Title

Analysis of SSR dynamics in chloroplast genomes of Brassicaceae family

Authors

Sumit G. Gandhi*, Praveen Awasthi, Yashbir S. Bedi

Affiliation

Plant Biotechnology Division and Systems Biology Division, Indian Institute of Integrative Medicine (Council of Scientific and Industrial Research), Canal Road, Jammu – 180 001, India

Email

sumit@iiim.res.in; * Corresponding author

Article Type

Hypothesis

Date

recieved March 04, 2010 ; accepted April 09, 2010, published June 16, 2010

Abstract

Simple sequence repeats (SSRs) are present abundantly in most eukaryotic genomes. They affect several cellular processes like chromatin organization, regulation of gene activity, DNA repair, DNA recombination, etc. Though considerable data exists on using nuclear SSRs to infer phylogenetic relationships, the potential of chloroplast microsatellites (cpSSR), in this regard, remains largely unexplored. In the present study we probe various nucleotide repeat motifs (NRMs) / types of SSRs present in chloroplast genomes (cpDNA) of 12 species belonging to Brassicaceae family. NRMs show a non-random distribution in coding and non-coding compartments of cpDNA. As expected, trinucleotide repeats are more common in coding regions while other repeat motifs are prominent in non-coding DNA. Total numbers of SSRs in coding region show little variation between species while considerable variation is exhibited by SSRs in non-coding regions. Finally, we have designed universal primers that yield polymorphic amplicons from all 12 species. Our analysis also suggests that amplicon length polymorphism shows no significant relationship with sequence based phylogeny of SSRs in cpDNA of Brassicaceae family.

Keywords

SSR, microsatellites, phylogenetic relationship, chloroplast DNA, Brassicales, coding DNA, non-coding DNA

Citation

Gandhi et al. Bioinformation 5(1): 16-20 (2010)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.