Journal article
A chromosomal genomics approach to assess and validate thedesiandkabulidraft chickpea genome assemblies
Plant Biotechnology Journal, Vol.12(6), pp.778-786
2014
Abstract
With the expansion of next-generation sequencing technology and advanced bioinformatics, there has been a rapid growth of genome sequencing projects. However, while this technology enables the rapid and cost-effective assembly of draft genomes, the quality of these assemblies usually falls short of gold standard genome assemblies produced using the more traditional BAC by BAC and Sanger sequencing approaches. Assembly validation is often performed by the physical anchoring of genetically mapped markers, but this is prone to errors and the resolution is usually low, especially towards centromeric regions where recombination is limited. New approaches are required to validate reference 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 chromosome sizes and published assemblies highlights significant differences. Our chromosomal genomics analysis highlights short defined regions that appear to have been misassembled in the kabuli genome and identifies large-scale misassembly in the draft desi genome. The integration of chromosomal genomics tools within genome sequencing projects has the potential to significantly improve the construction and validation of genome assemblies. The approach could be applied both for new genome assemblies as well as published assemblies, and complements currently applied genome assembly strategies.
Details
- Title
- A chromosomal genomics approach to assess and validate thedesiandkabulidraft chickpea genome assemblies
- Authors/Creators
- P. Ruperao (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsC-K.K. Chan (Author/Creator) - The University of QueenslandS. Azam (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsM. Karafiátová (Author/Creator) - Czech Academy of Sciences, Institute of Experimental BotanyS. Hayashi (Author/Creator) - The University of QueenslandJ. Čížková (Author/Creator) - Czech Academy of Sciences, Institute of Experimental BotanyR.K. Saxena (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsH. Šimková (Author/Creator) - Czech Academy of Sciences, Institute of Experimental BotanyC. Song (Author/Creator) - BGI Group (China)J. Vrána (Author/Creator) - Czech Academy of Sciences, Institute of Experimental BotanyA. Chitikineni (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsP. Visendi (Author/Creator) - The University of QueenslandP.M. Gaur (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsT. Millan (Author/Creator) - University of CórdobaK.B. Singh (Author/Creator) - Plant IndustryB. Taran (Author/Creator)J. Wang (Author/Creator) - BGI Group (China)J. Batley (Author/Creator) - The University of QueenslandJ. Doležel (Author/Creator) - Czech Academy of Sciences, Institute of Experimental BotanyR.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsD. Edwards (Author/Creator) - Australian Centre for Plant Functional Genomics
- Publication Details
- Plant Biotechnology Journal, Vol.12(6), pp.778-786
- Publisher
- Blackwell Publishing Inc.
- Identifiers
- 991005542948507891
- Copyright
- © 2014 Society for Experimental Biology
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
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- Plant Sciences
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- Plant & Animal Science