A Chromosomal Genomics Approach to Assess and Validate the Desi and Kabuli Draft Chickpea Genome Assemblies

The ability to isolate individual chromosomes combined with next generation sequencing permits the validation of genome assemblies at the chromosome level. We demonstrate this approach by the assessment of the recently published chickpea kabuli and desi genomes. While previous genetic analysis suggests that these genomes should be very similar, a comparison of their published assemblies highlights significant differences. Our chromosomal genomics analysis highlights regions that appear to have been mis-assembled in the kabuli genome and identifies large scale mis-assembly in the draft desi genome. The integration of chromosomal genomics with skimGBS based genome assembly tools has the potential to significantly improve genome assemblies. The approach could be applied both for new genome assemblies as well as published assemblies, and complements currently applied genome assembly strategies.