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Large-insert genome analysis technology detects structural variation in Pseudomonas aeruginosa clinical strains from cystic fibrosis patients

2008; Elsevier BV; Volume: 91; Issue: 6 Linguagem: Inglês

10.1016/j.ygeno.2008.02.005

1089-8646

Hillary S. Hayden, Will Gillett, Channakhone Saenphimmachak, Regina Lim, Yang Zhou, Michael A. Jacobs, Jean Chang, Laurence Rohmer, David A. D’Argenio, Anthony Palmieri, Ruth Levy, Eric Haugen, Gane Ka‐Shu Wong, Mitch Brittnacher, Jane L. Burns, Samuel I. Miller, Maynard V. Olson, Rajinder Kaul,

Plant Pathogenic Bacteria Studies

Large-insert genome analysis (LIGAN) is a broadly applicable, high-throughput technology designed to characterize genome-scale structural variation. Fosmid paired-end sequences and DNA fingerprints from a query genome are compared to a reference sequence using the Genomic Variation Analysis (GenVal) suite of software tools to pinpoint locations of insertions, deletions, and rearrangements. Fosmids spanning regions that contain new structural variants can then be sequenced. Clonal pairs of Pseudomonas aeruginosa isolates from four cystic fibrosis patients were used to validate the LIGAN technology. Approximately 1.5 Mb of inserted sequences were identified, including 743 kb containing 615 ORFs that are absent from published P. aeruginosa genomes. Six rearrangement breakpoints and 220 kb of deleted sequences were also identified. Our study expands the "genome universe" of P. aeruginosa and validates a technology that complements emerging, short-read sequencing methods that are better suited to characterizing single-nucleotide polymorphisms than structural variation.