Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads

被引：169

作者：

Etter, Paul D. ^{[1
]}

Preston, Jessica L. ^{[1
]}

Bassham, Susan ^{[2
]}

Cresko, William A. ^{[2
]}

Johnson, Eric A. ^{[1
]}

机构：

[1] Univ Oregon, Inst Mol Biol, Eugene, OR 97403 USA

[2] Univ Oregon, Ctr Ecol & Evolutionary Biol, Eugene, OR 97403 USA

来源：

PLOS ONE | 2011年 / 6卷 / 04期

关键词：

PARALLEL; GENOME;

D O I：

10.1371/journal.pone.0018561

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

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