Sequencing and annotation of the Ophiostoma ulmi genome

The ascomycete fungus Ophiostoma ulmi was responsible for the initial pandemic of the massively destructive Dutch elm disease in Europe and North America in early 1910. Dutch elm disease has ravaged the elm tree population globally and is a major threat to the remaining elm population. O. ulmi is al...

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Published in:BMC genomics 2013-03, Vol.14 (1), p.162-162
Main Authors: Khoshraftar, Shima, Hung, Stacy, Khan, Sadia, Gong, Yunchen, Tyagi, Vibha, Parkinson, John, Sain, Mohini, Moses, Alan M, Christendat, Dinesh
Format: Article
Language:English
Subjects:
Ascomycetes
Colleges & universities
Comparative analysis
Expressed Sequence Tags
Fungal Proteins - chemistry
Fungal Proteins - genetics
Fungal Proteins - metabolism
Genetics
Genome, Fungal
Genomes
Genomics
Growth rate
Ophiostoma - classification
Ophiostoma - genetics
Ophiostoma ulmi
Phylogeny
Plant diseases
Proteins
RNA, Messenger - chemistry
RNA, Messenger - genetics
RNA, Messenger - metabolism
Sequence Analysis, DNA
Sequence Analysis, RNA
Trees
Virulence - genetics
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container_end_page 162
container_issue 1
container_start_page 162
container_title BMC genomics
container_volume 14
creator Khoshraftar, Shima
Hung, Stacy
Khan, Sadia
Gong, Yunchen
Tyagi, Vibha
Parkinson, John
Sain, Mohini
Moses, Alan M
Christendat, Dinesh
description The ascomycete fungus Ophiostoma ulmi was responsible for the initial pandemic of the massively destructive Dutch elm disease in Europe and North America in early 1910. Dutch elm disease has ravaged the elm tree population globally and is a major threat to the remaining elm population. O. ulmi is also associated with valuable biomaterials applications. It was recently discovered that proteins from O. ulmi can be used for efficient transformation of amylose in the production of bioplastics. We have sequenced the 31.5 Mb genome of O.ulmi using Illumina next generation sequencing. Applying both de novo and comparative genome annotation methods, we predict a total of 8639 gene models. The quality of the predicted genes was validated using a variety of data sources consisting of EST data, mRNA-seq data and orthologs from related fungal species. Sequence-based computational methods were used to identify candidate virulence-related genes. Metabolic pathways were reconstructed and highlight specific enzymes that may play a role in virulence. This genome sequence will be a useful resource for further research aimed at understanding the molecular mechanisms of pathogenicity by O. ulmi. It will also facilitate the identification of enzymes necessary for industrial biotransformation applications.
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source Open Access: PubMed Central; Publicly Available Content Database
subjects Ascomycetes
Colleges & universities
Comparative analysis
Expressed Sequence Tags
Fungal Proteins - chemistry
Fungal Proteins - genetics
Fungal Proteins - metabolism
Genetics
Genome, Fungal
Genomes
Genomics
Growth rate
Ophiostoma - classification
Ophiostoma - genetics
Ophiostoma ulmi
Phylogeny
Plant diseases
Proteins
RNA, Messenger - chemistry
RNA, Messenger - genetics
RNA, Messenger - metabolism
Sequence Analysis, DNA
Sequence Analysis, RNA
Trees
Virulence - genetics
title Sequencing and annotation of the Ophiostoma ulmi genome
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