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

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Title De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification
 
Creator Garg, Rohini
Patel, Ravi K.
Tyagi, Akhilesh K.
Jain, Mukesh
 
Subject De novo assembly
chickpea
next generation sequencing
transcriptome
short read
 
Description 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.
 
Date 2014-04-07T09:45:46Z
2014-04-07T09:45:46Z
2011
2 November 2010
 
Type Article
 
Identifier DNA Res., 18(1): 53-63
http://hdl.handle.net/123456789/179
 
Language en
 
Publisher Oxford University Press