AAG/CTT ACG/CTG AGC/CGT ACC/GGT AGG/CCT AAC/GTT CCG/CGG AC/GT AG/CT ACT/ATG AAT/ATT AAAC/GTTT AAAT/ATTT AGT/ATC AT/AT P. infestans 258 158 128 114 86 68 67 55 54 53 52 50 36 25 23 15.54 9.52 7.71 6.87 5.18 4.10 4.04 3.31 3.25 3.19 3.13 3.01 2.17 1.51 1.39 AGC/CGT ACG/CTG AAG/CTT AGG/CCT CCG/CGG ACC/GGT AAC/GTT ACT/ATG AGCG/CGCT CG/CG AGGC/CCGT AGT/ATC ACCG/CTGG AAGG/CCTT ACGG/CCTG P. sojae 1318 964 833 710 554 215 134 99 70 46 33 32 29 28 28 BMC Genomics 2006, 7:245 http://www.biomedcentral.com/1471-2164/7/245 Table 3: Most common repeat motifs identified from perfect and compound microsatellites in the three oomycetes analyzed. Motif a Count Percentage Motif Count Percentage Motif Count Percentage P. ramorum AGC/CGT ACG/CTG AAG/CTT AGG/CCT CCG/CGG ACC/GGT AAC/GTT ACT/ATG AGCG/CGCT ACGC/CGTG CG/CG ACCG/CTGG ACCACG/CTGGTG AGT/ATC AGCC/CGGT 630 527 383 315 220 131 74 64 49 27 23 23 15 14 14 22.20 16.23 14.03 11.96 9.33 3.62 2.26 1.67 1.18 0.77 0.56 0.54 0.49 0.47 0.47 2500,00 2000,00 ) b M /(pb 1500,00 y t i s n e ed 1000,00 v i t a l e R 500,00 0,00 22.20 18.57 13.50 11.10 7.75 4.62 2.61 2.26 1.73 0.95 0.81 0.81 0.53 0.49 0.49 P. infestans P. sojae P. ramorum a The same constraints on minimum length cited for Table 1 were used. Repeats containing motifs between 7 and 14 bp were scarce in the three oomycetes transcriptome analyzed, accounting for less than 1% of the total number of SSRs. They did not merit further attention in our study because of their low abundance. Regarding SSR lengths, we found that di-, tetra- and penta-nucleotide motif types did not exceed 30 bp (Table 4), while tri and hexanucleotides were clearly longer in all organisms. Although P. sojae had the longest SSR for di-, tetra-, penta- and hexa-nucleotide repeat types, longer than reported for other organisms (Karaoglu et al., 2004), only a very few of these lengths can be considered "long microsatellites" (> 15 repetitions [39]). The motif sequences of the longest SSRs are not shared among organisms, indicating that this factor is independent in each species. Thus, our results suggest that long SSRs are absent from these consensus EST or tran- scripts sequences. The number of repeats found in SSR loci ranged from 3 to 33, from 3 to 32 and from 3 to 15 in P. infestans, P. sojae and P. ramorum, respectively. Most SSR loci showed seven repeats or less (96% P. infestans, 98% P. sojae and 99%P. ramorum), with a repeat number of four being the most common in all species (Fig. 3). SSRs in pathogenicity factors In total, 136, 318 and 171 sequences corresponding to pathogenicity factors or annotated as putatively involved in pathogenicity were selected for P. infestans, P. sojae and 180,00 160,00 ) 140,00 b M /s120,00 R S (e100,00 S c n ad 80,00 n u a b 60,00 e v i t lea 40,00 R 20,00 0,00 P. infestans P. sojae P. ramorum di tri penta hexa tetra Repeat type di tri penta hexa tetra Repeat type aRFneigdlautrivaeen1sacbruipntdasneqceueonfcSeS RsestasminotnhgeoooommyycceetetecsoannsaelnyszuesdESTs Relative abundance of SSRs among oomycete con- sensus ESTs and transcript sequence sets in the oomycetes analyzed. Abundance is defined as the total number of SSRs per Mb of sequence analyzed. aRFneigdlautrivaeen2sdcernipstityseoqfuSeSnRces ascertosss consensus oomycete ESTs Relative density of SSRs across consensus oomycete ESTs and transcript sequence sets. Density is defined as the total sequence length (bp) contributed by each SSR per Mb of sequence analyzed. Page 5 of 11 (page number not for citation purposes)