ArticlePlant physiology2011
Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development.
Article in Plant physiology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 122 papers, 1 of them a synthesis that pooled it.
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Who cites it
122 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Chickpea Biofortification for Cytokinin DehydrogenaseFrontiers in genetics · 2022Pooled it
- Pan-transcriptome analysis of diverse chickpea accessions reveals specific expression patterns and genetic variations associated with agronomic traits.Plant molecular biology · 2026Article
- Genome-wide identification and characterization of CaM and CML gene family in chickpea (Cicer arietinum L.).Scientific reports · 2026Article
- Genome-Wide Identification and In Silico Analysis of Annexins in Chickpea (Cicer arietinum L.).Biochemical genetics · 2025Article
- The BBX family and their response to abiotic stress in ginger (Zingiber officinale Roscoe).BMC genomics · 2025Article
- Advancing Chickpea Breeding: Omics Insights for Targeted Abiotic Stress Mitigation and Genetic Enhancement.Biochemical genetics · 2025Review
- Comprehensive analysis of housekeeping genes, tissue-specific genes, and dynamic regulation across developmental stages in pearl millet.BMC genomics · 2024Article
- Elucidating the Mesocarp Drupe Transcriptome of Açai (International journal of molecular sciences · 2023Article
- De Novo Transcriptome Profiling for the Generation and Validation of Microsatellite Markers, Transcription Factors, and Database Development forInternational journal of molecular sciences · 2023Article
- Breeding and Genomic Approaches towards Development of Fusarium Wilt Resistance in Chickpea.Life (Basel, Switzerland) · 2023Review
- Transcriptomic Analysis of Flowering Time Genes in Cultivated Chickpea and WildInternational journal of molecular sciences · 2023Article
- Underutilized legumes: nutrient status and advanced breeding approaches for qualitative and quantitative enhancement.Frontiers in nutrition · 2023Review
- Molecular Breeding and Drought Tolerance in Chickpea.Life (Basel, Switzerland) · 2022Review
- An integrated transcriptome mapping the regulatory network of coding and long non-coding RNAs provides a genomics resource in chickpea.Communications biology · 2022Article
- Herbal Arsenal against Skin Ailments: A Review Supported by In Silico Molecular Docking Studies.Molecules (Basel, Switzerland) · 2022Review
- Transcriptomic Analysis of Early Flowering Signals in 'Royal' Flax.Plants (Basel, Switzerland) · 2022Article
- Stage specific comparative transcriptomic analysis to reveal gene networks regulating iron and zinc content in pearl millet [Pennisetum glaucum (L.) R. Br.].Scientific reports · 2022Article
- Identification of Pueraria spp. through DNA barcoding and comparative transcriptomics.BMC plant biology · 2022Article
- Genomics Associated Interventions for Heat Stress Tolerance in Cool Season Adapted Grain Legumes.International journal of molecular sciences · 2021Review
- Evolutionary and functional analysis of two-component system in chickpea reveals CaRR13, a TypeB RR, as positive regulator of symbiosis.Plant biotechnology journal · 2021Article
62 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chickpea (Cicer arietinum) is an important food legume crop but lags in the availability of genomic resources. In this study, we have generated about 2 million high-quality sequences of average length of 372 bp using pyrosequencing technology. The optimization of de novo assembly clearly indicated that hybrid assembly of long-read and short-read primary assemblies gave better results. The hybrid assembly generated a set of 34,760 transcripts with an average length of 1,020 bp representing about 4.8% (35.5 Mb) of the total chickpea genome. We identified more than 4,000 simple sequence repeats, which can be developed as functional molecular markers in chickpea. Putative function and Gene Ontology terms were assigned to at least 73.2% and 71.0% of chickpea transcripts, respectively. We have also identified several chickpea transcripts that showed tissue-specific expression and validated the results using real-time polymerase chain reaction analysis. Based on sequence comparison with other species within the plant kingdom, we identified two sets of lineage-specific genes, including those conserved in the Fabaceae family (legume specific) and those lacking significant similarity with any non chickpea species (chickpea specific). Finally, we have developed a Web resource, Chickpea Transcriptome Database, which provides public access to the data and results reported in this study. The strategy for optimization of de novo assembly presented here may further facilitate the transcriptome sequencing and characterization in other organisms. Most importantly, the data and results reported in this study will help to accelerate research in various areas of genomics and implementing breeding programs in chickpea.
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