Characterization of chloroplast DNA microsatellites from Saccharum spp and related species

Abstract

ABSTRACT. Microsatellites, or simple sequence repeats (SSRs), and their flanking regions in chloroplast genomes (plastomes) of some species of the family Poaceae were analyzed in silico to look for DNA sequence variations. Comparison of the complete chloroplast DNA sequences (cpDNAs) of sugarcane (Saccharum hybrid cv. SP-80-3280 and S. officinarum cv. NCo310) and related species, Agrostis stolonifera, Brachypodium distachyon, Hordeum vulgare subsp vulgare, Lolium perenne, Oryza nivara, O. sativa subsp indica, O. sativa subsp japonica, Sorghum bicolor, Triticum aestivum, Zea mays, and Z. mays cv. B73, allowed us to examine the organization of chloroplast SSRs (cpSSRs) in genic and intergenic regions. We identified 204 cpSSRs in the sugarcane cpDNA; 22.5% were in genic regions. The ndh, rps, trn, and rpl gene clusters of the chloroplasts had the most repeats. Mononucleotide repeats were the most abundant cpSSRs in these species; however, di-, tri-, tetra-, penta-, and hexanucleotide repeats were also identified. Chloroplast SSRs in Poaceae variability possible; repeat motifs are not uniformly distributed across the Poaceae plastomes, but are mostly confined to intergenic regions. Phylogeny was determined by maximum parsimony and neighborjoining inference methods. The cpSSRs of these species were found to be polymorphic. It appears that individual cpSSRs in the Poaceae are stable, at least over short periods of evolutionary time. We conclude that the plastome database can be exploited for phylogenetic analysis and biotechnological development.

In Silico chloroplast SSRs mining of Olea species

“…A total of 340 cpSSRs (30.5%) were found to be in genic regions while a total of 809 cpSSRs (69.5%) were found to be in intergenic regions and genic cpSSRs were identified only mono and trinucleotide motifs. In general, intergenic cpSSR (69.5%) in Olea species were more abundant than genic cpSSR (29.6%) and this result is consistent with earlier studies Asteraceae (Timme et al 2007), Fabaceae (Saski et al 2005), and Solanaceae (Daniell et al 2006), Saccharum (Melotto-passarin et al 2011). According to the analysis, the most abundant genic cpSSRs were found for trinucleotide motifs (57.2%).…”

“…The higher AT/TA frequencies in chloroplast genomes can be explained to be the conclusion of the high A/T content of the genomes. Among the trinucleotide repeats, AAG/CTT motif was the most common (28.9%) followed by AAT/TTA (24.9%) and AAC/GTT (16%) and this finding was not consistent with earlier studies results (Rajendrakumar et al 2007;Melotto-passarin et al 2011;Kuntal et al 2012). In tetranucleotide SSR motifs, the maximum frequency of 47.1% was showed by AAAG/CTTT followed by AAAT/ATTT (29.4%).…”

Completion of the Chloroplast Genomes of Five Chinese Juglans and Their Contribution to Chloroplast Phylogeny

“…The SSRs in the five Juglans Cp genomes we investigated were AT rich. Poly (A)/(T) SSRs are more common than poly (G)/(C) in many plant families (Melotto-Passarin et al, 2011; Nie et al, 2012; Martin et al, 2013). The cpSSRs of the five Juglans we studied are expected to be useful for assays detecting polymorphisms at population-level as well as comparing more distantly phylogenetic relationships among Juglans species.…”

Simple sequence repeats mining using computational approach in chloroplast genome of Marchantia polymorpha

“…(Melotto-Passarin et al, 2011) and Olea species (Filiz & Koc, 2012). Moreover the abundance of cpSSRs in non-coding regions is also in agreement with previous studies (Hancock, 1995;Shanker, 2013d …”