Assessment of chloroplast microsatellite from pine family (Pinaceae) by using bioinformatics tools
Küçük Resim Yok
Tarih
2014
Yazarlar
Dergi Başlığı
Dergi ISSN
Cilt Başlığı
Yayıncı
Natl Inst Science Communication-Niscair
Erişim Hakkı
info:eu-repo/semantics/closedAccess
Özet
Microsatellites, 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.
Açıklama
Filiz, Ertugrul/0000-0001-9636-6389
WOS: 000336821100004
WOS: 000336821100004
Anahtar Kelimeler
cpDNA, cpSSR, Pinaceae, pine, plastome
Kaynak
Indian Journal Of Biotechnology
WoS Q Değeri
Q4
Scopus Q Değeri
Q4
Cilt
13
Sayı
1
