Table 2.
Total numbers of polymorphisms found in RNAseq and confirmed in bait capture DNAseq of 124 accessions for the 21 target U. ruziziensis genes
| Type | Effects | ||||||
|---|---|---|---|---|---|---|---|
| Gene | snp/mnp | Indel | Complex | Low | Moderate | High | |
| Cell wall genes | Ur.4CL | 200 | 0 | 44 | 186 | 58 (N: 15) | 0 |
| Ur.4CL_p1 | 195 | 3 | 39 | 169 | 67 (N: 17) | 1 | |
| Ur.BAHD01 | 146 | 1 | 33 | 144 | 35 (N: 5) | 1 | |
| Ur.BAHD05 | 183 | 0 | 29 | 159 | 53 (N: 19) | 0 | |
| Ur.CAD | 109 | 0 | 15 | 100 | 24 (N: 6) | 0 | |
| Ur.CAD_p1 | 117 | 1 | 17 | 88 | 46 (N: 11) | 1 | |
| Ur.CCoAOMT | 81 | 1 | 6 | 72 | 15 (N: 7) | 1 | |
| Ur.CCoAOMT_p1 | 49 | 0 | 22 | 64 | 7 (N: 3) | 0 | |
| Ur.CCR | 76 | 1 | 12 | 74 | 15 (N: 4) | 0 | |
| Ur.CGI58 | 54 | 0 | 14 | 39 | 29 (N: 7) | 0 | |
| Ur.CGI58_p1 | 68 | 0 | 15 | 47 | 35 (N: 11) | 1 | |
| Ur.COMT | 104 | 0 | 26 | 108 | 22 (N: 8) | 0 | |
| Lipid genes | Ur.GT43A | 169 | 0 | 30 | 159 | 40 (N: 13) | 0 |
| Ur.PXA1 | 284 | 0 | 42 | 228 | 97 (N: 26) | 1 | |
| Ur.PXA1-like | 337 | 0 | 21 | 228 | 130 (N: 50) | 0 | |
| Ur.SDP1 | 236 | 2 | 32 | 169 | 99 (N: 33) | 2 | |
| Ur.SDP1-like | 234 | 5 | 28 | 181 | 82 (N: 8) | 4 | |
| Ur.TGD1 | 81 | 0 | 12 | 78 | 15 (N: 3) | 0 | |
| Ur.TGD2 | 71 | 0 | 7 | 51 | 27 (N: 10) | 0 | |
| Ur.TGD3 | 118 | 0 | 17 | 90 | 45 (N: 0) | 0 | |
| total | 2912 | 14 | 461 | 2434 | 941 (N: 256) | 12 |
Genes are classified by type or predicted effect on protein. Type ‘snp/mnp’ includes SNPs and a small number of contiguous multiple nucleotide polymorphisms in the same haplotype; ‘complex’ denotes a mixture of SNPs and indels. ‘Low’ effects are synonymous variants, ‘Moderate’ are missense, in-frame indels, start or stop lost, and ‘High’ are frameshift or stop gained, predicted to cause loss of function (LOF). From moderate missense variants, counts of those predicted to be non-tolerated by the SIFT web server are shown ‘(N:)’.