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

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Title An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.)
 
Creator Parween, Sabiha
Nawaz, Kashif
Roy, Riti
Pole, Anil K.
Venkata Suresh, B.
Misra, Gopal
Jain, Mukesh
Yadav, Gitanjali
Parida, Swarup K.
Tyagi, Akhilesh K.
Bhatia, Sabhyata
Chattopadhyay, Debasis
 
Subject Plant genetics
Natural variation in plants
 
Description Accepted date: 06 July 2015
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.
We acknowledge funding from the Department of Biotechnology, Ministry of Science and Technology,
Government of India, under the Next Generation Challenge Programme in Chickpea Genomics (Grant
no. BT/PR12919/AGR/02/676/2009 from 2009-14). We acknowledge ‘Distributed Information Science
Centre’ (DISC) at the National Institute of Plant Genome Research, New Delhi for curating the data.
Authors declare no conflict of interest.
 
Date 2016-01-21T06:01:54Z
2016-01-21T06:01:54Z
2015
 
Type Article
 
Identifier Scientific Reports, 5: 12806
2045-2322
http://172.16.0.77:8080/jspui/handle/123456789/562
http://www.nature.com/articles/srep12806
10.1038/srep12806
 
Language en_US
 
Publisher Nature Publishing Group