A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies

Ruperao, P and Bayer, P E and Chan, C K K and Azam, S and Karafiatova, M and Hayashi, S and Cizkova, J and Saxena, R K and Simkova, H and Song, C and Vrána, J and Chitikineni, A and Visendi, P and Gaur, P M and Millan, T and Singh, K B and Taran, B and Wang, J and Batley, J and Dolezel, J and Varshney, R K and Edwards, D (2014) A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. The University of Queensland, Australia.

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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 (Varshney et al 2013) and desi (Jain et al 2013) 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.

Item Type: Other
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Chickpea; Genome assemblies; Chromosomal Genomics
Subjects: Mandate crops > Chickpea
Depositing User: Mr Ramesh K
Date Deposited: 07 Aug 2015 04:59
Last Modified: 04 Sep 2017 09:06
URI: http://oar.icrisat.org/id/eprint/8909
Acknowledgement: The authors would like to acknowledge funding support from the Australian Research Council (Projects LP0882095, LP0883462, LP110100200 and DP0985953) and the AISRF grand challenge fund GCF010013. This work was supported AGRF, QCIF, APAC.
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