title: Local de novo assembly of RAD paired-end contigs using short sequencing reads.
abstract: Despite the power of massively parallel sequencing platforms, a drawback is the short length of the sequence reads produced. We demonstrate that short reads can be locally assembled into longer contigs using paired-end sequencing of restriction-site associated DNA (RAD-PE) fragments. We use this RAD-PE contig approach to identify single nucleotide polymorphisms (SNPs) and determine haplotype structure in threespine stickleback and to sequence E. coli and stickleback genomic DNA with overlapping contigs of several hundred nucleotides. We also demonstrate that adding a circularization step allows the local assembly of contigs up to 5 kilobases (kb) in length. The ease of assembly and accuracy of the individual contigs produced from each RAD site sequence suggests RAD-PE sequencing is a useful way to convert genome-wide short reads into individually-assembled sequences hundreds or thousands of nucleotides long.
authors.affiliation: Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America.
authors.forename: Paul D
authors.initials: PD
authors.lastname: Etter
authors.forename: Jessica L
authors.initials: JL
authors.lastname: Preston
authors.forename: Susan
authors.initials: S
authors.lastname: Bassham
authors.forename: William A
authors.initials: WA
authors.lastname: Cresko
authors.forename: Eric A
authors.initials: EA
authors.lastname: Johnson
mesh_terms: D000818:Animals; D001483:Base Sequence; D020451:Contig Mapping; D004247:DNA / Q000235:genetics*; D004252:DNA Mutational Analysis; D004926:Escherichia coli / Q000235:genetics*; D015723:Gene Library; D016678:Genome / Q000235:genetics; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D015203:Reproducibility of Results; D015183:Restriction Mapping / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D023701:Smegmamorpha / Q000235:genetics*
chemical_list: D004247:DNA