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PLoS One. 2014 Jan 23;9(1):e86039. doi: 10.1371/journal.pone.0086039. eCollection 2014.

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

Author information

1
Research Program on Grain Legumes, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh, India.
2
National Research Council Canada (NRC-CNRC), Saskatoon, Saskatchewan, Canada.
3
Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
4
Department of Agronomy, University of Iowa, Ames, Iowa, United States of America.
5
National Center for Genome Resources (NCGR), Santa Fe, New Mexico, United States of America.
6
Department of Agronomy, University of Iowa, Ames, Iowa, United States of America ; United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Corn Insects and Crop Genetics Research Unit (USDA-ARS-CICGRU), Ames, Iowa, United States of America.
7
Research Program on Grain Legumes, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh, India ; CGIAR Generation Challenge Programme (GCP), c/o CIMMYT, Mexico DF, Mexico.

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.

PMID:
24465857
PMCID:
PMC3900451
DOI:
10.1371/journal.pone.0086039
[Indexed for MEDLINE]
Free PMC Article
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