Journal Article

<i>De Novo</i> Assembly of Chickpea Transcriptome Using Short Reads for Gene Discovery and Marker Identification

Rohini Garg, Ravi K. Patel, Akhilesh K. Tyagi and Mukesh Jain

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 18, issue 1, pages 53-63
Published in print February 2011 | ISSN: 1340-2838
Published online January 2011 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/dsq028

Show Summary Details

Preview

Chickpea ranks third among the food legume crops production in the world. However, the genomic resources available for chickpea are still very limited. In the present study, the transcriptome of chickpea was sequenced with short reads on Illumina Genome Analyzer platform. We have assessed the effect of sequence quality, various assembly parameters and assembly programs on the final assembly output. We assembled ∼107million high-quality trimmed reads using Velvet followed by Oases with optimal parameters into a non-redundant set of 53 409 transcripts (≥100 bp), representing about 28 Mb of unique transcriptome sequence. The average length of transcripts was 523 bp and N50 length of 900 bp with coverage of 25.7 rpkm (reads per kilobase per million). At the protein level, a total of 45 636 (85.5%) chickpea transcripts showed significant similarity with unigenes/predicted proteins from other legumes or sequenced plant genomes. Functional categorization revealed the conservation of genes involved in various biological processes in chickpea. In addition, we identified simple sequence repeat motifs in transcripts. The chickpea transcripts set generated here provides a resource for gene discovery and development of functional molecular markers. In addition, the strategy for de novo assembly of transcriptome data presented here will be helpful in other similar transcriptome studies.

Keywords: De novo assembly; chickpea; next generation sequencing; transcriptome; short read

Journal Article.  6034 words.  Illustrated.

Subjects: Genetics and Genomics

Users without a subscription are not able to see the full content. Please, subscribe or login to access all content.