Ruperao, P., Chan, C.K., Azam, S., Karafiátová, M., Hayashi, S., Cížková, J., Saxena, R.K., Šimková, H., Song, C., Vrána, J., Chitikineni, A., Visendi, P., Gaur, P.M., Millán, T., Singh, K.B., Taran, B., Wang, J., Batley, J., Doležel, J., Varshney, R.K., Edwards, D.
PLANT BIOTECHNOLOGY JOURNAL
12:
778-786,
2014
Keywords:
chickpea, genome assembly, cytogenetics, cicer
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.
Fulltext: contact IEB authors
IEB authors: Jana Čížková,
Jaroslav Doležel,
Miroslava Karafiá...,
Hana Šimková,
Jan Vrána
Čeština
English