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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]