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

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dc.contributor.authorFiliz, Ertuğrul
dc.contributor.authorDoğan, İlhan
dc.contributor.authorÖzyiğit, İbrahim İlker
dc.date.accessioned2020-04-30T22:39:20Z
dc.date.available2020-04-30T22:39:20Z
dc.date.issued2016
dc.departmentDÜ, Çilimli Meslek Yüksekokulu, Bitkisel ve Hayvansal Üretim Bölümüen_US
dc.descriptionFiliz, Ertugrul/0000-0001-9636-6389; Ozyigit, Ibrahim Ilker/0000-0002-0825-5951en_US
dc.descriptionWOS: 000375452300017en_US
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.identifier.doi10.1007/s11676-015-0182-1en_US
dc.identifier.endpage646en_US
dc.identifier.issn1007-662X
dc.identifier.issn1993-0607
dc.identifier.issue3en_US
dc.identifier.scopusqualityQ1en_US
dc.identifier.startpage639en_US
dc.identifier.urihttps://doi.org/10.1007/s11676-015-0182-1
dc.identifier.urihttps://hdl.handle.net/20.500.12684/2690
dc.identifier.volume27en_US
dc.identifier.wosWOS:000375452300017en_US
dc.identifier.wosqualityQ3en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.language.isoenen_US
dc.publisherNortheast Forestry Univen_US
dc.relation.ispartofJournal Of Forestry Researchen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectSilver birch (Betula pendula)en_US
dc.subjectBetulaceaeen_US
dc.subjectEST-SSRen_US
dc.subjectSSR miningen_US
dc.subjectIn silico analysisen_US
dc.titleAnalysis of EST-SSRs in silver birch (Betula pendula Roth.)en_US
dc.typeArticleen_US

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