SSRs mining of Brassica species in mitochondrial genomes: Bioinformatic approaches

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dc.contributor.authorFiliz, Ertuğrul
dc.date.accessioned2020-04-30T23:32:12Z
dc.date.available2020-04-30T23:32:12Z
dc.date.issued2013
dc.departmentDÜ, Çilimli Meslek Yüksekokulu, Bitkisel ve Hayvansal Üretim Bölümüen_US
dc.descriptionFiliz, Ertugrul/0000-0001-9636-6389en_US
dc.descriptionWOS: 000329943000012en_US
dc.description.abstractSimple 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%).en_US
dc.identifier.doi10.1007/s13580-013-0026-xen_US
dc.identifier.endpage553en_US
dc.identifier.issn2211-3452
dc.identifier.issn2211-3460
dc.identifier.issue6en_US
dc.identifier.scopusqualityQ1en_US
dc.identifier.startpage548en_US
dc.identifier.urihttps://doi.org/10.1007/s13580-013-0026-x
dc.identifier.urihttps://hdl.handle.net/20.500.12684/4643
dc.identifier.volume54en_US
dc.identifier.wosWOS:000329943000012en_US
dc.identifier.wosqualityQ3en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.language.isoenen_US
dc.publisherKorean Soc Horticultural Scienceen_US
dc.relation.ispartofHorticulture Environment And Biotechnologyen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/closedAccessen_US
dc.subjectin silico analysisen_US
dc.subjectmicrosatelliteen_US
dc.subjectmitochondrial SSRsen_US
dc.titleSSRs mining of Brassica species in mitochondrial genomes: Bioinformatic approachesen_US
dc.typeArticleen_US

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