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Open Access Research article

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

Queenie WT Chan1, R Scott Cornman2, Inanc Birol3, Nancy Y Liao3, Simon K Chan3, T Roderick Docking3, Shaun D Jackman3, Greg A Taylor3, Steven JM Jones3, Dirk C de Graaf4, Jay D Evans2 and Leonard J Foster1*

Author Affiliations

1 Department of Biochemistry ž Molecular Biology, Centre for High-throughput Biology, University of British Columbia, 2125 East Mall, Vancouver, British Columbia, V6T 1Z4 Canada

2 Bee Research Laboratory, Agricultural Research Service, United States Department of Agriculture, 10300 Baltimore Avenue, Beltsville, Maryland, 20705, USA

3 Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, V5Z 4S6, Canada

4 Ghent University, Laboratory of Zoophysiology, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium and Institute of Marine Sciences Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany

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BMC Genomics 2011, 12:450  doi:10.1186/1471-2164-12-450

Published: 16 September 2011

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.

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.

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.