A new strategy for genome assembly using short sequence reads and reduced representation libraries.

Genome Research
Andrew L YoungElliott H Margulies

Abstract

We have developed a novel approach for using massively parallel short-read sequencing to generate fast and inexpensive de novo genomic assemblies comparable to those generated by capillary-based methods. The ultrashort (<100 base) sequences generated by this technology pose specific biological and computational challenges for de novo assembly of large genomes. To account for this, we devised a method for experimentally partitioning the genome using reduced representation (RR) libraries prior to assembly. We use two restriction enzymes independently to create a series of overlapping fragment libraries, each containing a tractable subset of the genome. Together, these libraries allow us to reassemble the entire genome without the need of a reference sequence. As proof of concept, we applied this approach to sequence and assembled the majority of the 125-Mb Drosophila melanogaster genome. We subsequently demonstrate the accuracy of our assembly method with meaningful comparisons against the current available D. melanogaster reference genome (dm3). The ease of assembly and accuracy for comparative genomics suggest that our approach will scale to future mammalian genome-sequencing efforts, saving both time and money without sacrific...Continue Reading

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Citations

Jun 8, 2011·Proceedings of the National Academy of Sciences of the United States of America·Korbinian SchneebergerDetlef Weigel
Jun 4, 2010·Briefings in Bioinformatics·Daniel C KoboldtRichard K Wilson
Aug 21, 2010·Briefings in Bioinformatics·Konrad Paszkiewicz, David J Studholme
Sep 12, 2013·BMC Bioinformatics·Tilo Buschmann, Leonid V Bystrykh
Jul 24, 2013·BMC Research Notes·Leonid V Bystrykh
Jul 28, 2011·Molecular Ecology Resources·Kevin C RoweCraig C Moritz
Apr 30, 2014·The Plant Journal : for Cell and Molecular Biology·Clícia GrativolPaulo Cavalcanti Gomes Ferreira
Oct 17, 2015·Journal of Biological Research·Bingguang XiaoYongping Li
Jun 10, 2015·Nature Reviews. Genetics·Ludovic OrlandoEske Willerslev
Jan 27, 2015·Molecular Breeding : New Strategies in Plant Improvement·Ravinder SinghIsobel A P Parkin
May 1, 2016·Current Protocols in Plant Biology·Nathan J Bivens, Mingyi Zhou

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