title: Gene-boosted assembly of a novel bacterial genome from very short reads.
abstract: Recent improvements in technology have made DNA sequencing dramatically faster and more efficient than ever before. The new technologies produce highly accurate sequences, but one drawback is that the most efficient technology produces the shortest read lengths. Short-read sequencing has been applied successfully to resequence the human genome and those of other species but not to whole-genome sequencing of novel organisms. Here we describe the sequencing and assembly of a novel clinical isolate of Pseudomonas aeruginosa, strain PAb1, using very short read technology. From 8,627,900 reads, each 33 nucleotides in length, we assembled the genome into one scaffold of 76 ordered contiguous sequences containing 6,290,005 nucleotides, including one contig spanning 512,638 nucleotides, plus an additional 436 unordered contigs containing 416,897 nucleotides. Our method includes a novel gene-boosting algorithm that uses amino acid sequences from predicted proteins to build a better assembly. This study demonstrates the feasibility of very short read sequencing for the sequencing of bacterial genomes, particularly those for which a related species has been sequenced previously, and expands the potential application of this new technology to most known prokaryotic species.
authors.affiliation: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America. salzberg@umd.edu
authors.forename: Steven L
authors.initials: SL
authors.lastname: Salzberg
authors.forename: Daniel D
authors.initials: DD
authors.lastname: Sommer
authors.forename: Daniela
authors.initials: D
authors.lastname: Puiu
authors.forename: Vincent T
authors.initials: VT
authors.lastname: Lee
mesh_terms: D001419:Bacteria / Q000235:genetics*; D019295:Computational Biology; D004269:DNA, Bacterial / Q000235:genetics; D005818:Genetic Engineering; D005821:Genetic Techniques; D016680:Genome, Bacterial; D006801:Humans; D008957:Models, Genetic; D011550:Pseudomonas aeruginosa / Q000235:genetics / Q000302:isolation & purification / Q000472:pathogenicity
chemical_list: D004269:DNA, Bacterial