MASiVEdb: the sirevirus plant retrotransposon database

J 2012

MASiVEdb: the sirevirus plant retrotransposon database

BOUSIOS, A.; E. MINGA; N. KALITSOU; M. PANTERMALI; A. TSABALLA et. al.

Základní údaje

Originální název

MASiVEdb: the sirevirus plant retrotransposon database

Autoři

BOUSIOS, A.; E. MINGA; N. KALITSOU; M. PANTERMALI; A. TSABALLA a Nikos DARZENTAS

Vydání

BMC Genomics, London, BioMed Central Ltd, 2012, 1471-2164

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

30200 3.2 Clinical medicine

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 4.397

Kód RIV

RIV/00216224:14740/12:00062999

Organizační jednotka

Středoevropský technologický institut

DOI

https://doi.org/10.1186/1471-2164-13-158

UT WoS

000307361500001

Klíčová slova anglicky

sirevirus plant; database

Štítky

ok, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 11. 4. 2013 12:35, Olga Křížová

Anotace

V originále

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.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

EE2.3.20.0045, projekt VaV

Název: Podpora profesního růstu a mezinárodní integrace výzkumných týmů v oblasti molekulární medicíny

Citovat

BOUSIOS, A.; E. MINGA; N. KALITSOU; M. PANTERMALI; A. TSABALLA a Nikos DARZENTAS. MASiVEdb: the sirevirus plant retrotransposon database. BMC Genomics. London: BioMed Central Ltd, 2012, roč. 13, Apr, s. "nestránkováno", 10 s. ISSN 1471-2164. Dostupné z: https://doi.org/10.1186/1471-2164-13-158.

@article{1082998,
   author = {Bousios, A. and Minga, E. and Kalitsou, N. and Pantermali, M. and Tsaballa, A. and Darzentas, Nikos},
   article_location = {London},
   article_number = {Apr},
   doi = {https://doi.org/10.1186/1471-2164-13-158},
   keywords = {sirevirus plant; database},
   language = {eng},
   issn = {1471-2164},
   journal = {BMC Genomics},
   title = {MASiVEdb: the sirevirus plant retrotransposon database},
   url = {http://www.biomedcentral.com/1471-2164/13/158},
   volume = {13},
   year = {2012}
}

TY  - JOUR
ID  - 1082998
AU  - Bousios, A. - Minga, E. - Kalitsou, N. - Pantermali, M. - Tsaballa, A. - Darzentas, Nikos
PY  - 2012
TI  - MASiVEdb: the sirevirus plant retrotransposon database
JF  - BMC Genomics
VL  - 13
IS  - Apr
SP  - "nestránkováno"
EP  - "nestránkováno"
PB  - BioMed Central Ltd
SN  - 14712164
KW  - sirevirus plant
KW  - database
UR  - http://www.biomedcentral.com/1471-2164/13/158
L2  - http://www.biomedcentral.com/1471-2164/13/158
N2  - 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.
ER  -

BOUSIOS, A.; E. MINGA; N. KALITSOU; M. PANTERMALI; A. TSABALLA a Nikos DARZENTAS. MASiVEdb: the sirevirus plant retrotransposon database. \textit{BMC Genomics}. London: BioMed Central Ltd, 2012, roč.~13, Apr, s.~''nestránkováno'', 10 s. ISSN~1471-2164. Dostupné z: https://doi.org/10.1186/1471-2164-13-158.

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