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

Queenie WT Chan, R Scott Cornman, Inanc Birol, Nancy Y Liao, Simon K Chan, T Roderick Docking, Shaun D Jackman, Greg A Taylor, Steven JM Jones and Dirk de Graaf UGent, et al. (2011) BMC GENOMICS. 12.
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
BACILLUS-SUBTILIS, APIS-MELLIFERA, STAPHYLOCOCCUS-AUREUS, IN-VITRO, BACTERIA, BIOSYNTHESIS, SURFACTIN, PROTEASES, PATHWAYS, PATHOGEN
journal title
BMC GENOMICS
BMC Genomics
volume
12
article_number
450
pages
15 pages
Web of Science type
Article
Web of Science id
000295740800001
JCR category
BIOTECHNOLOGY & APPLIED MICROBIOLOGY
JCR impact factor
4.073 (2011)
JCR rank
26/157 (2011)
JCR quartile
1 (2011)
ISSN
1471-2164
DOI
10.1186/1471-2164-12-450
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
2059334
handle
http://hdl.handle.net/1854/LU-2059334
date created
2012-03-05 12:40:17
date last changed
2012-04-05 13:49:35
@article{2059334,
  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.},
  articleno    = {450},
  author       = {Chan, Queenie WT and Cornman, R Scott and Birol, Inanc and Liao, Nancy Y and Chan, Simon K and Docking, T Roderick and Jackman, Shaun D and Taylor, Greg A and Jones, Steven JM and de Graaf, Dirk and Evans, Jay D and Foster, Leonard J},
  issn         = {1471-2164},
  journal      = {BMC GENOMICS},
  keyword      = {BACILLUS-SUBTILIS,APIS-MELLIFERA,STAPHYLOCOCCUS-AUREUS,IN-VITRO,BACTERIA,BIOSYNTHESIS,SURFACTIN,PROTEASES,PATHWAYS,PATHOGEN},
  language     = {eng},
  pages        = {15},
  title        = {Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees},
  url          = {http://dx.doi.org/10.1186/1471-2164-12-450},
  volume       = {12},
  year         = {2011},
}

Chicago
Chan, Queenie WT, R Scott Cornman, Inanc Birol, Nancy Y Liao, Simon K Chan, T Roderick Docking, Shaun D Jackman, et al. 2011. “Updated Genome Assembly and Annotation of Paenibacillus Larvae, the Agent of American Foulbrood Disease of Honey Bees.” Bmc Genomics 12.
APA
Chan, Q. W., Cornman, R. S., Birol, I., Liao, N. Y., Chan, S. K., Docking, T. R., Jackman, S. D., et al. (2011). Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees. BMC GENOMICS, 12.
Vancouver
1.
Chan QW, Cornman RS, Birol I, Liao NY, Chan SK, Docking TR, et al. Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees. BMC GENOMICS. 2011;12.
MLA
Chan, Queenie WT, R Scott Cornman, Inanc Birol, et al. “Updated Genome Assembly and Annotation of Paenibacillus Larvae, the Agent of American Foulbrood Disease of Honey Bees.” BMC GENOMICS 12 (2011): n. pag. Print.