Constructing improved chickpea genome assemblies using skimGBS

Chickpea (Cicer arietinum L.) is the second most important grain legume after soybean and plays an important role in food security. The application of genomics provides the potential to increase the productivity and resilience of this important crop. We have developed a novel strategy to assess and improve the chickpea reference genomes. The quality of both chickpea desi and kabuli draft genomes were assessed using sequence data from flow cytometry isolated chromosomes to identify misplaced contigs. Using SNPs derived from whole genome sequence data of ICC 4958 x PI 489777, and skim sequence-based genotyping of this population, we could validate and correct the draft assembly. In addition to placing the misplaced sequence regions into corresponding chromosome positions, most of the previously unplaced contig sequences have now been incorporated into the pseudomolecules of the improved version. The total chromosome sequence length has increased from 124.38 Mb and 347.24 Mb to 375.06 Mb and 423.28 Mb for the desi and kabuli genomes respectively. Both genomes have been re-annotated. A total of 33,473 genes from kabuli and 31,419 genes from desi were predicted. Both improved genomes are available at http://cicer.info.