Assessment of chloroplast microsatellite from pine family (Pinaceae) by using bioinformatics tools

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dc.contributor.authorFiliz, Ertuğrul
dc.contributor.authorKoç, İbrahim
dc.date.accessioned2020-04-30T22:39:44Z
dc.date.available2020-04-30T22:39:44Z
dc.date.issued2014
dc.departmentDÜ, Çilimli Meslek Yüksekokulu, Bitkisel ve Hayvansal Üretim Bölümüen_US
dc.descriptionFiliz, Ertugrul/0000-0001-9636-6389en_US
dc.descriptionWOS: 000336821100004en_US
dc.description.abstractMicrosatellites, also known as simple sequence repeats (SSRs), are repeating sequences of 2-6 base pairs of DNA and affect chromatin organization, regulation of gene activity, DNA repair, DNA recombination, etc. Chloroplast DNA (cpDNA) has been used extensively in plant studies at different taxonomic levels. Therefore, the aim of this study Was to understand the distrubution of microsatellites in the coding and non-coding regions of organellar genomes (cpDNAs) of Major species of pine family (Pinaceae), viz., Cathaya argyrophylla, Cedrus deodara, Larix decidua, Picea morrisonicola, P. sitchensis, Pinus contorta, P. gerardiana, P. koraiensis, P. krempfii, P. lambertiana, P. monophylla, P. nelsonii, P. thunbergii, Pseudotsuga sinensis var. wilsoniana. 1623 cpSSRs were identified in pine species with an average frequency of 9.79 cpSSR per kb, of which 584 (22.5%) were in genic regions. Mononucleotide repeats were the most abundant cpSSRs (52.4%) in these species, followed by trinucleotide SSRs (37.3%), dinucleotide (5%), tetranucleotide (3.9%), pentanucleotide (0.8%), and hexanucleotide (0.6%). As expected, trinucleotide repeats are more common in coding regions, while other repeat motifs are abundant in non-coding cpDNA. G+C content of these species have closely similar frequency, ranging from 31.67 to 38.80%. Our analyses suggest that plastome database can be used for comparative genomics in different plant species.en_US
dc.identifier.endpage40en_US
dc.identifier.issn0972-5849
dc.identifier.issn0975-0967
dc.identifier.issue1en_US
dc.identifier.scopusqualityQ4en_US
dc.identifier.startpage34en_US
dc.identifier.urihttps://hdl.handle.net/20.500.12684/2810
dc.identifier.volume13en_US
dc.identifier.wosWOS:000336821100004en_US
dc.identifier.wosqualityQ4en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.language.isoenen_US
dc.publisherNatl Inst Science Communication-Niscairen_US
dc.relation.ispartofIndian Journal Of Biotechnologyen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/closedAccessen_US
dc.subjectcpDNAen_US
dc.subjectcpSSRen_US
dc.subjectPinaceaeen_US
dc.subjectpineen_US
dc.subjectplastomeen_US
dc.titleAssessment of chloroplast microsatellite from pine family (Pinaceae) by using bioinformatics toolsen_US
dc.typeArticleen_US

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