Abstract:The distribution frequency and characteristic of base repeats of EST-SSR (expressed sequence tag - simple sequence repeats) were induced and analyzed in 21 kinds of decapod crustaceans by applying bioinformatics methods. The results showed that EST-SSR abundances were different between various crustacean species. Exopalaemon carinicauda had the most abundant EST-SSR (868.02/Mb), whereas Scylla paramamosain had the least (286.48/Mb) in pleocyemata. Penaeus monodon had the most abundant EST-SSR (641.19/Mb), whereas Litopenaeus setiferus had the least (166.96/Mb) in dendrobranchiata. The abundance of EST-SSR with di-, tri-, and tetra-nucleotide motifs was more than that of those with penta- and hex- nucleotide motifs, which accounts for 41.11% in pleocyemata and 28.00% in dendrobranchiata. EST-SSR of compound (Ⅰ) type occupied a large proportion in the pleocyemata (51.38%) and dendrobranchiata (65.13%). The frequency of the AC/GT repeat motif distribution was highest in dinucleotides, and ACC/GGT and AAT/ATT repeat motifs were the most abundant in the trinucleotide repeats in the pleocyemata. The frequency of AG/CT repeat motif distribution was highest in dinucleotides, and the distribution frequency of AAT/ATT motifs was significantly higher than other motifs of dinucleotide repeats in the dendrobranchiata. A total of 12,155 sequences containing SSRs were predicted; moreover, Gene Ontology (GO) Classification with the blast2go application was performed based on sequences containing SSRs of Exopalaemon carinicauda. The results demonstrated that ‘cellular process’ comprised the largest proportion in the biological process category, whereas ‘binding’ comprised the largest proportion in the molecular function category. Additionally, the cellular component category showed that many sequences likely possessed ‘cell parts’ and ‘cell’ by GO annotation. This study compared the characteristics of EST-SSR in different species of crustaceans and the diverse regions of the species genome. The consequences deepened our understanding of the distribution of SSRs and provided a reference for the development and practical applications of EST-SSR markers. The results also provided powerful information for future conservation and breeding research.
