Sequencing and annotation of the Ophiostoma ulmigenome

BMC Genomics

Research Article

Yunchen Gong¹  Vibha Tyagi²  Mohini Sain²  Alan M Moses³  Shima Khoshraftar³  Sadia Khan³  Dinesh Christendat³  Stacy Hung⁴  John Parkinson⁵ 

[1] Center for Analysis of Genome Evolution and Function, Toronto, Canada;Centre for Biocomposites and Biomaterials Processing, Faculty of Forestry, Toronto, Canada;Department of Cell & Systems Biology, University of Toronto, Toronto, Canada;Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Canada;Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Canada;Molecular Structure and Function Hospital for Sick Children, Toronto, Canada;

关键词: Bark Beetle;    Metabolic Reconstruction;    Cercosporin;    Gene Prediction Method;    Glycan Degradation;   

DOI  :  10.1186/1471-2164-14-162

 received in 2012-11-01, accepted in 2013-02-28,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsWe 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.ConclusionsThis 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.

【 授权许可】

Unknown   
© Khoshraftar et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.