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Table 1 Characterization of seven SSH libraries

From: Characterization of resistance to pine wood nematode infection in Pinus thunbergiiusing suppression subtractive hybridization

SSH librariesa

Total ESTs sequences

Length of sequence (bp)

Contigs

Singletons

Non-redundant ESTs

Redundant (%)

Unique (%)

Hit rate using the BLAST program in Blast2GO tool (%)b

Hit rate using the local BLAST program (%)

Automatic annotation rate (%)

Manual annotation rate (%)d

Total annotation rate (%)

Tester

Drivers

       

blastx to nrDB1)

tblastx to nrDB2)

tblastx to estDB3)

blastn to estDB4)

no hit

blastn to PGIC

   

R_1dpi

S_1dpi

437

102-775

14

406

420

3.9

96.1

71.0

17.1

7.0

3.8

1.1

97.1

65.8

9.7

75.5

S_1dpi

R_1dpi

449

108-777

52

214

266

40.8

59.2

79.7

10.8

7.5

1.6

0.4

96.9

73.3

6.9

80.2

R_3dpi

S_3dpi

455

102-775

43

344

387

14.9

85.1

72.4

15.7

7.5

3.5

0.9

97.6

65.1

10.6

75.7

S_3dpi

R_3dpi

440

101-760

43

272

315

28.4

71.6

81.1

12.2

4.1

1.4

1.2

96.4

77.0

7.4

84.4

R_7dpi

S_7dpi

528

100-767

41

394

435

17.6

82.4

79.5

10.3

6.9

3.0

0.3

98.0

74.1

7.8

81.9

S_7dpi

R_7dpi

508

104-780

48

90

138

72.8

27.2

91.8

5.9

1.7

0.6

0.0

99.4

84.7

6.3

91.0

R_14dpi

S_7dpi

482

106-764

52

299

351

27.2

72.8

73.8

15.3

7.2

3.3

0.4

98.0

66.7

11.0

77.7

  1. a R = resistant, S = susceptible, dpi = days post-inoculation
  2. b The edited sequences in each library were compared to the NCBI database using the following algorithms: 1) blastx program against the non-redundant protein database of NCBI with a threshold value of e-6, 2) tblastx program against the nucleotide database of NCBI with a threshold value of e-6, 3) tblastx program against the EST database of NCBI with a threshold value of e-6, 4) blastn program against the EST database of NCBI with a threshold value of e-10
  3. c The edited sequences in each library were compared to the PGI database (DFCI Pine Gene Index, release 8.0) using the blastn program with a threshold value of e-10
  4. d Manual annotation based on the annotated gene information in the PGI database