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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC AND BIOLOGICAL DETERMINANTS OF RESPIRATORY DISEASES OF RUMINANTS

Location: Genetics, Breeding, & Animal Health

Title: Application of SMRT genome sequencing to reveal the methylomes of bacteria associated with respiratory disease outbreaks in beef cattle

Authors
item Harhay, Gregory
item McVey, D Scott
item Korlach, Jonas -
item Roberts, Richard -
item Chitko Mckown, Carol
item Clawson, Michael
item Heaton, Michael
item Harhay, Dayna
item Smith, Timothy
item Anton, Brian -

Submitted to: Advances in Genome Biology and Technology
Publication Type: Abstract Only
Publication Acceptance Date: December 20, 2012
Publication Date: February 20, 2013
Citation: Harhay, G.P., McVey, D.S., Korlach, J., Roberts, R., Chitko-McKown, C.G., Clawson, M.L., Heaton, M.P., Harhay, D.M., Smith, T.P.L., Anton, B.P. 2013. Application of SMRT genome sequencing to reveal the methylomes of bacteria associated with respiratory disease outbreaks in beef cattle [Abstract]. Advances in Genome Biology and Technology Conference, February 20-23, 2013, Marco Island, FL. Page 99.

Technical Abstract: DNA base modification systems are common in bacteria and can modulate gene expression as well as act in defense against invading viruses. Recent advances in the direct identification of modified bases in the genome via Single Molecule Real Time (SMRT) sequencing supports an integrated analytical approach involving genome sequencing, assembly and base modification detection. We applied this approach to the genomes of multiple isolates of livestock pathogens. SMRT sequencing was used to identify the methyltransferase mediated base modification 6-methyladenine in the Bovine Respiratory Disease Complex (BRDC) pathogens Bibersteinia trehalosi and Mannheimia haemolytica. Novel methyltransferase genes and recognition motifs were observed in multiple strains of M. haemolytica and B. trehalosi that were isolated from BRDC-affected feedlot cattle from the Midwest United States. BRDC is the most costly disease (about 1 billion USD per year) affecting beef cattle in the United States. The most severe manifestations of the disease appear to involve immune suppression by viral infection, followed by lung invasion from a normally commensal organism, M. haemolytica. Some strains of M. haemolytica appear more aggressive and communicable than others and, thus, may be responsible for increased disease severity, economic losses and a reduction in animal well-being. The rich methylome content we observed in these pathogens suggest that an examination of the relationship between the methylome and virulence may reveal important virulence determinants. We present our analysis of the methylomes of these pathogens in the context of known genomic virulence factors, biochemical phenotypes and limited epidemiological data.

Last Modified: 4/20/2014
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