Constructing improved chickpea genome assemblies using skimGBS uri icon


  • Chickpea (Cicer arietinum L.) is the second most important grainlegume after soybean and plays an important role in food security.The application of genomics provides the potential to increase theproductivity and resilience of this important crop. We have developeda novel strategy to assess and improve the chickpea referencegenomes. The quality of both chickpea desi and kabuli draftgenomes were assessed using sequence data from flow cytometryisolated chromosomes to identify misplaced contigs. UsingSNPs derived from whole genome sequence data of ICC 4958 xPI 489777, and skim sequence-based genotyping of this population,we could validate and correct the draft assembly. In additionto placing the misplaced sequence regions into correspondingchromosome positions, most of the previously unplaced contigsequences have now been incorporated into the pseudomoleculesof the improved version. The total chromosome sequence lengthhas increased from 124.38 Mb and 347.24 Mb to 375.06 Mb and423.28 Mb for the desi and kabuli genomes respectively. Bothgenomes have been re-annotated. A total of 33,473 genes fromkabuli and 31,419 genes from desi were predicted. Both improvedgenomes are available at

publication date

  • 2017