ArticleJournal of biomolecular techniques : JBT2013
Sequencing of the Dutch elm disease fungus genome using the Roche/454 GS-FLX Titanium System in a comparison of multiple genomics core facilities.
Article in Journal of biomolecular techniques : JBT, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
35 citing papers in PubMed, 63 citations in OpenAlex.
- An Ammonium Transporter Gene Contributes to the Aggressiveness of the Dutch Elm Disease PathogenJournal of fungi (Basel, Switzerland) · 2026Article
- Ulmus minor response to Dutch elm disease: de novo transcriptome assembly and annotation.Scientific data · 2025Article
- What are the 100 most cited fungal genera?Studies in mycology · 2024Article
- Unraveling the transcriptional features and gene expression networks of pathogenic and saprotrophicMicrobiology spectrum · 2024Article
- Article
- Methods to improve the accuracy of next-generation sequencing.Frontiers in bioengineering and biotechnology · 2023Review
- Independent Evolution Has Led to Distinct Genomic Signatures in Dutch Elm Disease-Causing Fungi and Other Vascular Wilts-Causing Fungal Pathogens.Journal of fungi (Basel, Switzerland) · 2022Article
- Evaluation of the correctable decoding sequencing as a new powerful strategy for DNA sequencing.Life science alliance · 2022Article
- Molecular basis of cycloheximide resistance in the Ophiostomatales revealed.Current genetics · 2022Article
- Generic boundaries in theStudies in mycology · 2022Article
- Comparative Analysis of Transcriptomes ofJournal of fungi (Basel, Switzerland) · 2022Article
- Draft Genome Sequences for ThreeMicrobiology resource announcements · 2022Article
- Clinical Oral Condition Analysis and the Influence of Highly Active Antiretroviral Therapy on Human Salivary Microbial Community Diversity in HIV-Infected/AIDS Patients.Frontiers in cellular and infection microbiology · 2022Article
- Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing.International journal of molecular sciences · 2021Review
- Ophiostomatoid fungi associated with pine bark beetles and infested pines in south-eastern Australia, including Graphilbum ipis-grandicollis sp. nov.IMA fungus · 2021Article
- Article
- An Efficient Strategy for Obtaining Mutants by Targeted Gene Deletion inFrontiers in microbiology · 2021Article
- Comparative Genomics Analyses of Lifestyle Transitions at the Origin of an Invasive Fungal Pathogen in the GenusmSphere · 2020Article
- A Review of the Scientific Rigor, Reproducibility, and Transparency Studies Conducted by the ABRF Research Groups.Journal of biomolecular techniques : JBT · 2020Review
- Hybridization and introgression drive genome evolution of Dutch elm disease pathogens.Nature ecology & evolution · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
20 authors at 10 institutions in 3 countries.
Funding
Abstract
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.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.