De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification

Publication Overview
TitleDe novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification
AuthorsGarg R, Patel RK, Tyagi AK, Jain M
TypeJournal Article
Journal NameDNA research : an international journal for rapid publication of reports on genes and genomes
Volume18
Issue1
Year2011
Page(s)53-63
CitationGarg R, Patel RK, Tyagi AK, Jain M. De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA research : an international journal for rapid publication of reports on genes and genomes. 2011 Feb; 18(1):53-63.

Abstract

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.
Properties
Additional details for this publication include:
Property NameValue
Publication ModelPrint-Electronic
ISSN1756-1663
Publication TypeJournal Article
Elocation10.1093/dnares/dsq028
eISSN1756-1663
Publication Date2011 Feb
Journal AbbreviationDNA Res.
DOI10.1093/dnares/dsq028
LanguageEnglish
Language Abbreng
Journal CountryEngland
Publication TypeResearch Support, Non-U.S. Gov't
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DatabaseAccession
PMID: PubMedPMID:21217129