Please use this identifier to cite or link to this item: https://hdl.handle.net/11147/5818
Title: Analysis of EST-SSRs in silver birch (Betula pendula Roth.)
Authors: Filiz, Ertuğrul
Doğan, İlhan
Özyigit, İbrahim İlker
Doğan, İlhan
Keywords: Betulaceae
EST-SSR
Silver birch
Betula pendula
In silico analysis
Issue Date: Jun-2016
Publisher: Northeast Forestry University
Source: Filiz, 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/s11676-015-0182-1
Abstract: 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 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.
URI: https://doi.org/10.1007/s11676-015-0182-1
http://hdl.handle.net/11147/5818
ISSN: 1007-662X
1007-662X
Appears in Collections:Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection

Files in This Item:
File Description SizeFormat 
5818.pdfMakale529.51 kBAdobe PDFThumbnail
View/Open
Show full item record

CORE Recommender

SCOPUSTM   
Citations

2
checked on Oct 16, 2021

WEB OF SCIENCETM
Citations

2
checked on Oct 16, 2021

Page view(s)

30
checked on Oct 18, 2021

Download(s)

18
checked on Oct 18, 2021

Google ScholarTM

Check

Altmetric


Items in GCRIS Repository are protected by copyright, with all rights reserved, unless otherwise indicated.