Sequencing of the Dutch elm disease fungus genome using the Roche/454 GS-FLX titanium system in a comparison of multiple genomics core facilities

Journal of Biomolecular Techniques

Volumn 24, Issue 1, 2013, Pages 39-49

  Forgetta, Vincenzo ^a,b   Leveque, Gary ^b   Dias, Joana ^b   Grove, Deborah ^c,d   Lyons, Robert ^c,e   Genik, Suzanne ^e   Wright, Chris ^f   Singh, Sushmita ^c,g   Peterson, Nichole ^g   Zianni, Michael ^c,h   Kieleczawa, Jan ^c,i   Steen, Robert ^c,j   Perera, Anoja ^c,k   Bintzler, Doug ^c,l   Adams, Scottie ^c,m   Hintz, Will ⁿ   Jacobi, Volker ^o   Bernier, Louis ^o   Levesque, Roger ^o   Dewar, Ken ^a,b,c  

^a MCGILL UNIVERSITY   (Canada)

^b MCGILL UNIVERSITY   (Canada)

^c DNA Sequencing Research Group of the Association of Biomolecular Resourcev Facilities   (United States)

^d PENNSYLVANIA STATE UNIVERSITY   (United States)

^e UNIVERSITY OF MICHIGAN   (United States)

^f UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^g UNIVERSITY OF MINNESOTA   (United States)

^h OHIO STATE UNIVERSITY   (United States)

ⁱ Wyzer Biosciences   (United States)

^j HARVARD MEDICAL SCHOOL   (United States)

^k STOWERS INSTITUTE FOR MEDICAL RESEARCH   (United States)

^l UNIVERSITY OF CINCINNATI COLLEGE OF MEDICINE   (United States)

^m TRUDEAU INSTITUTE   (United States)

ⁿ UNIVERSITY OF VICTORIA   (Canada)

^o UNIVERSITÉ LAVAL   (Canada)

more..

Author keywords

Fungal genomics; Massively parallel DNA sequencing; Ophiostoma novo ulmi

Indexed keywords

CONTIG;

AGAR GEL ELECTROPHORESIS; ARTICLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; DUTCH ELM DISEASE; EXPRESSED SEQUENCE TAG; FUNGAL GENOME; GENE SEQUENCE; GENOME SIZE; NONHUMAN; OPHIOSTOMA; PYROSEQUENCING; REPRODUCIBILITY; SEQUENCE ANALYSIS; SPECTROMETRY;

EID: 84875759967     PISSN: 15240215     EISSN: 19434731     Source Type: Journal    
DOI: 10.7171/jbt.12-2401-005     Document Type: Article

References (18)

1. Margulies M, Egholm M, Altman WE, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005;437:376-380.
2. Dewar K, Bousquet J, Dufour J, Bernier L. A meiotically reproducible chromosome length polymorphism in the ascomycete fungus Ophiostoma ulmi (sensu lato). Mol Gen Genet 1997;255: 38-44.
3. Et-Touil A, Brasier CM, Bernier L. L.calization of a pathogenicity gene in Ophiostoma novo-ulmi and evidence that it may be introgressed from. O. ulmi. Mol Plant-Microbe Interact 1999; 12:6-15.
4. Aoun M, Jacobi V, Boyle B, Bernier L. Identification and monitoring of Ulmus americana transcripts during in vitro interactions with the Dutch elm disease pathogen Ophiostoma novoulmi. Physiol Mol Plant Pathol 2010;74:254-266.
5. Zolan ME, Pukkila PJ. Inheritance of DNA methylation in Coprinus cinereus. Mol Cell Biol 1986;6:195-200.
6. Ter-Hovhannisyan V, Lomsadze A, Chernoff YO, Borodovsky M. Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res 2008;12: 1979-1990.
7. Hintz W, Pinchback M, de la Bastide P, et al. Functional categorization of unique expressed sequence tags obtained from the yeast-like growth phase of the elm pathogen Ophiostoma novo-ulmi. BMC Genomics 2011;12:431-443.
8. Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res 2002;12:656-664.
9. DiGuistini S, Wang Y, Liao NY, et al. Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen. Proc Natl Acad Sci USA 2011;108:2504-2509.
10. Bates MR, Buck KW, Brasier CM. Molecular relationships of the mitochondrial DNA of Ophiostoma ulmi and the NAN and EAN races of O. novo-ulmi determined by restriction fragment length polymorphisms. Mycol Res 1993;97:1093-1100.
11. Campbell PJ, Pleasance ED, Stephens PJ, et al. Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing. Proc Natl Acad Sci USA 2008;105:13081-13086.
12. Ennis PD, Zemmour J, Salter RD, Parham P. Rapid cloning of HLA-A,B cDNA by using the polymerase chain reaction: frequency and nature of errors produced in amplification. Proc Natl Acad Sci USA 1990;87:2833-2837.
13. Bracho MA, Moya A, Barrio E. Contribution of Taq polymerase-induced errors to the estimation of RNA virus diversity. J Gen Virol 1998;79:2921-2928.
14. Dunning AM, Talmud P, Humphries SE. Errors in the polymerase chain reaction. Nucleic Acids Res 1988;16:10393- 10399.
15. Diguistini S, Liao NJ, Platt D., et al. De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. Genome Biol 2009;10:R94.
16. Jacobi V, Dufour J, Bouvet G, Aoun M, Bernier L. Identification of transcripts up-regulated in asexual and sexual fruiting bodies of the Dutch elm disease pathogen Ophiostoma novoulmi. Can J Microbiol 2010;56:697-705.
17. Brasier CM, Kirk SA. Designation of the EAN and NAN races of Ophiostoma novo-ulmi as subspecies. Myol Res 2001; 105:547-554.
18. Brasier CM. Low genetic diversity of the Ophiostoma novo-ulmi population in North America. Mycologia 1996;88:951-964.