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Open Access Highly Accessed Research article

Sequencing and annotation of the Ophiostoma ulmi genome

Shima Khoshraftar1, Stacy Hung3, Sadia Khan1, Yunchen Gong2, Vibha Tyagi5, John Parkinson34, Mohini Sain5, Alan M Moses1* and Dinesh Christendat1*

Author Affiliations

1 Department of Cell & Systems Biology University of Toronto, Toronto, Canada

2 Center for Analysis of Genome Evolution and Function, Toronto, Canada

3 Departments of Biochemistry and Molecular Genetics University of Toronto, Toronto, Canada

4 Molecular Structure and Function Hospital for Sick Children, Toronto, Canada

5 Centre for Biocomposites and Biomaterials Processing, Faculty of Forestry, Toronto, Canada

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BMC Genomics 2013, 14:162  doi:10.1186/1471-2164-14-162

Published: 12 March 2013

Abstract

Background

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.

Results

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.

Conclusions

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.