We sought to deter mine regardless of whether this high frequency of tri SSRs occurred in CjCon1, and irrespective of whether the distribution within the SSRs was non uniform and dependent on their spot. So as to estimate the spot of every SSR, the amino acid sequences of CjCon1 had been identi fied working with prot4EST pipeline, The coding sequences were then re mapped onto the nucleotide sequences to ob tain coordinates to the coding areas and estimate the destinations within the EST SSRs. The complete length of your esti mated coding region was 43. 88 Mbp, representing 69. 0% with the total sequence length for CjCon1. The average length of your coding area in every contig was 179. 9 amino acids, ranging from 14 to 1483 aa. The examination of coding areas using prot4EST did not ensure the inclusion of get started and or halt codons, but rough estimated loca tions had been obtained for three,942 on the 4,059 SSRs.
no spot may be established to the remaining 117 for the reason that they extended over the two estimated coding and non coding areas. Significantly less than half from the di Ueno et al. BMC Genomics 2012, 13.136 Page ten of sixteen UTR 3 UTR Coding di tetra penta hexa Figure 4 Partnership among genome dimension and SSR frequency. SSR frequencies were plotted against genome size on a log scale. a total noob The gene indices are assigned since the following abbreviations. AGI. Arabidopsis thaliana, HAGI. Helianthus annuus, NTGI. Nicotiana tabacum, OGI. Oak, OSGI. Oryza sativa, PGI. Pinus and SGI. Picea. Genome dimension for Pinus taeda and Picea abies was employed for PGI and SGI, respectively. SSRs had been estimated to be coding, but 72. 8% in the tri SSRs and 64.
3% on the hexa SSRs had been in coding regions, Because the addition or deletion of di SSR repeats located within coding regions can cause frame shifts, selective pressures disfavour the presence of di SSRs in coding areas, We also examination ined the locations of precise SSR motifs. Just about the most com mon motifs during the 3 UTR and coding regions were full report AT and AG, respectively, with AT motifs accounting for 154 of all di SSRs within the three UTRs and AG motifs representing 155 of all di SSRs motifs in coding areas. AT was also the most typical motif inside the 5 UTR, accounting for 70 of all di SSRs in this re gion, despite the fact that it was a lot much less frequent here than within the three UTR. The most typical tri SSRs within the coding, 3 UTR, and five UTR regions had been AAG, AAT and AGG, respectively. GC percentage Simply because the genomic GC percentage may well affect microsatel lite evolution, we analyzed the GC articles of the con tigs, contigs with SSRs, and SSR motifs of CjCon1. The average GC percentage for CjCon1 was 40. 23%, with max imum and minimal values of 87. 12% and 12. 08%, respect ively. No homologues of sequences with this kind of intense GC percentages may be recognized employing BLAST searches towards the NCBI nr database.