Show simple item record

dc.contributor.authorÖzyiǧit, Ibrahim Ilker
dc.contributor.authorDoğan, İlhan
dc.description.abstractSimple sequence repeats (SSRs) defined as sequence repeat units between 1 and 6 bp occur abundantly in both coding and non-coding regions in eukaryotic genomes 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 5′ UTR (58.43 %), followed by in ORF (31.46 %) and in 3′ 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. © 2015 Northeast Forestry University and Springer-Verlag Berlin Heidelbergen_US
dc.subjectBetulaceae; EST-SSR; In silico analysis; Silver birch (Betula pendula); SSR miningen_US
dc.titleAnalysis of EST-SSRs in silver birch (Betula pendula Roth.)en_US
dc.relation.journalJournal of Forestry Researchen_US
dc.contributor.departmentDepartment of Biology, Faculty of Science and Arts, Marmara Universityen_US

Files in this item


There are no files associated with this item.

This item appears in the following Collection(s)

Show simple item record