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 | Â | |||||||||
C3H1 | Potri.006G033300 | 23 | 5 | Exon | 347 | 118 | 63 | 40 | 0 | 6 |
Intron | 0 | / | / | / | / | Â | ||||
C4H | Potri.013G157900 | 13 | 6 | Exon | 609 | 76 | 16 | 21 | 0 | 3 |
Intron | 0 | / | / | / | / | Â | ||||
CesA2 | Potri.005G194200 | 22 | 4 | Exon | 244 | 53 | 20 | 20 | 0 | 0 |
Intron | 87 | 195 | 92 | 11 | 2 | Â | ||||
Pal1 | Potri.006G126800 | 20 | 6 | Exon | 474 | 99 | 46 | 40 | 0 | 0 |
Intron | 0 | / | / | / | / | Â | ||||
CesA1 | Potri.002G257900 | 20 | 6 | Exon | 629 | 68 | 11 | 38 | 0 | 2 |
Intron | 130 | 208 | 146 | 31 | 3 | Â | ||||
Knat7 | Potri.001G112200 | 17 | 2 | Exon | 120 | 25 | 8 | 8 | 0 | 0 |
Intron | 95 | 284 | 221 | 42 | 3 | Â | ||||
Kor1 | Potri.003G151700 | 23 | 5 | Exon | 192 | 63 | 10 | 36 | 0 | 0 |
Intron | 117 | 179 | 111 | 17 | 0 | Â | ||||
SAD | Potri.016G078300 | 15 | 4 | Exon | 395 | 142 | 78 | 30 | 1 | 28 |
Intron | 19 | 158 | 0 | 158 | 0 | Â | ||||
B) COMBINED RESULTS (from direct sequencing and cloning) | Â | |||||||||
CesA1 | Potri.002G257900 | 20 | 6 | Exon | 629 | 107 | 33 | 54 | 0 | 14 |
Intron | 130 | 315 | 177 | 46 | 8 | Â | ||||
Knat7 | Potri.001G112200 | 17 | 2 | Exon | 372 | 70 | 38 | 30 | 0 | 13 |
Intron | 392 | 209 | 117 | 56 | 15 | Â | ||||
Kor1 | Potri.003G151700 | 23 | 5 | Exon | 319 | 94 | 38 | 34 | 0 | 19 |
Intron | 438 | 201 | 98 | 23 | 11 | Â | ||||
SAD | Potri.016G078300 | 15 | 4 | Exon | 582 | 165 | 93 | 24 | 1 | 38 |
Intron | 217 | 475 | 207 | 69 | 4 | Â | ||||
C) CLONING | Â | |||||||||
4CL2 | Potri.019G049500 | 7 | 2 | Exon | 249 | 116 | 48 | 8 | 0 | 20 |
Intron | 289 | 325 | 83 | 35 | 14 | Â | ||||
GA-20 | Potri.015G134600 | 6 | 2 | Exon | 620 | 176 | 58 | 105 | 0 | 27 |
Intron | 290 | 462 | 117 | 210 | 31 | Â | ||||
CAD | Potri.009G095800 | 7 | 2 | Exon | 439 | 125 | 96 | 16 | 1 | 34 |
Intron | 436 | 273 | 128 | 76 | 21 | Â | ||||
Mybr2r3 | Potri.015G033600 | 6 | 2 | Exon | 351 | 117 | 23 | 26 | 1 | 11 |
 |  |  |  | Intron | 259 | 228 | 108 | 31 | 11 |  |