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An efficient approach to BAC based assembly of complex genomes
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SYSNO ASEP 0456187 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title An efficient approach to BAC based assembly of complex genomes Author(s) Visendi, P. (AU)
Berkman, P.J. (AU)
Hayashi, S. (AU)
Golicz, A.A. (AU)
Bayer, P.E. (AU)
Ruperao, P. (AU)
Hurgobin, B. (AU)
Montenegro, J. (AU)
Chan, C.K.K. (AU)
Staňková, Helena (UEB-Q) RID
Batley, J. (AU)
Šimková, Hana (UEB-Q) RID, ORCID
Doležel, Jaroslav (UEB-Q) RID, ORCID
Edwards, D. (AU)Source Title Plant Methods. - : BioMed Central
Roč. 12, JAN 20 (2016), s. 2Number of pages 9 s. Language eng - English Country GB - United Kingdom Keywords Next-generation sequencing ; SASSY ; BAC Subject RIV EB - Genetics ; Molecular Biology R&D Projects LO1204 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) GAP501/12/2554 GA ČR - Czech Science Foundation (CSF) Institutional support UEB-Q - RVO:61389030 UT WOS 000368412000001 DOI 10.1186/s13007-016-0107-9 Annotation Background: There has been an exponential growth in the number of genome sequencing projects since the introduction of next generation DNA sequencing technologies. Genome projects have increasingly involved assembly of whole genome data which produces inferior assemblies compared to traditional Sanger sequencing of genomic fragments cloned into bacterial artificial chromosomes (BACs). While whole genome shotgun sequencing using next generation sequencing (NGS) is relatively fast and inexpensive, this method is extremely challenging for highly complex genomes, where polyploidy or high repeat content confounds accurate assembly, or where a highly accurate 'gold' reference is required. Several attempts have been made to improve genome sequencing approaches by incorporating NGS methods, to variable success.
Results: We present the application of a novel BAC sequencing approach which combines indexed pools of BACs, Illumina paired read sequencing, a sequence assembler specifically designed for complex BAC assembly, and a custom bioinformatics pipeline. We demonstrate this method by sequencing and assembling BAC cloned fragments from bread wheat and sugarcane genomes.
Conclusions: We demonstrate that our assembly approach is accurate, robust, cost effective and scalable, with applications for complete genome sequencing in large and complex genomes.Workplace Institute of Experimental Botany Contact David Klier, knihovna@ueb.cas.cz, Tel.: 220 390 469 Year of Publishing 2016
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