BMC Genomics 2006, 7:245 http://www.biomedcentral.com/1471-2164/7/245 Table 1: Number and distribution of SSRs in consensus EST and transcript sequences. Total number of sequences examined Total size covered by examined sequences (Mb) Total number of SSRs identified Number of SSR-containing sequences: Number of sequences containing more than one SSR Total relative abundance (SSRs/Mb) Total relative density (bp/Mb) Perfect a Within a compound formation b P. infestans 25965 12.573 1660 1466 (88.31 %) 194 (11.69 %) 1466 (5.65 %) 152 (0.59 %) 132.02 1803.66 Organism P. sojae 19276 29.249 5938 4859 (81.83 %) 1079 (18.17%) 4265 (22.13 %) 1142 (5.92 %) 203.01 2819.08 P. ramorum 16066 22.097 2838 2554 (89.99 %) 284 (10.01 %) 2320 (14.44 %) 377 (2.35 %) 128.43 1723.24 Analysis was based on the MISA script, which identified di- to hexa-nucleotide repeat motifs (perfect and compound microsatellites) that are at least 12 bases in length. a Perfect microsatellites consist of a single repeat motif and are not interrupted anywhere by a base that does not fit the repeat structure b Compound microsatellites consist of two or more adjacent microsatellites with different repeat types Since the most common motifs in the three organisms analyzed were trinucleotide repeats, we attempted to identify the amino acid(s) encoded by these. Twenty sequences from each organism, containing the most com- mon triplet in each case, were randomly selected and used for ORF analyses. The most probable open reading frame and consequently the location of the SSR in this reading frame were determined. The triplets analyzed (in their canonical forms and possible variations) were (AGC)n for P. sojae and P. ramorum and (AAG)n for P. infestans respec- tively. In P. sojae and P. ramorum, CAG (glutamine) was predominant at 80% and 60% respectively, followed by AGC (serine) at 10% and 35%, and finally GCA (alanine) at 10% and 5%. In P. infestans, GAG (glutamic acid) was predominant at 50%, followed by AAG (lysine) at 30% and finally CTT (leucine) at 10%. These results were fur- ther investigated for correlations between the amino acids encoded by the trinucleotide repetitions and the codon usage preferences reported for each organism in the Codon Usage Database from the Kazuka DNA Research Institute [38]. In all cases, the triplets analyzed encoded for amino acids that were normally overrepresented in the corresponding organism. The differences detected between P. infestans and P. sojae-P.ramorum emerging in our trinucleotide analysis were also corroborated by codon usage frequencies. Table 2: Percentage, relative abundance and relative density of SSRs in the P. infestans, P. sojae, and P. ramorum sequence sets. Motif length Count Percentage Relative abundance Relative density 10.82 80.25 26.64 5.09 9.23 2.67 166.26 14.84 3.01 16.24 1.27 106.71 9.01 1.13 10.32 165.91 1054.66 328.01 77.55 177.53 34.60 2214.72 187.22 47.35 335.19 15.39 1377.36 108.79 16.97 204.74 Page 4 of 11 (page number not for citation purposes) P. infestans P. sojae P. ramorum di tri tetra penta hexa di tri tetra penta hexa di tri tetra penta hexa 136 1009 335 64 116 78 4863 434 88 475 28 2358 199 25 228 8.19 60.78 20.18 3.86 6.99 1.31 81.90 7.31 1.48 8.00 0.99 83.09 7.01 0.88 8.03 a Percentage was calculated for each organism on the basis of the corresponding total SSRs count b Relative abundance is defined as the total number of SSR s per Mb of sequence analyzed c Relative density is defined as a the total sequence length (bp) contributed by each SSR per Mb of DNA of total sequence analyzed