ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2011
Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L.).
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 34 papers.
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Who cites it
34 citing papers in PubMed, 102 citations in OpenAlex.
- Waterlogging tolerance in pigeonpea: current understanding of physiological responses, genetic resources, and genomic prospects.Frontiers in plant science · 2026Review
- The cacao gene atlas: a transcriptome developmental atlas reveals highly tissue-specific and dynamically-regulated gene networks in Theobroma cacao L.BMC plant biology · 2024Article
- Developments and Prospects in Imperative Underexploited Vegetable Legumes Breeding: A Review.International journal of molecular sciences · 2020Review
- Genomics-assisted breeding for pigeonpea improvement.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Review
- An "Axiom Cajanus SNP Array" based high density genetic map and QTL mapping for high-selfing flower and seed quality traits in pigeonpea.BMC genomics · 2019Article
- Association mapping to discover significant marker-trait associations for resistance against fusarium wilt variant 2 in pigeonpea [Cajanus cajan (L.) Millspaugh] using SSR markers.Journal of applied genetics · 2017Article
- Genomics-assisted characterization of a breeding collection of Apios americana, an edible tuberous legume.Scientific reports · 2016Article
- First-generation HapMap in Cajanus spp. reveals untapped variations in parental lines of mapping populations.Plant biotechnology journal · 2016Article
- Emerging Genomic Tools for Legume Breeding: Current Status and Future Prospects.Frontiers in plant science · 2016Review
- De novo transcriptome analysis of Medicago falcata reveals novel insights about the mechanisms underlying abiotic stress-responsive pathway.BMC genomics · 2015Article
- The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies.BMC genomics · 2015Article
- Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.).DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
- Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects.Frontiers in plant science · 2015Review
- Article
- Genomics-assisted breeding for boosting crop improvement in pigeonpea (Cajanus cajan).Frontiers in plant science · 2015Review
- An integrated SNP mining and utilization (ISMU) pipeline for next generation sequencing data.PloS one · 2014Article
- Article
- Populus euphratica: the transcriptomic response to drought stress.Plant molecular biology · 2013Article
- Article
- An RNA-Seq transcriptome analysis of orthophosphate-deficient white lupin reveals novel insights into phosphorus acclimation in plants.Plant physiology · 2013Article
Corrections and comments
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Authors and funding
19 authors at 8 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This study reports generation of large-scale genomic resources for pigeonpea, a so-called 'orphan crop species' of the semi-arid tropic regions. FLX/454 sequencing carried out on a normalized cDNA pool prepared from 31 tissues produced 494 353 short transcript reads (STRs). Cluster analysis of these STRs, together with 10 817 Sanger ESTs, resulted in a pigeonpea trancriptome assembly (CcTA) comprising of 127 754 tentative unique sequences (TUSs). Functional analysis of these TUSs highlights several active pathways and processes in the sampled tissues. Comparison of the CcTA with the soybean genome showed similarity to 10 857 and 16 367 soybean gene models (depending on alignment methods). Additionally, Illumina 1G sequencing was performed on Fusarium wilt (FW)- and sterility mosaic disease (SMD)-challenged root tissues of 10 resistant and susceptible genotypes. More than 160 million sequence tags were used to identify FW- and SMD-responsive genes. Sequence analysis of CcTA and the Illumina tags identified a large new set of markers for use in genetics and breeding, including 8137 simple sequence repeats, 12 141 single-nucleotide polymorphisms and 5845 intron-spanning regions. Genomic resources developed in this study should be useful for basic and applied research, not only for pigeonpea improvement but also for other related, agronomically important legumes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.