Skip to main content

Advertisement

Table 1 Variation for each gene region showing the P. trichocarpa gene models used as reference, the number of Salix genotypes and Populus species studied, the total number of SNPs detected, the number of SNPs within Salix and within Populus; the number of insertions/deletions

From: High levels of variation in Salix lignocellulose genes revealed using poplar genomic resources

Gene region P. trichocarpa reference(Phytozome gene model)a No.ofSalix genotypes studied No.ofPopulus species studied(See Table2) Predicted Exons/intronsa Studied length (bp) Total SNPs per kbpb SNPs withinSalix per kbpc SNPs withinPopulus per kbpc Total Indels Total non synonymous sites amongSalix per kbp
A) DIRECT SEQUENCING  
C3H1 Potri.006G033300 23 5 Exon 347 118 63 40 0 6
Intron 0 / / / /  
C4H Potri.013G157900 13 6 Exon 609 76 16 21 0 3
Intron 0 / / / /  
CesA2 Potri.005G194200 22 4 Exon 244 53 20 20 0 0
Intron 87 195 92 11 2  
Pal1 Potri.006G126800 20 6 Exon 474 99 46 40 0 0
Intron 0 / / / /  
CesA1 Potri.002G257900 20 6 Exon 629 68 11 38 0 2
Intron 130 208 146 31 3  
Knat7 Potri.001G112200 17 2 Exon 120 25 8 8 0 0
Intron 95 284 221 42 3  
Kor1 Potri.003G151700 23 5 Exon 192 63 10 36 0 0
Intron 117 179 111 17 0  
SAD Potri.016G078300 15 4 Exon 395 142 78 30 1 28
Intron 19 158 0 158 0  
B) COMBINED RESULTS (from direct sequencing and cloning)  
CesA1 Potri.002G257900 20 6 Exon 629 107 33 54 0 14
Intron 130 315 177 46 8  
Knat7 Potri.001G112200 17 2 Exon 372 70 38 30 0 13
Intron 392 209 117 56 15  
Kor1 Potri.003G151700 23 5 Exon 319 94 38 34 0 19
Intron 438 201 98 23 11  
SAD Potri.016G078300 15 4 Exon 582 165 93 24 1 38
Intron 217 475 207 69 4  
C) CLONING  
4CL2 Potri.019G049500 7 2 Exon 249 116 48 8 0 20
Intron 289 325 83 35 14  
GA-20 Potri.015G134600 6 2 Exon 620 176 58 105 0 27
Intron 290 462 117 210 31  
CAD Potri.009G095800 7 2 Exon 439 125 96 16 1 34
Intron 436 273 128 76 21  
Mybr2r3 Potri.015G033600 6 2 Exon 351 117 23 26 1 11
     Intron 259 228 108 31 11  
  1. aBased on P. trichocarpa v3 assembly retrieved from Phytozome (http://www.phytozome.net/poplar).
  2. b(No. total SNPs / length) × 1,000.
  3. c(No. SNPs within Salix or within Populus / length) × 1,000.
  4. Both direct sequencing and cloning techniques were used.