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A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies
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SYSNO ASEP 0432721 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies Author(s) Ruperao, P. (AU)
Chan, C.K.K. (AU)
Azam, S. (IN)
Karafiátová, Miroslava (UEB-Q) RID, ORCID
Hayashi, S. (AU)
Čížková, Jana (UEB-Q) RID, ORCID
Šimková, Hana (UEB-Q) RID, ORCID
Vrána, Jan (UEB-Q) RID, ORCID
Doležel, Jaroslav (UEB-Q) RID, ORCID
Varshney, R.K. (IN)
Edwards, D. (AU)Number of authors 21 Source Title Plant Biotechnology Journal. - : Wiley - ISSN 1467-7644
Roč. 12, č. 6 (2014), s. 778-786Number of pages 9 s. Language eng - English Country US - United States Keywords chickpea ; genome assembly ; cytogenetics Subject RIV EB - Genetics ; Molecular Biology R&D Projects GBP501/12/G090 GA ČR - Czech Science Foundation (CSF) LO1204 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) Institutional support UEB-Q - RVO:61389030 UT WOS 000339488200014 DOI 10.1111/pbi.12182 Annotation 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. Workplace Institute of Experimental Botany Contact David Klier, knihovna@ueb.cas.cz, Tel.: 220 390 469 Year of Publishing 2015
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