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

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.

Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea

“…The transcription factor (TF) genes with MAD- and TAD-SNPs belonging to TF families like basic helix-loop-helix ( bHLH ), basic leucine zipper ( bZIP ) and APETALA2 ethylene-responsive element binding proteins ( AP2-EREBP ) were found predominant.

Figure 2Proportionate distribution of MAD- and TAD-SNPs in different coding (synonymous and non-synonymous) and non-coding (intron, URR and DRR) sequence components of genes and intergenic regions annotated from desi chickpea genome. The gene annotation of desi genome 4 was considered as reference to infer the coding DNA sequence (CDS)/exons, introns, up/downstream regulatory region (URR/DRR) sequence components of genes. Digits within the round and square Parentheses indicate the (number of gene-derived SNPs) and [number of genes with SNPs], respectively, representing each class of coding and non-coding regions of chickpea genes.

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“…The gene annotation of desi genome 4 was considered as reference to infer the coding DNA sequence (CDS)/exons, introns, up/downstream regulatory region (URR/DRR) sequence components of genes. Digits within the round and square Parentheses indicate the (number of gene-derived SNPs) and [number of genes with SNPs], respectively, representing each class of coding and non-coding regions of chickpea genes.…”

‘Omics’ and Plant Responses to Botrytis cinerea

“…The genetic map of the grape ( Vitis vinifera ) was completed in 2007 by the shotgun sequencing approach (Jaillon et al, 2007). In addition, genome sequence of chickpea ( Cicer arietinum ) was also assembled by two independent groups (Jain et al, 2013; Varshney et al, 2013; Parween et al, 2015; Thudi et al, 2016). The releases of genome sequences of B. cinerea and its hosts have helped identify candidate genes associated with virulence of B. cinerea and potential target genes associated with resistance in host crops.…”

Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy

“…Genome sequences for most of the grain legumes are now available, for instance soybean (Schmutz et al, 2010), groundnut progenitors (Bertioli et al, 2016;Chen et al, 2016), chickpea (Varshney et al, 2013d;Parween et al, 2015), pigeonpea (Varshney et al, 2012a), common bean (Schmutz et al, 2014;Yang et al, 2015), and adzuki bean (Kang et al, 2015;Yang et al, 2015) (Table 1). Efforts are underway to sequence the remaining legume genomes.…”