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Table 5 Comparative sequence analysis of Upland cotton BESs with the D genome sequence of G. raimondii (DOE Joint Genome Institute, Cotton D V1.0, http://http://www.phytozome.net/cotton.php )

From: Construction of a plant-transformation-competent BIBAC library and genome sequence analysis of polyploid Upland cotton (Gossypium hirsutumL.)

Inquired upland cotton BESs

Criteria of the analysis

Sequence similarity

 

Continuous MinMatch (bp)

100

100

100

100

100

100

All AD-subgenome BESs

Sequence identity (%)

100

95

90

80

70

60

(No. of BESs = 9,711; total sequence length = 3,842,009 bp)

No. of BESs aligned

57

4,587

6,588

7,118

7,257

7,277

 

% of BESs aligned

0.59

47.24

67.84

73.30

74.73

74.94

 

Total sequence length of BESs aligned to the raimondii sequence (bp)

15,539

1,367,385

1,960,413

2,048,311

1,996,820

1,975,511

 

% of sequence length of BESs aligned to the raimondii sequence

0.41

35.59

51.10

53.31

51.95

51.42

 

Continuous MinMatch (bp)

100

100

100

100

100

100

A-subgenome-specific BESs

Sequence identity (%)

100

95

90

80

70

60

(No. of BESs = 418; total sequence length = 169,533 bp)

No. of BESs aligned

7

205

294

310

317

317

 

% of BESs aligned

1.67

49.04

70.33

74.16

75.84

75.84

 

Continuous MinMatch (bp)

100

100

100

100

100

100

D-subgenome-specific BESs

Sequence identity (%)

100

95

90

80

70

60

(No. of BESs = 184; total sequence length = 71,410 bp)

No. of BESs aligned

1

88

128

136

139

139

 

% of BESs aligned

0.54

47.83

69.57

73.91

75.54

75.54