Skip to main content

Table 1 Number of ESTs, clusters, SSRs and polymorphic SSRs of chicken, rice, Arabidopsis, Brassica, potato and tomato

From: Large-scale identification of polymorphic microsatellites using an in silico approach

  chicken rice Arabidopsis Brassica potato tomato
ESTs 599,330 1,211,078 734,275 163,750 219,765 249,794
Non-redundant sequences1 283,434 493,818 224,994 58,260 72,381 54,182
Clusters1 44,654 35,154 33,052 20,468 25,228 21,229
Singletons1 238,780 458,664 191,942 37,792 47,153 32,953
ESTs with SSRs (%)2 74,297 (12%) 336,569 (28%) 127,757 (17%) 14,968 (9%) 29,481 (13%) 28,728 (11%)
SSRs Non-redundant sequences (%)2 40,020 (14%) 133,861 (27%) 38,096 (17%) 13,251 (23%) 10,537 (15%) 7,163 (13%)
Singletons with SSRs (%)2 31,119 (13%) 118,649 (26%) 29,843 (16%) 7,328 (19%) 5,717 (12%) 3,261 (10%)
SSR in clusters (%)2 8,901 (20%) 15,212 (43%) 8,253 (25%) 5,923 (29%) 4,820 (19%) 3,902 (18%)
Polymorphic SSRs3 (%) 1,724 (19%) 2,646 (17%) 1,248 (15%) 997 (17%) 1,080 (22%) 265 (7%)
Polymorphic SSRs with primers (%) 1,667 (97%) 2,555 (97%) 1,163 (93%) 937 (94%) 1,053 (97%) 263 (99%)
% polymorphism in long SSRs4 15% 11% 12% 13% 17% 6%
% polymorphism in short SSRs5 36% 23% 30% 40% 46% 14%
  1. 1 clusters and singletons were produced using CAP3 with 95% similarity for 100 nucleotides overlaps; 'non-redundant sequences' includes clusters and singletons
  2. 2 SSR detected by Sputnik [13] using default settings
  3. 3polymorphic SSRs detected by PolySSR (settings used are described in Materials and Methods); % = percentage of SSRs in clusters that are polymorphic SSRs.
  4. 4 long polymorphic SSRs are SSRs with at least 10 repeats for dinucleotide SSRs, 6 repeats for trinuleotide SSRs, 5 repeats for tetra-, penta- or hexanucleotide SSRs; % = percentage of polymorphic SSRs in long SSRs;
  5. 5short polymorphic SSRs are SSRs with a maximum of 5 repeats for dinucleotide SSRs, and 4 repeats for tri-, tetra-, penta- and hexanucleotide SSRs; the minimum number of repeats was in this case set to 3 for all SSR types; % = percentage of polymorphic SSR in short SSRs