ArticlePloS one2014
Comprehensive transcriptome assembly of Chickpea (Cicer arietinum L.) using sanger and next generation sequencing platforms: development and applications.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers, 1 of them a synthesis that pooled it.
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Who cites it
52 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Epigenomics as Potential Tools for Enhancing Magnitude of Breeding Approaches for Developing Climate Resilient Chickpea.Frontiers in genetics · 2022Pooled it
- Genome-wide identification and characterization of CaM and CML gene family in chickpea (Cicer arietinum L.).Scientific reports · 2026Article
- Advancing Chickpea Breeding: Omics Insights for Targeted Abiotic Stress Mitigation and Genetic Enhancement.Biochemical genetics · 2025Review
- Haplotypes of ATP-Binding CassetteBiomolecules · 2024Article
- Integrated multi-omics analysis reveals drought stress response mechanism in chickpea (Cicer arietinum L.).The plant genome · 2024Article
- Chickpea: Its Origin, Distribution, Nutrition, Benefits, Breeding, and Symbiotic Relationship withPlants (Basel, Switzerland) · 2024Review
- Transcriptome analysis of ovules offers early developmental clues after fertilization in3 Biotech · 2023Article
- Breeding and Genomic Approaches towards Development of Fusarium Wilt Resistance in Chickpea.Life (Basel, Switzerland) · 2023Review
- Comprehensive Transcriptome Profiling Uncovers Molecular Mechanisms and Potential Candidate Genes Associated with Heat Stress Response in Chickpea.International journal of molecular sciences · 2023Article
- An integrated transcriptome mapping the regulatory network of coding and long non-coding RNAs provides a genomics resource in chickpea.Communications biology · 2022Article
- De novo transcriptome assembly and analysis of gene expression in different tissues of moth bean (Vigna aconitifolia) (Jacq.) Marechal.BMC plant biology · 2022Article
- Proteotranscriptomics - A facilitator in omics research.Computational and structural biotechnology journal · 2022Review
- Global transcriptome and coexpression network analyses reveal cultivar-specific molecular signatures associated with different rooting depth responses to drought stress in potato.Frontiers in plant science · 2022Article
- Genetic mapping of QTLs for drought tolerance in chickpea (Frontiers in genetics · 2022Article
- Systems biology for crop improvement.The plant genome · 2021Review
- Molecular mapping of quantitative trait loci for ascochyta blight and botrytis grey mould resistance in an inter-specific cross in chickpea (Breeding science · 2021Article
- Identification of stable heat tolerance QTLs using inter-specific recombinant inbred line population derived from GPF 2 and ILWC 292.PloS one · 2021Article
- Molecular and Physiological Alterations in Chickpea under Elevated CO2 Concentrations.Plant & cell physiology · 2020Article
- Integrating genomics for chickpea improvement: achievements and opportunities.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Review
- Genome wide transcriptome analysis reveals vital role of heat responsive genes in regulatory mechanisms of lentil (Lens culinaris Medikus).Scientific reports · 2019Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A comprehensive transcriptome assembly of chickpea has been developed using 134.95 million Illumina single-end reads, 7.12 million single-end FLX/454 reads and 139,214 Sanger expressed sequence tags (ESTs) from >17 genotypes. This hybrid transcriptome assembly, referred to as Cicer arietinumTranscriptome Assembly version 2 (CaTA v2, available at http://data.comparative-legumes.org/transcriptomes/cicar/lista_cicar-201201), comprising 46,369 transcript assembly contigs (TACs) has an N50 length of 1,726 bp and a maximum contig size of 15,644 bp. Putative functions were determined for 32,869 (70.8%) of the TACs and gene ontology assignments were determined for 21,471 (46.3%). The new transcriptome assembly was compared with the previously available chickpea transcriptome assemblies as well as to the chickpea genome. Comparative analysis of CaTA v2 against transcriptomes of three legumes - Medicago, soybean and common bean, resulted in 27,771 TACs common to all three legumes indicating strong conservation of genes across legumes. CaTA v2 was also used for identification of simple sequence repeats (SSRs) and intron spanning regions (ISRs) for developing molecular markers. ISRs were identified by aligning TACs to the Medicago genome, and their putative mapping positions at chromosomal level were identified using transcript map of chickpea. Primer pairs were designed for 4,990 ISRs, each representing a single contig for which predicted positions are inferred and distributed across eight linkage groups. A subset of randomly selected ISRs representing all eight chickpea linkage groups were validated on five chickpea genotypes and showed 20% polymorphism with average polymorphic information content (PIC) of 0.27. In summary, the hybrid transcriptome assembly developed and novel markers identified can be used for a variety of applications such as gene discovery, marker-trait association, diversity analysis etc., to advance genetics research and breeding applications in chickpea and other related legumes.
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