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

Overview
TitleComprehensive transcriptome assembly of Chickpea (Cicer arietinum L.) using sanger and next generation sequencing platforms: development and applications
AuthorsKudapa Himabindu, Azam Sarwar, Sharpe Andrew G, Taran Bunyamin, Li Rong, Deonovic Benjamin, Cameron Connor, Farmer Andrew D, Cannon Steven B, Varshney Rajeev K
TypeJournal Article
JournalPloS one
Volume9
Issue1
DOI10.1371/journal.pone.0086039
eISSN1932-6203
Elocation10.1371/journal.pone.0086039
ISSN1932-6203
Journal AbbreviationPLoS ONE
Journal CountryUnited States
LanguageEnglish
Language Abbreng
Publication Date2014
Publication ModelElectronic-eCollection

Abstract

<p>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.</p>

Citation

Kudapa H, Azam S, Sharpe AG, Taran B, Li R, Deonovic B, Cameron C, Farmer AD, Cannon SB, Varshney RK. Comprehensive transcriptome assembly of Chickpea (Cicer arietinum L.) using sanger and next generation sequencing platforms: development and applications. PloS one. 2014; 9(1):e86039.

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There are three main kinds of chickpeas: Desi, which has small, darker seeds and a rough coat; Bombay, which has slightly larger dark seeds; and Kabuli, which has lighter coloured seeds with a smooth coat. Chickpeas are an excellent source of the essential nutrients, iron, folate, phosphorus, protein and dietary fiber. Chickpeas are low in fat and most of this is polyunsaturated. Desi chickpeas have a markedly higher fiber content than Kabulis and hence a very low glycemic index which may make them suitable for people with blood sugar problems. The plant grows to between 20–50 cm high and has small feathery leaves on either side of the stem. Chickpea pods are short in length containing 2-3 seeds. ... [more]

 
Cross References
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DatabaseAccession
PMID: PubMedPMID:24465857
Research Area
Research Area: 
Breeding & Genetics

Plant breeding is the art and science of changing the traits of plants in order to produce desired characteristics. Plant breeding can be accomplished through many different techniques ranging from simply selecting plants with desirable characteristics for propagation, to more complex molecular techniques. ... [more]