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Table 1 Characteristics of nuclear genome sequence in Dioscorea rotundata and other angiosperms

From: Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination

Feature

Value

D. rotundata (v0.1)

A. thaliana (TAIR10)

B. distachyon (v3.1)

O. sativa (v7_JGI 323)

Total length (Mbp)

594.23

119.67

271.16

374.47

GC (%)

35.83

36.06

46.40

43.57

Number of scaffolds (≥ 0 bp)

4723

7

10

14

Number of scaffolds (≥ 1000 bp)

4704

7

10

14

Largest scaffold (Mbp)

13.61

30.43

75.07

43.27

N50 (Mbp)

2.12

23.46

59.13

29.96

N75 (Mbp)

0.77

19.70

48.59

28.44

Number of Ns per 100 kb

282.45a

155.60

155.85

44.13

Ambiguous bases

1,413,029

Number of genes

26,198

27,416

34,310

42,189

Exons

 Number

158,059

141,044

154,104

178,353

 Average number per gene

6.03

5.14

4.49

4.25

 Total length (Mbp)

42.43

33.49

39.01

46.85

 Average size (bp)

268.43

237.46

253.15

262.70

 Average GC (%)

44.08

43.70

51.02

51.12

Introns

 Number

105,663

86,212

85,484

94,345

 Average number per gene

4.03

3.14

2.49

2.25

 Total length (Mbp)

83.12

17.87

47.70

53.34

 Average size (bp)

630.33

157.25

398.18

391.23

 Average GC (%)

32.37

32.45

38.29

37.20

Transposable elementsb

 % Total interspersed

46.07

13.32

37.39

44.40

 Total interspersed total length (Mbp)

274.51

15.94

101.39

166.27

 % Short interspersed nuclear elements (SINEs)

0.02

0.17

0.38

0.88

 SINEs total length (Mbp)

0.13

0.20

1.02

3.31

 % Long interspersed nuclear elements (LINEs)

2.43

1.07

2.91

1.29

 LINEs total length (Mbp)

14.46

1.29

7.90

4.83

 % Long terminal repeat (LTR) elements

22.82

6.35

19.31

21.09

 LTR elements total length (Mbp)

135.71

7.61

52.36

78.98

 % DNA elements

6.70

3.08

7.11

16.7

 DNA elements total length (Mbp)

39.83

3.69

19.27

62.82

 % Unclassified

14.20

2.64

7.68

4.36

 Unclassified total length (Mbp)

84.38

3.16

20.84

16.32

  1. aNumber of Ns per 100 kb using the D. rotundata broken scaffolds
  2. bTransposable elements were identified by masking the genomes using RepeatModeler and RepeatMasker, with the same parameters across all species