TY - JOUR
T1 - Sequencing of the Dutch elm disease fungus genome using the Roche/454 GS-FLX titanium system in a comparison of multiple genomics core facilities
AU - Forgetta, Vincenzo
AU - Leveque, Gary
AU - Dias, Joana
AU - Grove, Deborah
AU - Lyons, Robert
AU - Genik, Suzanne
AU - Wright, Chris
AU - Singh, Sushmita
AU - Peterson, Nichole
AU - Zianni, Michael
AU - Kieleczawa, Jan
AU - Steen, Robert
AU - Perera, Anoja
AU - Bintzler, Doug
AU - Adams, Scottie
AU - Hintz, Will
AU - Jacobi, Volker
AU - Bernier, Louis
AU - Levesque, Roger
AU - Dewar, Ken
PY - 2013/3
Y1 - 2013/3
N2 - As part of the DNA Sequencing Research Group of the Association of Biomolecular Resource Facilities, we have tested the reproducibility of the Roche/454 GS-FLX Titanium System at five core facilities. Experience with the Roche/454 system ranged from <10 to >340 sequencing runs performed. All participating sites were supplied with an aliquot of a common DNA preparation and were requested to conduct sequencing at a common loading condition. The evaluation of sequencing yield and accuracy metrics was assessed at a single site. The study was conducted using a laboratory strain of the Dutch elm disease fungus Ophiostoma novo-ulmi strain H327, an ascomycete, vegetatively haploid fungus with an estimated genome size of 30-50 Mb. We show that the Titanium System is reproducible, with some variation detected in loading conditions, sequencing yield, and homopolymer length accuracy. We demonstrate that reads shorter than the theoretical minimum length are of lower overall quality and not simply truncated reads. The O. novo-ulmi H327 genome assembly is 31.8 Mb and is comprised of eight chromosome-length linear scaffolds, a circular mitochondrial conti of 66.4 kb, and a putative 4.2-kb linear plasmid. We estimate that the nuclear genome encodes 8613 protein coding genes, and the mitochondrion encodes 15 genes and 26 tRNAs.
AB - As part of the DNA Sequencing Research Group of the Association of Biomolecular Resource Facilities, we have tested the reproducibility of the Roche/454 GS-FLX Titanium System at five core facilities. Experience with the Roche/454 system ranged from <10 to >340 sequencing runs performed. All participating sites were supplied with an aliquot of a common DNA preparation and were requested to conduct sequencing at a common loading condition. The evaluation of sequencing yield and accuracy metrics was assessed at a single site. The study was conducted using a laboratory strain of the Dutch elm disease fungus Ophiostoma novo-ulmi strain H327, an ascomycete, vegetatively haploid fungus with an estimated genome size of 30-50 Mb. We show that the Titanium System is reproducible, with some variation detected in loading conditions, sequencing yield, and homopolymer length accuracy. We demonstrate that reads shorter than the theoretical minimum length are of lower overall quality and not simply truncated reads. The O. novo-ulmi H327 genome assembly is 31.8 Mb and is comprised of eight chromosome-length linear scaffolds, a circular mitochondrial conti of 66.4 kb, and a putative 4.2-kb linear plasmid. We estimate that the nuclear genome encodes 8613 protein coding genes, and the mitochondrion encodes 15 genes and 26 tRNAs.
KW - Fungal genomics
KW - Massively parallel DNA sequencing
KW - Ophiostoma novo-ulmi
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U2 - 10.7171/jbt.12-2401-005
DO - 10.7171/jbt.12-2401-005
M3 - Article
C2 - 23542132
AN - SCOPUS:84875759967
SN - 1524-0215
VL - 24
SP - 39
EP - 49
JO - Journal of Biomolecular Techniques
JF - Journal of Biomolecular Techniques
IS - 1
ER -