Analysis of EST-SSRs in silver birch (Betula pendula Roth.)

摘要

Simple sequence repeats (SSRs) defined as sequence repeat units between 1 and 6 bp occur abundantly in both coding and non-coding regions in eukaryotic gen-omes and these repeats can affect gene expression. In this study, ESTs (expressed sequence tags) of Betula pendula (silver birch) were analyzed for in silico mining of EST-SSRs, protein annotation, open reading frames (ORFs), designing primers, and identifying codon repetitions. In B. pendula, the frequency of ESTs containing SSRs was 7.8%with an average of 1SSR/4. 78 kb of EST sequences. A total of 188 SSRs was identified by using MISA software and di-nucleotide SSR motifs (65.9%) were found to be the most abundant type of repeat motif followed by tri- (27.1%), tetra- (4.8%), and penta- (2.2%) motifs. Based on ORF analysis, 175 of 178 sequences were predicted as ORFs and the most frequent SSRs were detected in 50 UTR (58.43%), followed by in ORF (31.46%) and in 30 UTR (8.43%). 102 of 178 ESTs were annotated as ribosomal protein, transport protein, membrane protein, carrier protein, binding protein, and transferase protein. For a total of 102 SSRs (57.3%) with significant matches, a set of 102 primers (100%) with forward and reverse strands was designed by using Primer3 software. Serine (Ser, 19.6%) was predominant in putative encoded amino acids and most of amino acids showed nonpolar (35.3%) nature. Our data provide resources for B. pendula and can be useful for in silico comparative analyses of Betulaceae species, including SSR mining.