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

Abstract

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.