Table 1 Summary statistics of screening of the small-insert partial genomic library of robusta coffee for putative SSR positive clones/sequences and SSRs.
Summary of Screening/sequencing | |
|---|---|
Total Number of clones screened (X) | 15,744 |
Number of clones selected and sequenced after screening | 446 (2.83% of X) |
Number of good quality sequences obtained | 199 (1.27% of X) |
Total number of SSR containing clones (Y) | 76 (0.48% of X) |
Number of sequences containing more than 1 SSR core | 26 (34.21% of Y) |
Number of sequences containing compound SSRs | 15 (12.93% of Y) |
Number of SSR+ sequences used for primer design/synthesis | 58 (0.37% of X) |
Number of working primer pairs | 53 (0.34% of X) |
Average size of the cloned/sequenced insert | 773.5 bp |
Haploid genome size of C. canephora [13] | 809 Mb |
Estimated genome screened (number of library clones x. average insert size) | 12.2 Mb (1.5 % genome equivalent) |
C. canephora genome sequenced (good quality sequences × average insert size) | 0.15 Mb (0.01 % of robusta genome) |
Summary of SSRs identified in the library | |
Number of non-targeted MNRs of minimum 12-mer length (a) | 24 (0.15% of X) |
Number of targeted DNRs having a minimum of 6 repeats (b) | 46 (0.29% of X) |
Number of non-targeted DNRs having a minimum of 6 repeats (c) | 10 (0.06% of X) |
Total number of DNRs (b+c) | 56 (0.36% of X) |
Number of targeted TNRs having a minimum of 5 repeats (d) | 30 (0.19% of X) |
Total number of DNRs and TNRs (b+c+d) | 86 (0.55% of X) |
Total Number of non-targeted HO-NRs having a minimum of 5 repeats (e) | 6 (0.04% of X) |
Total Number of DNRs, TNRs and HO-NRs (b+c+d+e) | 92 (0.58% of X) |
Total Number of SSRs (a+b+c+d+e) | 116 (0.73% of X) |