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

<jats:title>Abstract</jats:title><jats:p>Chickpea (<jats:italic>Cicer arietinum</jats:italic> L.) is an important pulse legume crop. We previously reported a draft genome assembly of the <jats:italic>desi</jats:italic> 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 <jats:italic>desi</jats:italic> (ICC 4958) and the earlier reported <jats:italic>kabuli</jats:italic> (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 <jats:italic>desi</jats:italic> group and a <jats:italic>kabuli</jats:italic> group of chickpea genotypes.</jats:p>