TITLE

MASiVEdb: the Sirevirus Plant Retrotransposon Database

AUTHOR(S)
Bousios, Alexandros; Minga, Evangelia; Kalitsou, Nikoleta; Pantermali, Maria; Tsaballa, Aphrodite; Darzentas, Nikos
PUB. DATE
January 2012
SOURCE
BMC Genomics;2012, Vol. 13 Issue 1, p158
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: Sireviruses are an ancient genus of the Copia superfamily of LTR retrotransposons, and the only one that has exclusively proliferated within plant genomes. Based on experimental data and phylogenetic analyses, Sireviruses have successfully infiltrated many branches of the plant kingdom, extensively colonizing the genomes of grass species. Notably, it was recently shown that they have been a major force in the make-up and evolution of the maize genome, where they currently occupy ~21% of the nuclear content and ~90% of the Copia population. It is highly likely, therefore, that their life dynamics have been fundamental in the genome composition and organization of a plethora of plant hosts. To assist studies into their impact on plant genome evolution and also facilitate accurate identification and annotation of transposable elements in sequencing projects, we developed MASiVEdb (Mapping and Analysis of SireVirus Elements Database), a collective and systematic resource of Sireviruses in plants. Description: Taking advantage of the increasing availability of plant genomic sequences, and using an updated version of MASiVE, an algorithm specifically designed to identify Sireviruses based on their highly conserved genome structure, we populated MASiVEdb http://bat.infspire.org/databases/masivedb/) with data on 16,243 intact Sireviruses (total length >158Mb) discovered in 11 fully-sequenced plant genomes. MASiVEdb is unlike any other transposable element database, providing a multitude of highly curated and detailed information on a specific genus across its hosts, such as complete set of coordinates, insertion age, and an analytical breakdown of the structure and gene complement of each element. All data are readily available through basic and advanced query interfaces, batch retrieval, and downloadable files. A purpose-built system is also offered for detecting and visualizing similarity between user sequences and Sireviruses, as well as for coding domain discovery and phylogenetic analysis. Conclusion: MASiVEdb is currently the most comprehensive directory of Sireviruses, and as such complements other efforts in cataloguing plant transposable elements and elucidating their role in host genome evolution. Such insights will gradually deepen, as we plan to further improve MASiVEdb by phylogenetically mapping Sireviruses into families, by including data on fragments and solo LTRs, and by incorporating elements from newly-released genomes.
ACCESSION #
79964546

 

Related Articles

  • A Large Rearrangement Involving Genes and Low-Copy DNA Interrupts the Microcollinearity Between Rice and Barley at the Rph7 Locus. Brunner, S.; Keller, B.; Feuillet, C. // Genetics;Jun2003, Vol. 164 Issue 2, p673 

    Grass genomes differ greatly in chromosome number, ploidy level, and size. Despite these differences, very good conservation of the marker order (collinearity) was found at the genetic map level between the different grass genomes. Collinearity is particularly good between rice chromosome 1 and...

  • Evolutionary History of LTR Retrotransposon Chromodomains in Plants. Novikov, Anton; Smyshlyaev, Georgiy; Novikova, Olga // International Journal of Plant Genomics;2012, Vol. 2012, Special section p1 

    Chromodomain-containing LTR retrotransposons are one of the most successful groups of mobile elements in plant genomes. Previously, we demonstrated that two types of chromodomains (CHDs) are carried by plant LTR retrotransposons. Chromodomains from group I (CHD_I) were detected only in Tcn1-like...

  • Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants. Conte, Matthieu G.; Gaillard, Sylvain; Droc, Gaetan; Perin, Christophe // BMC Genomics;2008, Vol. 9, Special section p1 

    Background: Gene ortholog identification is now a major objective for mining the increasing amount of sequence data generated by complete or partial genome sequencing projects. Comparative and functional genomics urgently need a method for ortholog detection to reduce gene function inference and...

  • Phylogenetic analysis of Jarava (Poaceae, Pooideae, Stipeae) and related genera: testing the value of the awn indumentum in the circumscription of Jarava. Sclovich, Sergio; Giussani, Liliana; Cialdella, Ana; Sede, Silvana // Plant Systematics & Evolution;Jun2015, Vol. 301 Issue 6, p1625 

    Jarava, a genus of the tribe Stipeae with 31 American species, is considered polyphyletic. In previous phylogenetic analyses, despite a few species of Jarava were used, they were included in the Major American Clade (MAC) together with species of Achnatherum, Amelichloa and Nassella. The main...

  • Isolation, identification, and characterization of genomic LTR retrotransposon sequences from masson pine ( Pinus massoniana). Fan, Fuhua; Wen, Xiaopeng; Ding, Guijie; Cui, Bowen // Tree Genetics & Genomes;Oct2013, Vol. 9 Issue 5, p1237 

    Long terminal repeat (LTR) retrotransposons are ubiquitous in the plant kingdom and play an important role in plant genome evolution. Masson pine ( Pinus massoniana) is one of the most economically important forest trees. However, the masson pine genome is poorly understood. Conserved domains of...

  • NADP-Malate Dehydrogenase Gene Evolution in Andropogoneae (Poaceae): Gene Duplication Followed by Sub-functionalization. RONDEAU, P.; ROUCH, C.; BESNARD, G. // Annals of Botany;Dec2005, Vol. 96 Issue 7, p1307 

    • Background and Aims Plastid NADP-dependent malate dehydrogenase (MDH) catalyses the conversion of oxaloacetate to malate. In C4 plants, it is involved in photosynthetic carbon assimilation. In Poaceae, one NADP-MDH gene has been identified in rice (C3; Erhartoideae) and maize (C4;...

  • A phylogeographic study of the cosmopolitan genus Phragmites (Poaceae) based on AFLPs. Lambertini, C.; Gustafsson, M. H. G.; Frydenberg, J.; Lissner, J.; Speranza, M.; Brix, H. // Plant Systematics & Evolution;May2006, Vol. 258 Issue 3/4, p161 

    Within the genus Phragmites (Poaceae), the species P. australis (the common reed) is virtually cosmopolitan, and shows considerable variation in ploidy level and morphology. Genetic variation in Phragmites was studied using AFLPs, and analysed with parsimony and distance methods. Groups of P....

  • Gene rearrangement analysis and ancestral order inference from chloroplast genomes with inverted repeat. Feng Yue; Liying Cui; dePamphilis, Claude W.; Moret, Bernard M. E.; Jijun Tang // BMC Genomics;2008 Supplement 1, Vol. 9, Special section p1 

    Background: Genome evolution is shaped not only by nucleotide substitutions, but also by structural changes including gene and genome duplications, insertions, deletions and gene order rearrangements. The most popular methods for reconstructing phylogeny from genome rearrangements include GRAPPA...

  • MOLECULAR IDENTIFICATION OF Tinospora sinensis BY ITS2 SEQUENCE ANALYSIS. Khanapurkar, R. S.; Paul, Nilesh; Desai, D. M.; Lingojwar, D. P.; Raut, M. R.; Gangawane, A. K. // International Journal of Molecular Biology;2012, Vol. 3 Issue 2, p55 

    Intergenic spacer region 2 (ITS2) between 5.8S RNA and 28S RNA is well established genomic region for molecular identification of plant as potential universal barcode. The Present studies deals with molecular identification of Tinospora sinensis, by a unique ITS2 region. Briefly, the plant...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics