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Open Access Highly Accessed Research article

The genome and transcriptome of the pine saprophyte Ophiostoma piceae, and a comparison with the bark beetle-associated pine pathogen Grosmannia clavigera

Sajeet Haridas1, Ye Wang1, Lynette Lim1, Sepideh Massoumi Alamouti1, Shaun Jackman2, Rod Docking2, Gordon Robertson2, Inanc Birol2, Jörg Bohlmann3 and Colette Breuil1*

Author affiliations

1 Department of Wood Science, University of British Columbia, Vancouver, BC V6T1Z4, Canada

2 Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4E6, Canada

3 Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada

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Citation and License

BMC Genomics 2013, 14:373  doi:10.1186/1471-2164-14-373

Published: 2 June 2013

Abstract

Background

Ophiostoma piceae is a wood-staining fungus that grows in the sapwood of conifer logs and lumber. We sequenced its genome and analyzed its transcriptomes under a range of growth conditions. A comparison with the genome and transcriptomes of the mountain pine beetle-associated pathogen Grosmannia clavigera highlights differences between a pathogen that colonizes and kills living pine trees and a saprophyte that colonizes wood and the inner bark of dead trees.

Results

We assembled a 33 Mbp genome in 45 scaffolds, and predicted approximately 8,884 genes. The genome size and gene content were similar to those of other ascomycetes. Despite having similar ecological niches, O. piceae and G. clavigera showed no large-scale synteny. We identified O. piceae genes involved in the biosynthesis of melanin, which causes wood discoloration and reduces the commercial value of wood products. We also identified genes and pathways involved in growth on simple carbon sources and in sapwood, O. piceae’s natural substrate. Like the pathogen, the saprophyte is able to tolerate terpenes, which are a major class of pine tree defense compounds; unlike the pathogen, it cannot utilize monoterpenes as a carbon source.

Conclusions

This work makes available the second annotated genome of a softwood ophiostomatoid fungus, and suggests that O. piceae’s tolerance to terpenes may be due in part to these chemicals being removed from the cells by an ABC transporter that is highly induced by terpenes. The data generated will provide the research community with resources for work on host-vector-fungus interactions for wood-inhabiting, beetle-associated saprophytes and pathogens.

Keywords:
Ophiostoma piceae; Genome; Transcriptome; Wood-staining fungus; Saprobe