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dc.contributor.authorFiliz, Ertuğrul
dc.contributor.authorDoğan, İlhan
dc.contributor.authorÖzyiǧit, İbrahim İlker
dc.date.accessioned2017-06-30T08:12:49Z
dc.date.available2017-06-30T08:12:49Z
dc.date.issued2016-06
dc.identifier.citationFiliz, E., Doğan, İ., and Özyiğit, İ.İ. (2016). Analysis of EST-SSRs in silver birch (Betula pendula Roth.). Journal of Forestry Research, 27(3), 639-646. doi:10.1007/s11676-015-0182-1en_US
dc.identifier.issn1007-662X
dc.identifier.urihttps://doi.org/10.1007/s11676-015-0182-1
dc.identifier.urihttp://hdl.handle.net/11147/5818
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.en_US
dc.language.isoengen_US
dc.publisherNortheast Forestry Universityen_US
dc.relation.isversionof10.1007/s11676-015-0182-1en_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectBetulaceaeen_US
dc.subjectEST-SSRen_US
dc.subjectSilver birchen_US
dc.subjectBetula pendulaen_US
dc.subjectIn silico analysisen_US
dc.titleAnalysis of EST-SSRs in silver birch (Betula pendula Roth.)en_US
dc.typearticleen_US
dc.contributor.authorIDTR100479en_US
dc.contributor.iztechauthorDoğan, İlhan
dc.relation.journalJournal of Forestry Researchen_US
dc.contributor.departmentIzmir Institute of Technology. Molecular Biology and Geneticsen_US
dc.identifier.volume27en_US
dc.identifier.issue3en_US
dc.identifier.startpage639en_US
dc.identifier.endpage646en_US
dc.identifier.wosWOS:000375452300017
dc.identifier.scopusSCOPUS:2-s2.0-84949513813
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US


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