MASiVEdb: the Sirevirus Plant Retrotransposon Database

BMC Genomics

Table 1 Properties of the host species and their Sirevirus populations included in MASiVEdb

host species^a	common name	clade	genome size (Mb)^b	number of chr.	intact SVs	avg age (my)	withENV
Arabidopsis thaliana	thale cress	eudicot	116	5	4	0.95	2
Brachypodium distachyon	brome	monocot	262	5	22	1.97	14
Chlamydomonas reinhardtii	n/a	alga	99	17	0	n/a	0
Fragaria vesca	strawberry	eudicot	203	7	1	0.45	0
Glycine max	soybean	eudicot	915	20	1337	0.45	1294
Lotus japonicus	lotus	eudicot	291	7	282	0.35	270
Oryza sativa indica	rice	monocot	362	12	25	2.18	14
Oryza sativa japonica	rice	monocot	370	12	91	1.29	42
Ostreococcus lucimarinus	n/a	alga	13	21	0	n/a	0
Populus trichocarpa	poplar	eudicot	304	19	0	n/a	0
Sorghum bicolor	sorghum	monocot	633	10	522	0.80	227
Theobroma cocoa	cacao	eudicot	214	10	77	3.17	52
Vitis vinifera	grapevine	eudicot	414	19	49	1.73	45
Zea mays	maize	monocot	1969	10	13833	1.29	516
Total					16243	1.20	2476

^aThe chromosome sequence data for Arabidopsis were downloaded from http://www.arabidopsis.org/, for brachypodium, Chlamydomonas, soybean, poplar, sorghum and grapevine from http://www.phytozome.net/, for strawberry from http://www.strawberrygenome.org/, for lotus from http://www.kazusa.or.jp/lotus/, for rice (indica) from http://rice.genomics.org.cn/rice/, for rice (japonica) from http://rgp.dna.affrc.go.jp/E/IRGSP/Build5/build5, for Ostreococcus from http://genome.jgi-psf.org/, for cacao from http://cocoagendb.cirad.fr/, and for maize from http://www.maizesequence.org/; ^bThe genome sizes do not represent the real estimates for each species, but correspond to the cumulative Mb found in sequence files for chromosomes after removing unanchored contigs and scaffolds; chr, chromosome; SVs, Sireviruses; my, million years; ENV, envelope-like gene.

ISSN: 1471-2164