De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data

被引：107

作者：

DiGuistini, Scott ^{[2
]}

Liao, Nancy Y. ^{[1
]}

Platt, Darren ^{[3
]}

Robertson, Gordon ^{[1
]}

Seidel, Michael ^{[1
]}

Chan, Simon K. ^{[1
]}

Docking, T. Roderick ^{[1
]}

Birol, Inanc ^{[1
]}

Holt, Robert A. ^{[1
]}

Hirst, Martin ^{[1
]}

Mardis, Elaine ^{[4
]}

Marra, Marco A. ^{[1
]}

Hamelin, Richard C. ^{[5
]}

Bohlmann, Joerg ^{[6
]}

Breuil, Colette ^{[2
]}

Jones, Steven J. M. ^{[1
]}

机构：

[1] BC Canc Agcy Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada

[2] Univ British Columbia, Dept Wood Sci, Vancouver, BC V6T 1Z4, Canada

[3] Amyris Biotechnol Inc, Emeryville, CA 94608 USA

[4] Washington Univ, Sch Med, St Louis, MO 63108 USA

[5] Natl Res Canada, Ste Foy, PQ G1V 4C7, Canada

[6] Univ British Columbia, Michael Smith Labs, Vancouver, BC V6T 1Z3, Canada

来源：

GENOME BIOLOGY | 2009年 / 10卷 / 09期

基金：

加拿大自然科学与工程研究理事会;

关键词：

DNA; QUALITY; TOOL;

D O I：

10.1186/gb-2009-10-9-r94

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：

Sequencing-by-synthesis technologies can reduce the cost of generating de novo genome assemblies. We report a method for assembling draft genome sequences of eukaryotic organisms that integrates sequence information from different sources, and demonstrate its effectiveness by assembling an approximately 32.5 Mb draft genome sequence for the forest pathogen Grosmannia clavigera, an ascomycete fungus. We also developed a method for assessing draft assemblies using Illumina paired end read data and demonstrate how we are using it to guide future sequence finishing. Our results demonstrate that eukaryotic genome sequences can be accurately assembled by combining Illumina, 454 and Sanger sequence data.

引用

页数：12

共 21 条

[1] [Anonymous], Dust
[2] Quality scores and SNP detection in sequencing-by-synthesis systems
Brockman, William
Alvarez, Pablo
Young, Sarah
Garber, Manuel
Giannoukos, Georgia
Lee, William L.
Russ, Carsten
Lander, Eric S.
Nusbaum, Chad
Jaffe, David B.
[J]. GENOME RESEARCH, 2008, 18 (05) : 763 - 770
[3] ALLPATHS: De novo assembly of whole-genome shotgun microreads
Butler, Jonathan
MacCallum, Iain
Kleber, Michael
Shlyakhter, Ilya A.
Belmonte, Matthew K.
Lander, Eric S.
Nusbaum, Chad
Jaffe, David B.
[J]. GENOME RESEARCH, 2008, 18 (05) : 810 - 820
[4] The genome sequence of the rice blast fungus Magnaporthe grisea
Dean, RA
Talbot, NJ
Ebbole, DJ
Farman, ML
Mitchell, TK
Orbach, MJ
Thon, M
Kulkarni, R
Xu, JR
Pan, HQ
Read, ND
Lee, YH
Carbone, I
Brown, D
Oh, YY
Donofrio, N
Jeong, JS
Soanes, DM
Djonovic, S
Kolomiets, E
Rehmeyer, C
Li, WX
Harding, M
Kim, S
Lebrun, MH
Bohnert, H
Coughlan, S
Butler, J
Calvo, S
Ma, LJ
Nicol, R
Purcell, S
Nusbaum, C
Galagan, JE
Birren, BW
[J]. NATURE, 2005, 434 (7036) : 980 - 986
[5] Generation and annotation of lodgepole pine and oleoresin-induced expressed sequences from the blue-stain fungus Ophiostoma clavigerum, a Mountain pine beetle-associated pathogen
DiGuistini, Scott
Ralph, Steven G.
Lim, Young W.
Holt, Robert
Jones, Steven
Bohlmann, Jorg
Breuil, Colette
[J]. FEMS MICROBIOLOGY LETTERS, 2007, 267 (02) : 151 - 158
[6] FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology
Fejes, Anthony P.
Robertson, Gordon
Bilenky, Mikhail
Varhol, Richard
Bainbridge, Matthew
Jones, Steven J. M.
[J]. BIOINFORMATICS, 2008, 24 (15) : 1729 - 1730
[7] The genome sequence of the filamentous fungus Neurospora crassa
Galagan, JE
Calvo, SE
Borkovich, KA
Selker, EU
Read, ND
Jaffe, D
FitzHugh, W
Ma, LJ
Smirnov, S
Purcell, S
Rehman, B
Elkins, T
Engels, R
Wang, SG
Nielsen, CB
Butler, J
Endrizzi, M
Qui, DY
Ianakiev, P
Pedersen, DB
Nelson, MA
Werner-Washburne, M
Selitrennikoff, CP
Kinsey, JA
Braun, EL
Zelter, A
Schulte, U
Kothe, GO
Jedd, G
Mewes, W
Staben, C
Marcotte, E
Greenberg, D
Roy, A
Foley, K
Naylor, J
Stabge-Thomann, N
Barrett, R
Gnerre, S
Kamal, M
Kamvysselis, M
Mauceli, E
Bielke, C
Rudd, S
Frishman, D
Krystofova, S
Rasmussen, C
Metzenberg, RL
Perkins, DD
Kroken, S
[J]. NATURE, 2003, 422 (6934) : 859 - 868
[8] Consed: A graphical tool for sequence finishing
Gordon, D
Abajian, C
Green, P
[J]. GENOME RESEARCH, 1998, 8 (03) : 195 - 202
[9] Accuracy and quality of massively parallel DNA pyrosequencing
Huse, Susan M.
Huber, Julie A.
Morrison, Hilary G.
Sogin, Mitchell L.
Mark Welch, David
[J]. GENOME BIOLOGY, 2007, 8 (07)
[10] Circos: An information aesthetic for comparative genomics
Krzywinski, Martin
Schein, Jacqueline
Birol, Inanc
Connors, Joseph
Gascoyne, Randy
Horsman, Doug
Jones, Steven J.
Marra, Marco A.
[J]. GENOME RESEARCH, 2009, 19 (09) : 1639 - 1645

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