title: Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees.
abstract: BACKGROUND
  As scientists continue to pursue various 'omics-based research, there is a need for high quality data for the most fundamental 'omics of all: genomics. The bacterium Paenibacillus larvae is the causative agent of the honey bee disease American foulbrood. If untreated, it can lead to the demise of an entire hive; the highly social nature of bees also leads to easy disease spread, between both individuals and colonies. Biologists have studied this organism since the early 1900s, and a century later, the molecular mechanism of infection remains elusive. Transcriptomics and proteomics, because of their ability to analyze multiple genes and proteins in a high-throughput manner, may be very helpful to its study. However, the power of these methodologies is severely limited without a complete genome; we undertake to address that deficiency here.
  
  
  RESULTS
  We used the Illumina GAIIx platform and conventional Sanger sequencing to generate a 182-fold sequence coverage of the P. larvae genome, and assembled the data using ABySS into a total of 388 contigs spanning 4.5 Mbp. Comparative genomics analysis against fully-sequenced soil bacteria P. JDR2 and P. vortex showed that regions of poor conservation may contain putative virulence factors. We used GLIMMER to predict 3568 gene models, and named them based on homology revealed by BLAST searches; proteases, hemolytic factors, toxins, and antibiotic resistance enzymes were identified in this way. Finally, mass spectrometry was used to provide experimental evidence that at least 35% of the genes are expressed at the protein level.
  
  
  CONCLUSIONS
  This update on the genome of P. larvae and annotation represents an immense advancement from what we had previously known about this species. We provide here a reliable resource that can be used to elucidate the mechanism of infection, and by extension, more effective methods to control and cure this widespread honey bee disease.
authors.affiliation: Department of Biochemistry Ž Molecular Biology, Centre for High-throughput Biology, University of British Columbia, 2125 East Mall, Vancouver, British Columbia, V6T 1Z4 Canada.
authors.forename: Queenie W T
authors.initials: QW
authors.lastname: Chan
authors.forename: R Scott
authors.initials: RS
authors.lastname: Cornman
authors.forename: Inanc
authors.initials: I
authors.lastname: Birol
authors.forename: Nancy Y
authors.initials: NY
authors.lastname: Liao
authors.forename: Simon K
authors.initials: SK
authors.lastname: Chan
authors.forename: T Roderick
authors.initials: TR
authors.lastname: Docking
authors.forename: Shaun D
authors.initials: SD
authors.lastname: Jackman
authors.forename: Greg A
authors.initials: GA
authors.lastname: Taylor
authors.forename: Steven J M
authors.initials: SJ
authors.lastname: Jones
authors.forename: Dirk C
authors.initials: DC
authors.lastname: de Graaf
authors.forename: Jay D
authors.initials: JD
authors.lastname: Evans
authors.forename: Leonard J
authors.initials: LJ
authors.lastname: Foster
mesh_terms: D000818:Animals; D001516:Bees / Q000382:microbiology*; D055028:Comparative Genomic Hybridization; D019295:Computational Biology; D004269:DNA, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D058977:Molecular Sequence Annotation; D056507:Paenibacillus / Q000235:genetics*; D040901:Proteomics; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial