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Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest

Christopher I Keeling1, Macaire MS Yuen1, Nancy Y Liao2, T Roderick Docking2, Simon K Chan2, Greg A Taylor2, Diana L Palmquist2, Shaun D Jackman2, Anh Nguyen1, Maria Li1, Hannah Henderson1, Jasmine K Janes3, Yongjun Zhao2, Pawan Pandoh2, Richard Moore2, Felix AH Sperling3, Dezene P W Huber4, Inanc Birol25, Steven JM Jones256 and Joerg Bohlmann1*

Author affiliations

1 Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, Canada V6T 1A4

2 Canada's Michael Smith Genome Sciences Centre, 570 W 7th Ave #100 Vancouver, BC, Canada V5Z 4S6

3 Department of Biological Sciences, CW 405, Biological Sciences Bldg., University of Alberta, Edmonton, AB, Canada T6G 2E9

4 Ecosystem Science and Management Program, University of Northern British Columbia, 3333 University Way, Prince George, BC, Canada V2N 4Z9

5 Department of Medical Genetics, University of British Columbia, University of British Columbia, 4500 Oak St., Vancouver, BC, Canada V6H 3N1

6 Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, Canada V5A 1S6

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Citation and License

Genome Biology 2013, 14:R27  doi:10.1186/gb-2013-14-3-r27

Published: 27 March 2013

Abstract

Background

The mountain pine beetle, Dendroctonus ponderosae Hopkins, is the most serious insect pest of western North American pine forests. A recent outbreak destroyed more than 15 million hectares of pine forests, with major environmental effects on forest health, and economic effects on the forest industry. The outbreak has in part been driven by climate change, and will contribute to increased carbon emissions through decaying forests.

Results

We developed a genome sequence resource for the mountain pine beetle to better understand the unique aspects of this insect's biology. A draft de novo genome sequence was assembled from paired-end, short-read sequences from an individual field-collected male pupa, and scaffolded using mate-paired, short-read genomic sequences from pooled field-collected pupae, paired-end short-insert whole-transcriptome shotgun sequencing reads of mRNA from adult beetle tissues, and paired-end Sanger EST sequences from various life stages. We describe the cytochrome P450, glutathione S-transferase, and plant cell wall-degrading enzyme gene families important to the survival of the mountain pine beetle in its harsh and nutrient-poor host environment, and examine genome-wide single-nucleotide polymorphism variation. A horizontally transferred bacterial sucrose-6-phosphate hydrolase was evident in the genome, and its tissue-specific transcription suggests a functional role for this beetle.

Conclusions

Despite Coleoptera being the largest insect order with over 400,000 described species, including many agricultural and forest pest species, this is only the second genome sequence reported in Coleoptera, and will provide an important resource for the Curculionoidea and other insects.

Keywords:
Coleoptera; Curculionoidea; Scolytinae; bark beetles; conifer; cytochrome P450; glutathione S-transferase; plant cell wall-degrading enzymes; horizontal gene transfer; sex chromosomes