Review
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World J Biol Chem. May 26, 2014; 5(2): 161-168
Published online May 26, 2014. doi: 10.4331/wjbc.v5.i2.161
Value of a newly sequenced bacterial genome
Eudes GV Barbosa, Flavia F Aburjaile, Rommel TJ Ramos, Adriana R Carneiro, Yves Le Loir, Jan Baumbach, Anderson Miyoshi, Artur Silva, Vasco Azevedo
Eudes GV Barbosa, Flavia F Aburjaile, Anderson Miyoshi, Vasco Azevedo, Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901 MG, Brazil
Eudes GV Barbosa, Jan Baumbach, Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark
Flavia F Aburjaile, Yves Le Loir, INRA, UMR1253, Science et Technologie du Lait et de l’Œuf, F-35042 Rennes, France
Rommel TJ Ramos, Adriana R Carneiro, Artur Silva, Laboratório de Polimorfismo de DNA, Instituto de Ciências Biológicas, Univeridade Federal do Pará, Belém 66075-110, Brazil
Author contributions: All authors contributed extensively to the work presented in this review.
Supported by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) in Brazil, processes BEX 12954-12-8 and 11517-12-3, to Barbosa EGV and Aburjaile FF
Correspondence to: Vasco Azevedo, MD, PhD, Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Univeridade Federal de Minas Gerais, Av. Antônio Carlos 6627 Pampulha, Belo Horizonte 31270-901, Brazil. vasco@icb.ufmg.br
Telephone: +55-31-34092873 Fax: +55-31-34092610
Received: December 11, 2013
Revised: January 14, 2014
Accepted: April 3, 2014
Published online: May 26, 2014
Processing time: 181 Days and 10.5 Hours
Abstract

Next-generation sequencing (NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting in an exponential increase in draft (partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the “scientific value” of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses the factors that could be leading to the increase in the number of draft deposits and the consequent loss of relevant biological information.

Keywords: Next-generation sequencing; Drafts; Prokaryotic genomes; Computational tools; Omics

Core tip: Next-generation sequencing (NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of bacterial genomes has not only brought excitement to the field of genomics, it has also heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has consequences for genome quality, resulting in an exponential increase in draft genome deposits in public databases. This review will address the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology, as well as the impact of NGS on draft bacterial genomes.