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Table 3 Abundance of Atlantys Elements in the Oryza

From: Rapid and Differential Proliferation of the Ty3-Gypsy LTR Retrotransposon Atlantys in the Genus Oryza

Species # hits Estimated LTRs copy # % RS Complete s-LTRs MBp % genome
O. rufipogon 33 2762 0.85 460 1842 8743000 1.99
O. nivara 33 2417 0.86 403 1611 7655500 1.71
O. glaberrima 43 2110 0.79 352 1406 6685000 1.87
O. punctata 114 7956 2.48 1326 5304 25194000 5.93
O. officinalis 244 16293 3.47 2716 10861 51599500 7.93
O. minuta 484 28055 3.31 4676 18703 88842500 7.90
O. alta 456 26466 4.62 4411 17644 83809000 8.31
O. australiensis 326 22583 3.31 3764 15055 71514500 7.41
O. brachyantha 11 579 0.33 97 385 1838500 0.51
O. granulata 254 18578 2.45 3096 12386 58827000 6.67
O. coarctata 175 11500 1.25 1917 7666 36420000 2.84
O. ridleyi 332 20929 1.95 3488 13953 66273500 5.17
O. sativa 22 1426 - 285 856 4989000 1.28
  1. # hits is the number of significant hits obtained in BlastN searches using the LTRs as queries; “Estimated LTRs copy #” is the estimated copy number of Atlantys LTRs in that genome when the equation proposed by Hawkins et al. [17] was used; “% RS” is the percentage of base pairs in each random sheared library when Atlantys LTRs were used in a RepeatMasker search; “Complete” is the estimated number of complete Atlantys element in that genome (see text for details); “s-LTRs” is the estimated number of Atlantys solo-LTRs in that genome (see text for details); “Mbp” is the amount of complete and s-LTRs was translated into Mbp (see text for details); “% Genome” is the estimated percentage of each genome constituted by Atlantys elements. Values for O. sativa refer to the average of 10 samples of 3,000 pseudorandom sequences each generated from the O. sativa var. japonica complete genome sequence [20]