An efficient approach to BAC based assembly of complex genomes

P. Visendi, P.J. Berkman, S. Hayashi, A.A. Golicz, Philipp Bayer, Pradeep Ruperao, Bhavna Hurgobin, J. Montenegro, Kenneth Chan, H. Staňková, Jacqueline Batley, H. Šimková, J. Doležel, Dave Edwards

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    9 Citations (Scopus)

    Abstract

    © 2016 Visendi et al. 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.
    Original languageEnglish
    Article number2
    Pages (from-to)1
    JournalPlant Methods
    Volume12
    Issue number1
    DOIs
    Publication statusPublished - 20 Jan 2016

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