title: Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest.
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.
authors.forename: Christopher I
authors.initials: CI
authors.lastname: Keeling
authors.forename: Macaire M S
authors.initials: MM
authors.lastname: Yuen
authors.forename: Nancy Y
authors.initials: NY
authors.lastname: Liao
authors.forename: T Roderick
authors.initials: TR
authors.lastname: Docking
authors.forename: Simon K
authors.initials: SK
authors.lastname: Chan
authors.forename: Greg A
authors.initials: GA
authors.lastname: Taylor
authors.forename: Diana L
authors.initials: DL
authors.lastname: Palmquist
authors.forename: Shaun D
authors.initials: SD
authors.lastname: Jackman
authors.forename: Anh
authors.initials: A
authors.lastname: Nguyen
authors.forename: Maria
authors.initials: M
authors.lastname: Li
authors.forename: Hannah
authors.initials: H
authors.lastname: Henderson
authors.forename: Jasmine K
authors.initials: JK
authors.lastname: Janes
authors.forename: Yongjun
authors.initials: Y
authors.lastname: Zhao
authors.forename: Pawan
authors.initials: P
authors.lastname: Pandoh
authors.forename: Richard
authors.initials: R
authors.lastname: Moore
authors.forename: Felix A H
authors.initials: FA
authors.lastname: Sperling
authors.forename: Dezene P W
authors.initials: DP
authors.lastname: Huber
authors.forename: Inanc
authors.initials: I
authors.lastname: Birol
authors.forename: Steven J M
authors.initials: SJ
authors.lastname: Jones
authors.forename: Joerg
authors.initials: J
authors.lastname: Bohlmann
mesh_terms: D000818:Animals; D002473:Cell Wall / Q000378:metabolism; D001517:Coleoptera / Q000201:enzymology / Q000235:genetics*; D017753:Ecosystem; D005260:Female; D065928:Forests; D022761:Gene Transfer, Horizontal / Q000235:genetics; D008040:Genetic Linkage; D049750:Genome, Insect / Q000235:genetics*; D006579:Heterozygote; D008297:Male; D005810:Multigene Family; D010802:Phylogeny; D059828:Plant Cells / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D012730:Sex Chromosomes / Q000235:genetics; D026801:Synteny / Q000235:genetics
references.citation: Science. 2007 Dec 21;318(5858):1913-6
references.pmid: 18096805
references.citation: BMC Genomics. 2010 Oct 04;11:536
references.pmid: 20920358
references.citation: Comp Biochem Physiol B Biochem Mol Biol. 2010 Feb;155(2):145-54
references.pmid: 19895899
references.citation: Mol Ecol. 2010 Jun 1;19(12):2455-73
references.pmid: 20497324
references.citation: Gene. 2003 Oct 16;316:127-36
references.pmid: 14563559
references.citation: Genome Res. 2003 Sep;13(9):2178-89
references.pmid: 12952885
references.citation: New Phytol. 2005 Aug;167(2):353-75
references.pmid: 15998390
references.citation: J Biol Chem. 1993 Sep 15;268(26):19188-91
references.pmid: 8366071
references.citation: Genome Biol. 2008;9(3):R61
references.pmid: 18366801
references.citation: Science. 2011 Mar 18;331(6023):1386
references.pmid: 21415334
references.citation: Proc Natl Acad Sci U S A. 2008 Feb 5;105(5):1551-5
references.pmid: 18230736
references.citation: Insect Biochem Mol Biol. 2012 Aug;42(8):525-36
references.pmid: 22516182
references.citation: Bioinformatics. 2009 Jul 15;25(14):1754-60
references.pmid: 19451168
references.citation: Mol Ecol Resour. 2009 May;9(3):1071-3
references.pmid: 21564842
references.citation: FEMS Microbiol Lett. 2007 Feb;267(2):151-8
references.pmid: 17328114
references.citation: Environ Entomol. 2012 Jun;41(3):723-30
references.pmid: 22732632
references.citation: New Phytol. 2006;170(4):657-75
references.pmid: 16684230
references.citation: Proc Natl Acad Sci U S A. 2011 Feb 8;108(6):2504-9
references.pmid: 21262841
references.citation: Trends Ecol Evol. 2008 Apr;23(4):220-8
references.pmid: 18308422
references.citation: Nature. 2008 Apr 24;452(7190):987-90
references.pmid: 18432244
references.citation: BMC Genomics. 2010 Dec 14;11:703
references.pmid: 21156066
references.citation: J Bacteriol. 2011 Oct;193(19):5549-50
references.pmid: 21742884
references.citation: PLoS One. 2012;7(5):e36544
references.pmid: 22574182
references.citation: Insect Mol Biol. 2005 Jan;14(1):3-8
references.pmid: 15663770
references.citation: Mol Phylogenet Evol. 2011 Dec;61(3):924-32
references.pmid: 21930223
references.citation: Microb Ecol. 2012 Jul;64(1):268-78
references.pmid: 22234511
references.citation: Cytogenet Genome Res. 2005;110(1-4):462-7
references.pmid: 16093699
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D211-5
references.pmid: 18940856
references.citation: BMC Bioinformatics. 2005 Feb 15;6:31
references.pmid: 15713233
references.citation: Environ Entomol. 2012 Jun;41(3):478-86
references.pmid: 22732605
references.citation: Bioinformatics. 2005 Jun;21 Suppl 1:i351-8
references.pmid: 15961478
references.citation: BMC Genomics. 2010 Oct 25;11:602
references.pmid: 20973996
references.citation: Genes Dev. 2008 Jun 1;22(11):1522-33
references.pmid: 18519643
references.citation: Proc Natl Acad Sci U S A. 2012 Mar 13;109(11):4197-202
references.pmid: 22371593
references.citation: Proc Biol Sci. 2000 Dec 7;267(1460):2359-66
references.pmid: 11133024
references.citation: Nature. 2008 Apr 24;452(7190):949-55
references.pmid: 18362917
references.citation: PLoS One. 2010 Dec 17;5(12):e15635
references.pmid: 21179425
references.citation: Biochem Soc Trans. 2006 Dec;34(Pt 6):1252-5
references.pmid: 17073796
references.citation: J Biol Chem. 2001 Oct 5;276(40):37415-25
references.pmid: 11473129
references.citation: Genome Res. 2008 Jan;18(1):188-96
references.pmid: 18025269
references.citation: BMC Genomics. 2011 May 19;12:248
references.pmid: 21595916
references.citation: Bioinformatics. 2007 May 1;23(9):1061-7
references.pmid: 17332020
references.citation: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W475-8
references.pmid: 21470960
references.citation: Proc Natl Acad Sci U S A. 2009 Apr 28;106(17):7083-8
references.pmid: 19365072
references.citation: Biochem J. 2001 Nov 15;360(Pt 1):1-16
references.pmid: 11695986
references.citation: Nucleic Acids Res. 1998 Feb 15;26(4):1107-15
references.pmid: 9461475
references.citation: Mol Ecol. 2012 Jun;21(12):2931-48
references.pmid: 22554298
references.citation: Biochim Biophys Acta. 2011 Jan;1814(1):19-28
references.pmid: 20601227
references.citation: Annu Rev Entomol. 2010;55:609-32
references.pmid: 19754245
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: PLoS One. 2010 Mar 10;5(3):e9490
references.pmid: 20224823
references.citation: Microb Ecol. 2009 Nov;58(4):879-91
references.pmid: 19543937
references.citation: Mol Ecol. 2011 May;20(10):2157-71
references.pmid: 21457381
references.citation: J Chem Ecol. 2011 Aug;37(8):808-17
references.pmid: 21710365
references.citation: Genome Biol. 2009;10(9):R94
references.pmid: 19747388
references.citation: Bioinformatics. 2009 Aug 15;25(16):2078-9
references.pmid: 19505943
references.citation: BMC Genomics. 2013 Mar 21;14:198
references.pmid: 23517120
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D363-8
references.pmid: 16381887
references.citation: Genome Res. 2009 Jun;19(6):1117-23
references.pmid: 19251739
references.citation: J Biol Chem. 1974 Nov 25;249(22):7130-9
references.pmid: 4436300
references.citation: Biol Pharm Bull. 2012;35(6):838-43
references.pmid: 22687472
references.citation: Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
references.pmid: 15034147
references.citation: Genome Biol. 2006;7 Suppl 1:S11.1-8
references.pmid: 16925833
references.citation: Evolution. 1998 Dec;52(6):1731-1743
references.pmid: 28565330
references.citation: BMC Genomics. 2010 Mar 30;11:215
references.pmid: 20353591
references.citation: Insect Biochem Mol Biol. 2006 Nov;36(11):835-45
references.pmid: 17046597
references.citation: BMC Bioinformatics. 2004 May 14;5:59
references.pmid: 15144565