Table 3 The characteristics of TEs in the genomes of XYXZ, R498, and Nipponbare

Class I: Retrotransposon

152,593,462

38.63%

293,791

150,737,098

38.55%

292,231

135,624,823

36.34%

309,239

LTR-Retrotransposon

142,183,026

35.99%

252,194

140,192,746

35.86%

250,822

124,237,591

33.29%

265,728

 LTR/Gypsy

89,538,544

22.67%

106,882

84,915,354

21.72%

106,875

71,753,076

19.22%

109,588

 LTR/Copia

18,783,908

4.75%

38,386

18,653,262

4.77%

37,029

20,886,614

5.60%

46,509

 LTR/Other

33,860,574

8.57%

106,926

36,624,130

9.37%

106,918

31,597,901

8.47%

109,631

Non-LTR Retrotransposon

10,410,436

2.64%

41,597

10,544,352

2.70%

41,409

11,387,232

3.05%

43,511

 SINE

880,763

0.22%

4482

1,005,769

0.26%

4644

929,204

0.25%

4559

 LINE

9,529,673

2.41%

37,115

9,538,583

2.44%

36,765

10,458,028

2.80%

38,952

Class II: DNA Transposon

71,167,668

18.02%

287,904

70,466,702

18.02%

284,836

69,813,358

18.70%

277,817

 EnSpm/CACTA

2,860,768

0.72%

5146

2,624,568

0.67%

5080

3,760,181

1.01%

5443

 hAT

5,738,901

1.45%

22,713

4,539,718

1.16%

16,976

6,377,976

1.71%

25,049

 Harbinger

250,601

0.06%

957

268,432

0.07%

1051

247,626

0.07%

933

 Tc1/Mariner

10,260,759

2.60%

51,207

9,369,588

2.40%

49,076

8,890,174

2.38%

46,603

 MuDR

186,268

0.05%

809

173,445

0.04%

778

167,849

0.04%

749

 Helitron

3,320,855

0.84%

9233

3,410,449

0.87%

9754

3,571,714

0.96%

7947

 Other

48,549,516

12.29%

197,839

50,080,502

12.81%

202,121

46,797,838

12.54%

191,093

Unclassified

30,320

0.01%

265

27,697

0.01%

241

29,044

0.01%

253

Total content

214,682,827

54.34%

588,740

209,087,702

53.48%

595,353

192,700,449

51.63%

584,921

Total Genome Length

395,040,224

390,983,850

373,245,519