Comprehensive transcriptome assembly of chickpea (Cicer arietinum L.) using sanger and next generation sequencing platforms: development and applications

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DOIResolve DOI: http://doi.org/10.1371/journal.pone.0086039
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TypeArticle
Journal titlePLoS ONE
ISSN1932-6203
Volume9
Issue1
Article numbere86039
Subjectcontig; chickpea; expressed sequence tag; gene sequence; genetic conservation; genetic polymorphism; genetic transcription; genotype; intron; Medicago; next generation sequencing; Phaseolus vulgaris; plant chromosome; plant genome; Sanger sequencing; simple sequence repeat; soybean; species comparison; Cicer; Gene Expression Profiling; Genes, Plant; Genetic Linkage; Genetic Markers; High-Throughput Nucleotide Sequencing; Microsatellite Repeats; Molecular Sequence Annotation; Plant Proteins; Sequence Analysis, DNA; Synteny; transcriptome
AbstractA 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 arietinum Transcriptome 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.
Publication date
PublisherPLOS
LanguageEnglish
AffiliationNational Research Council Canada; Aquatic and Crop Resource Development
Peer reviewedYes
NPARC number21272918
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Record identifier6651f7cf-8278-4724-8472-9ac75fbf3b79
Record created2014-12-03
Record modified2016-05-09
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