CIENCIASMEDICASNEWS: Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics

domingo, 4 de noviembre de 2012

Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics

Bin Hu

Bin Hu is a postdoctoral researcher in computational biology and bioinformatics with interests in signal transduction pathways and how cells adapt to environmental perturbations.

Gary Xie

Gary Xie, PhD is a Technical Staff Member of the Bioscience Division at LANL, with a great deal of interest and expertise in comparative studies of human pathogens.

Chien-Chi Lo

Chien-Chi Lo is a research technologist and bioinformaticist at LANL with interests in sequencing analysis, comparative genomics and pathogen characterization from isolate and metagenomic samples.

Shawn R. Starkenburg

Shawn Starkenburg is a postdoctoral researcher who uses genomic and metagenomic information to study complex microbial communities.

Patrick S. G. Chain

Patrick S. G. Chain has had a long-standing interest in microbial comparative genomics and bioinformatics as they pertain to environmental and pathogenic microbes, from isolates to metagenomic samples.

Corresponding author. Patrick S. G. Chain, Genome Sciences, Bioscience Division, Los Alamos National Laboratory, MS-M888, HRL, Los Alamos, NM 87545, USA. Tel: (505) 665-4019; Fax: (505) 665-3024; E-mail: pchain@lanl.gov

Abstract

As soon as whole-genome sequencing entered the scene in the mid-1990s and demonstrated its use in revealing the entire genetic potential of any given microbial organism, this technique immediately revolutionized the way pathogen (and many other fields of) research was carried out. The ability to perform whole-genome comparisons further transformed the field and allowed scientists to obtain information linking phenotypic dissimilarities among closely related organisms and their underlying genetic mechanisms. Such comparisons have become commonplace in examining strain-to-strain variability, as well as comparing pathogens to less, or nonpathogenic near neighbors. In recent years, a bloom in novel sequencing technologies along with continuous increases in throughput has occurred, inundating the field with various types of massively parallel sequencing data and further transforming comparative genomics research. Here, we review the evolution of comparative genomics, its impact in understanding pathogen evolution and physiology and the opportunities and challenges presented by next-generation sequencing as applied to pathogen genome comparisons.