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MASiVEdb: the Sirevirus Plant Retrotransposon Database
Alexandros Bousios1, Evangelia Minga, Nikoleta Kalitsou
1Institute of Agrobiotechnology, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece. alexandros.bousios@gmail.com
BMC Genomics
|May 2, 2012
Summary
We developed MASiVEdb, a comprehensive database of Sireviruses, to aid in understanding their impact on plant genome evolution. This resource catalogs over 16,000 intact Sireviruses across 11 plant genomes, offering detailed structural and evolutionary insights.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Sireviruses are ancient LTR retrotransposons that have extensively colonized plant genomes, particularly grasses.
- They significantly contribute to the structure and evolution of plant genomes, as exemplified by their substantial presence in the maize genome.
- Understanding Sirevirus dynamics is crucial for plant genome composition and organization studies.
Purpose of the Study:
- To create a comprehensive and systematic resource for Sireviruses in plants, named MASiVEdb.
- To facilitate the identification and annotation of transposable elements in plant sequencing projects.
- To aid research into the impact of Sireviruses on plant genome evolution.
Main Methods:
- Utilized an updated MASiVE algorithm, designed for identifying Sireviruses based on conserved genome structure.
- Analyzed 11 fully-sequenced plant genomes to discover and catalog Sireviruses.
- Populated MASiVEdb with data on 16,243 intact Sireviruses, including coordinates, insertion age, and structural/gene complement analysis.
Main Results:
- MASiVEdb contains data on 16,243 intact Sireviruses, totaling over 158Mb, from 11 plant genomes.
- The database provides curated details on Sirevirus structure, gene content, insertion age, and coordinates.
- Includes tools for sequence similarity detection, visualization, coding domain discovery, and phylogenetic analysis.
Conclusions:
- MASiVEdb is the most comprehensive Sirevirus directory available, complementing existing transposable element catalogs.
- It offers valuable insights into the role of Sireviruses in host genome evolution.
- Future improvements include phylogenetic mapping, inclusion of fragments/solo LTRs, and integration of data from new genomes.
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