Collapse
|