A hybrid approach for the automated finishing of bacterial genomes

被引：134

作者：

Bashir, Ali ^{[1
,2
]}

Klammer, Aaron A. ^{[1
]}

Robins, William P. ^{[3
]}

Chin, Chen-Shan ^{[1
]}

Webster, Dale ^{[1
]}

Paxinos, Ellen ^{[1
]}

Hsu, David ^{[1
]}

Ashby, Meredith ^{[1
]}

Wang, Susana ^{[1
]}

Peluso, Paul ^{[1
]}

Sebra, Robert ^{[1
]}

Sorenson, Jon ^{[1
]}

Bullard, James ^{[1
]}

Yen, Jackie ^{[1
]}

Valdovino, Marie ^{[1
]}

Mollova, Emilia ^{[1
]}

Luong, Khai ^{[1
]}

Lin, Steven ^{[1
]}

Lamay, Brianna ^{[1
]}

Joshi, Amruta ^{[1
]}

Rowe, Lori ^{[4
]}

Frace, Michael ^{[4
]}

Tarr, Cheryl L. ^{[4
]}

Turnsek, Maryann ^{[4
]}

Davis, Brigid M. ^{[5
,6
]}

Kasarskis, Andrew ^{[1
]}

Mekalanos, John J. ^{[3
]}

Waldor, Matthew K. ^{[3
,5
,6
]}

Schadt, Eric E. ^{[1
,2
]}

机构：

[1] Pacific Biosci, Menlo Pk, CA USA

[2] Mt Sinai Sch Med, Dept Genet & Genom Sci, New York, NY USA

[3] Harvard Univ, Sch Med, Dept Microbiol & Mol Genet, Boston, MA 02115 USA

[4] Ctr Dis Control & Prevent, Natl Ctr Emerging & Zoonot Infect Dis, Atlanta, GA USA

[5] Harvard Univ, Sch Med, Dept Med, Boston, MA USA

[6] Howard Hughes Med Inst, Boston, MA 02115 USA

来源：

NATURE BIOTECHNOLOGY | 2012年 / 30卷 / 07期

基金：

美国国家卫生研究院;

关键词：

READ SEQUENCE DATA; VIBRIO-CHOLERAE; STRUCTURAL VARIATION; ORIGIN; GENERATION; INTEGRONS; ASSEMBLER; OUTBREAK; STRAIN; HAITI;

D O I：

10.1038/nbt.2288

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：

Advances in DNA sequencing technology have improved our ability to characterize most genomic diversity. However, accurate resolution of large structural events is challenging because of the short read lengths of second-generation technologies. Third-generation sequencing technologies, which can yield longer multikilobase reads, have the potential to address limitations associated with genome assembly. Here we combine sequencing data from second- and third-generation DNA sequencing technologies to assemble the two-chromosome genome of a recent Haitian cholera outbreak strain into two nearly finished contigs at >99.9% accuracy. Complex regions with clinically relevant structure were completely resolved. In separate control assemblies on experimental and simulated data for the canonical N16961 cholera reference strain, we obtained 14 scaffolds of greater than 1 kb for the experimental data and 8 scaffolds of greater than 1 kb for the simulated data, which allowed us to correct several errors in contigs assembled from the short-read data alone. This work provides a blueprint for the next generation of rapid microbial identification and full-genome assembly.

引用

页码：701 / +

页数：9

共 49 条

[1] Recent Clonal Origin of Cholera in Haiti [J].

Ali, Afsar ;

Chen, Yuansha ;

Johnson, Judith A. ;

Redden, Edsel ;

Mayette, Yfto ;

Rashid, Mohammed H. ;

Stine, O. Colin ;

Morris, J. Glenn, Jr. .

EMERGING INFECTIOUS DISEASES, 2011, 17 (04) :699-701

[2] APPLICATIONS OF NEXT-GENERATION SEQUENCING Genome structural variation discovery and genotyping [J].

Alkan, Can ;

Coe, Bradley P. ;

Eichler, Evan E. .

NATURE REVIEWS GENETICS, 2011, 12 (05) :363-375

[3] Limitations of next-generation genome sequence assembly [J].

Alkan, Can ;

Sajjadian, Saba ;

Eichler, Evan E. .

NATURE METHODS, 2011, 8 (01) :61-65

[4]

Batzoglou S, 2002, GENOME RES, V12, P177, DOI 10.1101/gr.208902

[5] ALLPATHS: De novo assembly of whole-genome shotgun microreads [J].

Butler, Jonathan ;

MacCallum, Iain ;

Kleber, Michael ;

Shlyakhter, Ilya A. ;

Belmonte, Matthew K. ;

Lander, Eric S. ;

Nusbaum, Chad ;

Jaffe, David B. .

GENOME RESEARCH, 2008, 18 (05) :810-820

[6] Genome Project Standards in a New Era of Sequencing [J].

Chain, P. S. G. ;

Grafham, D. V. ;

Fulton, R. S. ;

FitzGerald, M. G. ;

Hostetler, J. ;

Muzny, D. ;

Ali, J. ;

Birren, B. ;

Bruce, D. C. ;

Buhay, C. ;

Cole, J. R. ;

Ding, Y. ;

Dugan, S. ;

Field, D. ;

Garrity, G. M. ;

Gibbs, R. ;

Graves, T. ;

Han, C. S. ;

Harrison, S. H. ;

Highlander, S. ;

Hugenholtz, P. ;

Khouri, H. M. ;

Kodira, C. D. ;

Kolker, E. ;

Kyrpides, N. C. ;

Lang, D. ;

Lapidus, A. ;

Malfatti, S. A. ;

Markowitz, V. ;

Metha, T. ;

Nelson, K. E. ;

Parkhill, J. ;

Pitluck, S. ;

Qin, X. ;

Read, T. D. ;

Schmutz, J. ;

Sozhamannan, S. ;

Sterk, P. ;

Strausberg, R. L. ;

Sutton, G. ;

Thomson, N. R. ;

Tiedje, J. M. ;

Weinstock, G. ;

Wollam, A. ;

Detter, J. C. .

SCIENCE, 2009, 326 (5950) :236-237

[7] Fragment assembly with short reads [J].

Chaisson, M ;

Pevzner, P ;

Tang, HX .

BIOINFORMATICS, 2004, 20 (13) :2067-2074

[8] Short read fragment assembly of bacterial genomes [J].

Chaisson, Mark J. ;

Pevzner, Pavel A. .

GENOME RESEARCH, 2008, 18 (02) :324-330

[9] The Origin of the Haitian Cholera Outbreak Strain. [J].

Chin, Chen-Shan ;

Sorenson, Jon ;

Harris, Jason B. ;

Robins, William P. ;

Charles, Richelle C. ;

Jean-Charles, Roger R. ;

Bullard, James ;

Webster, Dale R. ;

Kasarskis, Andrew ;

Peluso, Paul ;

Paxinos, Ellen E. ;

Yamaichi, Yoshiharu ;

Calderwood, Stephen B. ;

Mekalanos, John J. ;

Schadt, Eric E. ;

Waldor, Matthew K. .

NEW ENGLAND JOURNAL OF MEDICINE, 2011, 364 (01) :33-42

[10] CTXφ contains a hybrid genome derived from tandemly integrated elements [J].

Davis, BM ;

Waldor, MK .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (15) :8572-8577

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