De Novo Assembly of Chickpea Transcriptome Using Short Reads for Gene Discovery and Marker Identification
Open accessAbstract
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.
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New assembly strategies such as merging the contigs of multiple assemblies and trimming of low-quality bases at the end of reads can give better assembly results.
“However, new assembly strategies such as merging the contigs of multiple assemblies [20], [21] and trimming of low-quality bases at the end of reads [22] can give better assembly results [9].”
From Digital Gene Expression Analysis Based on Integrated De Novo Transcriptome Assembly of Sweet Potato [Ipomoea batatas (L.) Lam.] (2012) · cites this paper as [22]
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- Authors
- Garg, R., Patel, R. K., Tyagi, A. K., & Jain, M.
- Affiliations
- National Institute of Plant Genome Research (IN)
- Corresponding author
- Jain, M.
- Venue
- DNA Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-01-07
- Volume
- 18
- Issue
- 1
- Pages
- 53-63
- ISSN
- 1340-2838 (ISSN-L)
- 1756-1663
- PMC
- PMC3041503
- OpenAlex
- W2160525528
- Cited by
- 457
- References
- 40
- Citations by year
- 2026: 6 · 2025: 3 · 2024: 2 · 2023: 12 · 2022: 15 · 2021: 14 · 2020: 19 · 2019: 35 · 2018: 24 · 2017: 29 · 2016: 51 · 2015: 63 · 2014: 70 · 2013: 53 · 2012: 42
- FWCI
- 70.97
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- DNA Research (publishedVersion)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Genetic and Environmental Crop Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- chickpea, de novo transcriptome assembly, gene discovery, genomic resources
- MeSH terms
- Base Composition, Plants, Sequence Analysis, DNA, Minisatellite Repeats, DNA, Plant, Gene Expression Profiling, Cicer
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