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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