SSRs mining of Brassica species in mitochondrial genomes: Bioinformatic approaches
Yükleniyor...
Dosyalar
Tarih
2013
Yazarlar
Dergi Başlığı
Dergi ISSN
Cilt Başlığı
Yayıncı
Korean Soc Horticultural Science
Erişim Hakkı
info:eu-repo/semantics/closedAccess
Özet
Simple sequence repeats (SSRs) are ubiquitous in eukaryotic genomes and SSRs have been used extensively in plant genetic studies. Five Brassica species (B. carinata, B. juncea, B. napus, B.oleracea, and B. rapa subsp. campestris) were analyzed to understand distribution and occurrence of mitochondrial SSRs (mtSSRs) in genic and intergenic regions. A total of 1295 mtSSRs were detected with an average density of 1.03 mtSSR per kb and about 18% of mtSSRs were determined in genic region. The A/T in mononucleotides, AG/CT in dinucleotides, AAG/CCT in trinucleotides, AATG/ATTC in tetranucleotides, and ACTAG/AGTCT in pentanucleotides were predominant mtSSR motifs, while there were not any hexanucleotides in all Brassica species. The most frequent repeat types were found as trinucleotides (8.6%) followed by mononucleotides (7.2%) and tetranucleotides (1.7%), while no pentanucleotides and hexanucleotides SSRs were present, in genic regions. The most abundant genic mtSSRs were observed in B. napus (21.7%), while the least genic mtSSRs were found in B. oleracea (12.9%). Based on putative amino acid triplets in coding regions, valine amino acid (15.4%) was predominant, followed by asparagine (14.4%), and glutamine (13.5%).
Açıklama
Filiz, Ertugrul/0000-0001-9636-6389
WOS: 000329943000012
WOS: 000329943000012
Anahtar Kelimeler
in silico analysis, microsatellite, mitochondrial SSRs
Kaynak
Horticulture Environment And Biotechnology
WoS Q Değeri
Q3
Scopus Q Değeri
Q1
Cilt
54
Sayı
6
