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Title: Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees

Author
item CHAN, Q.W.T - University Of British Columbia
item Cornman, Robert
item LIAO, N - University Of British Columbia
item CHAN, S. - University Of British Columbia
item DOCKING, R. - University Of British Columbia
item TAYLOR, G - University Of British Columbia
item JONES, S. - University Of British Columbia
item DE GRAAF, D.C - Ghent University
item Evans, Jay
item FOSTER, L.J. - University Of British Columbia

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/20/2011
Publication Date: 11/15/2011
Citation: Chan, Q., Cornman, R.S., Liao, N., Chan, S., Docking, R., Taylor, G., Jones, S., De Graaf, D., Evans, J.D., Foster, L. 2011. Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees. Biomed Central (BMC) Genomics. 12:450.

Interpretive Summary: Honey bees face numerous microbial threats, from bacteria and viruses to fungi. One of the most common diseases worldwide is American foulbrood disease (AFB). This disease is regulated tightly in the US, resulting in the destruction of bee hives and the use of expensive antibiotics. Understanding the genome of the bacteria causing AFB can lead to novel controls, diagnostics for antibiotic resistance and insights into how bees avoid AFB. This information can be used by bee scientists and regulators of bee health.

Technical Abstract: As life scientists continue to pursue various ‘omics-based research, there is a need make available, 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.We used the Illumina GAII platform and conventional Sanger sequencing, together with assembly through the Abyss system, to generate an 167-fold coverage of the P. larvae genome. A total of 353 contigs, whose lengths totaled 4.3Mbp, were assembled and ordered via comparison to a related, fully-sequenced soil bacterium P. JDR2. Interestingly, regions of poor conservation contained 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. This update on the genome of P .larvae and annotation represents an immense advancement from what we had previous 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 fatal honey bee disease.