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Table 2 Summary of variants from all Juglandaceae genomes based on comparison with Juglans regia whole genome sequences

From: Whole genome based insights into the phylogeny and evolution of the Juglandaceae

Species

cp-SNPs

nr-SNPs

cp-Indels

Ts/Tv ratio

Mapped %

Heterozygosity

Homozygosity

Het-ratio %

Alfaropsis roxburghiana

1959

215,357

166

1.17/1.66

55.74

10,655

204,702

4.94

Carya cathayensis

1131

253,730

288

1.04/1.43

53.16

9,006

244,724

3.54

Carya hunanensis

1066

275,372

241

1.14/1.45

84.00

21,179

254,193

7.69

Carya illinoensis

1100

761,308

268

1.05/2.28

44.90

263,845

497,463

34.65

Carya kweichwensis

1102

326,824

24

1.09/1.43

66.91

23,680

303,144

7.24

Carya sinensis

1041

344,322

5

1.01/1.56

69.18

26,548

325,860

6.88

Cyclocarya paliurus

676

483,874

9

0.77/1.43

56.99

40,571

443,303

8.38

Juglans ailantifolia

433

443,059

134

1.02/1.61

37.64

21,704

421,355

4.89

Juglans cathayensis

458

1,143,008

23

1.05/1.61

45.01

120,312

1,022,696

10.52

Juglans cinerea

482

1,014,615

109

0.99/1.64

71.72

80,304

934,311

7.91

Juglans hindsii

376

361,913

46

1.12/1.43

68.84

17,962

343,951

4.96

Juglans hopeiensis

368

990,423

26

0.83/1.82

61.78

540,892

449,531

54.61

Juglans major

472

943,553

15

0.93/1.65

84.57

73,817

869,736

7.82

Juglans mandshurica

455

1,059,545

32

0.97/1.63

92.58

110,349

9,49,196

10.41

Juglans microcarpa

374

949,180

106

1.23/1.66

98.11

111,259

837,921

11.72

Juglans regia

0

742,382

0

0.00/2.29

96.69

225,592

516,790

30.38

Juglans sigillata

6

1,051,470

2

0.20/2.29

46.02

421,420

630,050

40.07

Juglans nigra

478

682,382

3

0.94/1.66

69.12

166

1871

8.14

Platycarya strobilacea

1465

319,852

22

1.33/1.49

97.71

39,263

280,589

12.27

Pterocarya delavayi

495

686,705

123

1.09/1.43

64.74

45,839

640,866

6.67

Pterocarya fraxinifolia

506

621,411

103

1.11/1.42

23.93

37,402

584,009

6.01

Pterocarya hupehensis

505

515,964

75

1.17/1.45

36.97

35,974

479,990

6.97

Pterocarya insignis

506

589,290

116

1.00/1.43

98.45

41,877

547,413

7.10

Pterocarya macroptera

513

430,744

153

1.11/1.42

72.96

23,897

406,847

5.54

Pterocarya stenoptera

483

653,976

28

1.12/1.39

86.64

53,662

600,314

8.20

Pterocarya tonkinensis

487

547,524

133

1.05/1.44

68.29

33,764

513,760

6.16

Rhoiptelea chiliantha

2126

202,314

179

1.21/1.71

58.22

11,023

196,822

4.78

  1. cp-SNPs the number of SNPs of chloroplast genomes, nr-SNPs the number of SNPs of whole genome resequencing, cp-Indels the number of Indels of chloroplast genomes, Ts/Tv ratio the transition/transversion ratio based on chloroplast genomes and whole genome resequencing data respectively, Mapped the mapped ratio of whole genome resequencing data used common walnut genome sequence data, Het-ratio the Heterozygosity ratio of each samples based on the whole genome resequencing data
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BMC Ecology and Evolution

ISSN: 2730-7182

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