An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.)

Publication Overview
TitleAn advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.)
AuthorsParween S, Nawaz K, Roy R, Pole AK, Venkata Suresh B, Misra G, Jain M, Yadav G, Parida SK, Tyagi AK, Bhatia S, Chattopadhyay D
TypeJournal Article
Journal NameScientific reports
Volume5
Year2015
Page(s)12806
CitationParween S, Nawaz K, Roy R, Pole AK, Venkata Suresh B, Misra G, Jain M, Yadav G, Parida SK, Tyagi AK, Bhatia S, Chattopadhyay D. An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.). Scientific reports. 2015; 5:12806.

Abstract

Chickpea (Cicer arietinum L.) is an important pulse legume crop. We previously reported a draft genome assembly of the desi chickpea cultivar ICC 4958. Here we report an advanced version of the ICC 4958 genome assembly (version 2.0) generated using additional sequence data and an improved genetic map. This resulted in 2.7-fold increase in the length of the pseudomolecules and substantial reduction of sequence gaps. The genome assembly covered more than 94% of the estimated gene space and predicted the presence of 30,257 protein-coding genes including 2230 and 133 genes encoding potential transcription factors (TF) and resistance gene homologs, respectively. Gene expression analysis identified several TF and chickpea-specific genes with tissue-specific expression and displayed functional diversification of the paralogous genes. Pairwise comparison of pseudomolecules in the desi (ICC 4958) and the earlier reported kabuli (CDC Frontier) chickpea assemblies showed an extensive local collinearity with incongruity in the placement of large sequence blocks along the linkage groups, apparently due to use of different genetic maps. Single nucleotide polymorphism (SNP)-based mining of intra-specific polymorphism identified more than four thousand SNPs differentiating a desi group and a kabuli group of chickpea genotypes.

Properties
Additional details for this publication include:
Property NameValue
Publication ModelElectronic
ISSN2045-2322
eISSN2045-2322
Publication Date2015
Journal AbbreviationSci Rep
DOI10.1038/srep12806
Elocation10.1038/srep12806
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
Journal CountryEngland
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PMID: PubMedPMID:26259924