ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2011
De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 230 papers.
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230 citing papers in PubMed.
- Genome-wide identification and characterization of CaM and CML gene family in chickpea (Cicer arietinum L.).Scientific reports · 2026Article
- Metagenomic Data Preprocessing and Quality Control.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Exploring the drought-responsive miRNAs and their corresponding target genes in chickpea root tissue.Plant molecular biology · 2025Article
- CaLAP1 and CaLAP2 orchestrate anthocyanin biosynthesis in the seed coat of Cicer arietinum.Planta · 2024Article
- An Outstandingly Rare Occurrence of Mycoviruses in Soil Strains of the Plant-Beneficial Fungi from the GenusMicrobiology spectrum · 2023Article
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- Fusarivirus accessory helicases present an evolutionary link for viruses infecting plants and fungi.Virologica Sinica · 2022Article
- Harnessing the hidden allelic diversity of wild Cicer to accelerate genomics-assisted chickpea crop improvement.Molecular biology reports · 2022Review
- De novo transcriptome assembly and analysis of gene expression in different tissues of moth bean (Vigna aconitifolia) (Jacq.) Marechal.BMC plant biology · 2022Article
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- SNP Discovery Using BSR-Seq Approach for Spot Blotch Resistance in Wheat (Frontiers in genetics · 2022Article
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- Genomics Associated Interventions for Heat Stress Tolerance in Cool Season Adapted Grain Legumes.International journal of molecular sciences · 2021Review
- Development, characterization, functional annotation and validation of genomic and genic-SSR markers using de novo next generation sequencing in3 Biotech · 2021Article
- Genetics and breeding for climate change in Orphan crops.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Review
- Physiological and transcriptomic analyses characterized high temperature stress response mechanisms in Sorbus pohuashanensis.Scientific reports · 2021Article
- de novo transcriptomic profiling of differentially expressed genes in grass halophyte Urochondra setulosa under high salinity.Scientific reports · 2021Article
- Comparative transcriptome analysis of Rheum australe, an endangered medicinal herb, growing in its natural habitat and those grown in controlled growth chambers.Scientific reports · 2021Article
170 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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