title: High efficiency application of a mate-paired library from next-generation sequencing to postlight sequencing: Corynebacterium pseudotuberculosis as a case study for microbial de novo genome assembly.
abstract: With the advent of high-throughput DNA sequencing platforms, there has been a reduction in the cost and time of sequencing. With these advantages, new challenges have emerged, such as the handling of large amounts of data, quality assessment, and the assembly of short reads. Currently, benchtop high-throughput sequencers enable the genomes of prokaryotic organisms to be sequenced within two hours with a reduction in coverage compared with the SOLiD, Illumina and 454 FLX Titanium platforms, making it necessary to evaluate the efficiency of less expensive benchtop instruments for prokaryotic genomics. In the present work, we evaluate and propose a methodology for the use of the Ion Torrent PGM platform for decoding the gram-positive bacterium Corynebacterium pseudotuberculosis, for which 15 complete genome sequences have already been deposited based on fragment and mate-paired libraries with a 3-kb insert size. Despite the low coverage, a single sequencing run using a mate-paired library generated 39 scaffolds after de novo assembly without data curation. This result is superior to that obtained by sequencing using libraries generated from fragments marketed by the equipment's manufacturer, as well as that observed for mate-pairs sequenced by SOLiD. The generated sequence added an extra 91kb to the genome available at NCBI.
authors.affiliation: Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil.
authors.forename: Rommel Thiago Jucá
authors.initials: RT
authors.lastname: Ramos
authors.forename: Adriana Ribeiro
authors.initials: AR
authors.lastname: Carneiro
authors.forename: Siomar
authors.initials: S
authors.lastname: de Castro Soares
authors.forename: Silvanira
authors.initials: S
authors.lastname: Barbosa
authors.forename: Leonardo
authors.initials: L
authors.lastname: Varuzza
authors.forename: Guilherme
authors.initials: G
authors.lastname: Orabona
authors.forename: Andreas
authors.initials: A
authors.lastname: Tauch
authors.forename: Vasco
authors.initials: V
authors.lastname: Azevedo
authors.forename: Maria Paula
authors.initials: MP
authors.lastname: Schneider
authors.forename: Artur
authors.initials: A
authors.lastname: Silva
mesh_terms: D016925:Corynebacterium pseudotuberculosis / Q000235:genetics*; D023281:Genomics / Q000379:methods*
keywords: Corynebacterium; Genome sequencing; Ion Torrent; Mate-paired library