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

被引:29
作者
Hu, Bin [1 ]
Xie, Gary [1 ]
Lo, Chien-Chi [1 ]
Starkenburg, Shawn R. [1 ]
Chain, Patrick S. G. [1 ]
机构
[1] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM 87545 USA
关键词
comparative genomics; whole-genome alignment; next-generation sequencing; pathogen pangenomics; bioinformatics; BACTERIAL PAN-GENOME; SHORT READ ALIGNMENT; YERSINIA-PESTIS; ESCHERICHIA-COLI; BACILLUS-ANTHRACIS; STREPTOCOCCUS-PNEUMONIAE; GENE-EXPRESSION; DNA; DIVERSITY; EVOLUTION;
D O I
10.1093/bfgp/elr042
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
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.
引用
收藏
页码:322 / 333
页数:12
相关论文
共 118 条
[1]   AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision [J].
Abyzov, Alexej ;
Gerstein, Mark .
BIOINFORMATICS, 2011, 27 (05) :595-603
[2]   Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis [J].
Achtman, M ;
Zurth, K ;
Morelli, C ;
Torrea, G ;
Guiyoule, A ;
Carniel, E .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1999, 96 (24) :14043-14048
[3]   Microevolution and history of the plague bacillus, Yersinia pestis [J].
Achtman, M ;
Morelli, G ;
Zhu, PX ;
Wirth, T ;
Diehl, I ;
Kusecek, B ;
Vogler, AJ ;
Wagner, DM ;
Allender, CJ ;
Easterday, WR ;
Chenal-Francisque, V ;
Worsham, P ;
Thomson, NR ;
Parkhill, J ;
Lindler, LE ;
Carniel, E ;
Keim, P .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (51) :17837-17842
[4]   The RAST server: Rapid annotations using subsystems technology [J].
Aziz, Ramy K. ;
Bartels, Daniela ;
Best, Aaron A. ;
DeJongh, Matthew ;
Disz, Terrence ;
Edwards, Robert A. ;
Formsma, Kevin ;
Gerdes, Svetlana ;
Glass, Elizabeth M. ;
Kubal, Michael ;
Meyer, Folker ;
Olsen, Gary J. ;
Olson, Robert ;
Osterman, Andrei L. ;
Overbeek, Ross A. ;
McNeil, Leslie K. ;
Paarmann, Daniel ;
Paczian, Tobias ;
Parrello, Bruce ;
Pusch, Gordon D. ;
Reich, Claudia ;
Stevens, Rick ;
Vassieva, Olga ;
Vonstein, Veronika ;
Wilke, Andreas ;
Zagnitko, Olga .
BMC GENOMICS, 2008, 9 (1)
[5]   RETRACTED: Evaluation of next-generation sequencing software in mapping and assembly (Retracted article. See vol. 56, pg. 687, 2011) [J].
Bao, Suying ;
Jiang, Rui ;
Kwan, WingKeung ;
Wang, BinBin ;
Ma, Xu ;
Song, You-Qiang .
JOURNAL OF HUMAN GENETICS, 2011, 56 (06) :406-414
[6]   Population diversity and dynamics of Streptococcus mitis, Streptococcus oralis, and Streptococcus infantis in the upper respiratory tracts of adults, determined by a nonculture strategy [J].
Bek-Thomsen, Malene ;
Tettelin, Herve ;
Hance, Loana ;
Nelson, Karen E. ;
Kilian, Mogens .
INFECTION AND IMMUNITY, 2008, 76 (05) :1889-1896
[7]   Sequencing the species pan-genome [J].
Bentley, Stephen .
NATURE REVIEWS MICROBIOLOGY, 2009, 7 (04) :258-259
[8]   GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions [J].
Besemer, J ;
Lomsadze, A ;
Borodovsky, M .
NUCLEIC ACIDS RESEARCH, 2001, 29 (12) :2607-2618
[9]   Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies [J].
Boisvert, Sebastien ;
Laviolette, Francois ;
Corbeil, Jacques .
JOURNAL OF COMPUTATIONAL BIOLOGY, 2010, 17 (11) :1519-1533
[10]  
Burroughs A. M., 2007, V3, P48, DOI 10.1159/000107603