Mining of SSR markers from Expressed Sequence Tags of bamboo species.

Oviya Iyappan Ramalakshmi,Shanmughavel Piramanayagam

doi:10.6026/97320630005240

Abstract

With the ever increasing number of Expressed Sequence Tags (ESTs) from various sequencing projects, ESTs have become valuable and first-hand source of in-silico mining of simple sequence repeats (SSR) markers. We examined a total of 3419 EST sequences from three bamboo species, namely, Phyllostachys edulis, Bambusa oldhamii and Dendrocalamus sinicus for the presence of di- to hexa- microsatellites. The frequency of SSR containing ESTs varied from 5.36% in B. oldhamii to 13.05% in P. edulis. No SSRs were found in D. sinicus. Tri-nucleotide repeats (49.34%) were most frequent in P. edulis, while not much comparable difference in repeats was found in B. oldhamii. Flanking primer pairs were also designed in-silico for the sequences containing SSRs and their position on the genome hypothesized using similarity searching. SSRs located in open reading frame (ORF) were given functional annotation using Gene Ontology. Polymorphic SSRs were also detected using new pipeline- polySSR. Polymorphism level was very low (2.43%) and the position of the polymorphic SSRs was determined. The development of SSRs and the study of polymorphism will help in the further study of intra- and inter- gene flow, genetic structure, variability, linkage mapping and evolutionary relationships in bamboo.

Highlights

A large number of plant genomes are under consideration for whole genome sequencing but for most of them, due to their large genome size, the task has been little difficult and time consuming
Since the Expressed Sequence Tags (ESTs) are derived from cDNA, they provide direct evidence for the study of transcriptome and genome
In this study, we present the mining of EST-Simple Sequence Repeats (SSR) markers and detecting polymorphism in microsatellites in 3 bamboo species, namely, Phyllostachys edulis, Bambusa oldhamii, Dendrocalamus sinicus

Summary

Introduction

A large number of plant genomes are under consideration for whole genome sequencing but for most of them, due to their large genome size, the task has been little difficult and time consuming. Since EST represent the coding part of the genome, these serve as an important source for mining putative SSR markers and provide first hand insight into the organism’s genetic diversity. In this study, we present the mining of EST-SSR markers and detecting polymorphism in microsatellites in 3 bamboo species, namely, Phyllostachys edulis, Bambusa oldhamii, Dendrocalamus sinicus. By using MISA, SSR markers were predicted and functional annotation of those SSR containing sequences was done.

Results

Conclusion