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.
Highlights
Chickpea (Cicer arietinum L.) is an important pulse legume crop
Sequence gaps total of 27,381,655 bases within the scaffolds were filled with PE sequence data generated by the Illumina platform using SOAP de novo gap closure tool version 1.1 and, thereby, reduced the N-content from 13.8% in the previous assembly to 8.68%, much lower than the CDC Frontier assembly (15.20%)[31,28]
Total span of the advanced draft sequence was 510,879,539 bases, of which sixty-five percent (333,999,488 bases) of total assembly was assigned to eight linkage groups with ~340 kb/cM recombination rate resulting in 2.7-fold improvement in length from the previous assembly
Summary
Chickpea (Cicer arietinum L.) is an important pulse legume crop. We previously reported a draft genome assembly of the desi chickpea cultivar ICC 4958. High-throughput small RNA sequencing studies to discover tissue-specific and stress-responsive expression profile of chickpea microRNAs have been reported[25,26] All these efforts have brought about a significant enrichment of the in enriching chickpea genomic information, which are certainly useful for the marker-trait association, comparative sequence analyses of orthologous genes and improvement of chickpea by genetic transformation. Effective anchoring of sequence scaffolds to the genetic linkage groups based on genetic markers to have a chromosome-level genome assembly is essential to identify genetic loci governing traits followed by marker-assisted breeding and comparative mapping with other species To this end, two independent initiatives have published two draft sequences, one each of a kabuli type (CDC Frontier) and a desi type (ICC 4958) chickpea[27,28]. Comparison of the genome assemblies of desi and kabuli type chickpeas revealed an overall collinearity with some structural deviations, some of which might have resulted from the use of different genetic maps for anchoring
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