MASiVEdb @ the BAT cave

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17,903 Sireviruses in 37 hosts

Sireviruses is an exclusive-to-plants LTR retrotransposon genus of the Copia superfamily, characterized by its unique genome structure peppered with an envelope-like gene and intriguing highly conserved motifs in key domains. Sireviruses have extensively proliferated within plant genomes, often comprising the vast majority of Copia elements, as is the case in maize (~90% of Copia complement, ~20% of the genome) and sorghum (~70% of Copia complement). As evidence accumulate on the fundamental role of Sireviruses on the organization, function and evolution of plant genomes, we developed MASiVEdb, a collective resource of Sirevirus populations, aiming to assist in their further identification, annotation, and masking in plant sequences, and of course to support research into the evolutionary dynamics and impact of transposable elements across the Plant kingdom.

MASiVEdb is produced by deploying MASiVE, our tool for Sirevirus discovery and analysis, on all available whole genome sequences of plants - for now. Genomes in which we discovered Sireviruses, basic information, and primary results, can be reviewed in the table below.

This gateway has been designed to be straightforward yet powerful. It has four large buttons: query (simple and advanced), batch retrieval, sequence search, and a download section. Sequence search has been implemented through the use of our LTRphyler tool (soon to be available) which combines other technologies and know-how. Help is provided at every page through the 'usage' link. Enjoy your stay, get in touch if you need to.



species common name code clade chr Sireviruses with ENV-like radar
Arabidopsis thalianathale cressAthaeudicot542
Brachypodium distachyonpurple false bromeBdismonocot52214
Fragaria vescastrawberryFveseudicot71
Glycine maxsoybeanGmaxeudicot2013371294
Lotus japonicuslotusLjapeudicot7282270
Oryza sativa indicariceOsatimonocot122514
Oryza sativa japonicariceOsatjmonocot129142
Sorghum bicolorsorghumSbicmonocot10522227
Theobroma cocoacacaoTcoceudicot107752
Vitis viniferagrape vineVvineudicot194945
Zea maysmaizeZmaymonocot1013833516
Arabidopsis lyratalyrate rockcressAlyreudicot81511
Cajanus cajanpigeonpeaCcajeudicot1181
Capsella rubellared shepherd's purseCrubeudicot8158
Citrullus lanatuswatermelonClaneudicot112
Gossypium raimondiicottonGraieudicot133
Malus domesticaappleMdomeudicot171
Medicago truncatulabarrel medicMtrueudicot8163162
Setaria italicafoxtail milletSitamonocot9377
Solanum lycopersicumtomatoSlyceudicot126711
Solanum tuberosumpotatoStubeudicot123415
Eucalyptus grandiseucalyptusEgraeudicot11930878
Musa acuminatabananaMacumonocot117013
Prunus persicapeachPpereudicot862
with scaffolds, data only in 'downloads'
Aquilegia coeruleaColorado blue columbineAcoeeudicot79139
Citrus clementinaclementineCcleeudicot89136126
Thellungiella halophilasalt cressThaleudicot24345
no detectable Sireviruses
Chlamydomonas reinhardtiiCreialgae
Ostreococcus lucimaricusOlucalgae
Populus trichocarpapoplarPtrieudicot
Brassica rapaturnip mustardBrapeudicot
Carica papayapapayaCpapeudicot
Cucumis sativuscucumberCsateudicot
Physcomitrella patensPpatmoss
Ricinus communiscastor bean plantRcomeudicot
Selaginella moellendorffiispikemossSmoelycophyte
Volvox carteriVcaralgae

news and updates

03.12.2015 | Sireviruses and their epigenetic war in maize has been published in Genome Research
31.08.2012 | We now cover a total of 37 host species (23 new)
01.05.2012 | MASiVEdb has been published in BMC Genomics
05.03.2012 | Sireviruses go live on MaizeGDB
13.12.2011 | Sireviruses soon to appear in MaizeGDB
30.06.2011 | MASiVEdb has been released


publications

A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response.
Bousios A, Diez CM, Takuno S, Bystry V, Darzentas N, Gaut BS
Genome Research 2015 (Epub ahead of print). [Pubmed]

Sirevirus LTR retrotransposons: phylogenetic miconceptions in the plant world.
Bousios A, Darzentas N.
Mobile DNA 2013, 4:9. [Pubmed]

MASiVEdb: the Sirevirus Plant Retrotransposon Database.
Bousios A, Minga E, Kalitsou N, Pantermali M, Tsaballa A, Darzentas N.
BMC Genomics 2012;13:158. [PubMed]
Please cite the above article when using data from MASiVEdb.

The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story.
Bousios A, Kourmpetis YA, Pavlidis P, Minga E, Tsaftaris A, Darzentas N.
Plant Journal 2011;69: 475-488. [PubMed]

MASiVE: Mapping and Analysis of SireVirus Elements in plant genome sequences.
Darzentas N, Bousios A, Apostolidou V, Tsaftaris A.
Bioinformatics 2010;26: 2452-2454. [PubMed]

Highly conserved motifs in non-coding regions of Sirevirus retrotransposons: the key for their pattern of distribution within and across plants?
Bousios A, Darzentas N, Tsaftaris A, Pearce SR.
BMC Genomics 2010;11:89. [PubMed]


acknowledgements

The sequence data for maize were downloaded from http://www.maizesequence.org/ (genome version ZmB73_RefGen_v2), for rice (japonica) from http://rgp.dna.affrc.go.jp/E/IRGSP/Build5/build5 (Build 5 release), for rice (indica) from http://rice.genomics.org.cn/rice/, for strawberry from http://www.strawberrygenome.org/ (assembly v1.0 - Build 8), for cacao from http://cocoagendb.cirad.fr/ (v1.0 pseudomolecules), for lotus from http://www.kazusa.or.jp/lotus/ (Build 2.5), for Arabidopsis from http://www.arabidopsis.org/ (TAIR10 genome release), for Ostreococcus from http://genome.jgi-psf.org/ (v2.0), and for sorghum (Phytozome internal identifier [PII] for the current genome release is 79), grapevine (PII 145), soybean (PII 109), brachypodium (PII 114), poplar (PII 156) and Chlamydomonas (PII 169) from http://www.phytozome.net/. All sequence data were downloaded on May 2011.

The sequence data of the species that were included in the first major update (31.08.12) were downloaded for Medicago truncatula from http://medicago.jcvi.org/cgi-bin/medicago/download.cgi (Mt3.5v5 Release), for tomato from http://solgenomics.net/organism/solanum_lycopersicum/genome (version SL2.40), for potato from http://solanaceae.plantbiology.msu.edu/pgsc_download.shtml (PGSC_DM_v3_2.1.10_pseudomolecules), for cucumber (genome v2) and watermelon (genome v1) from http://www.icugi.org/, for apple from http://www.rosaceae.org/projects/apple_genome (genome v1.0), for peach from http://www.rosaceae.org/projects/peach_genome/ (genome v1.0) for Ricinus communis from http://castorbean.jcvi.org/ (release 0.1 assembly), for pigeonpea from http://www.icrisat.org/gt-bt/iipg/Home.html, for banana from http://banana-genome.cirad.fr/, and for Arabidopsis lyrata (PII 107), Setaria italica (PII 164), Brassica rapa (PII 197), Physcomitrella patens (PII 152), Volvox carteri (PII 199), Selaginella moellendorffii (PII 91), Aquilegia coerulea (PII 195), eucalyptus (PII 201), clementine (PII 165) papaya (PII 113), Thellungiella halophila (PII 173), Capsella rubella (PII 183), and cotton (Gossypium_raimondii.main_genome.scaffolds.fasta) from http://www.phytozome.net/.

The genomes of peach, watermelon, Aquilegia coerulea, eucalyptus, clementine, Thellungiella halophila, Capsella rubella and cotton are under reserved analysis, and, thus, no whole-genome analyses should be published before the primary manuscripts of the consortia are published.

A tab-delimited file for mapping the MASiVEdb sequence label used in the Sirevirus ID (e.g. Sbic_chr_10 in Sbic_chr_10-D-10263402) to the original sequence label in the above data is available here.


supported by CEITEC MU and project SuPReMMe, CERTH and projects co-funded by the GSRT, the Alexander S. Onassis Public Benefit Foundation

hosted at the Bioinformatics Analysis Team (BAT)