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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #298878

Research Project: Genomic and Metagenomic Approaches to Enhance Efficient and Sustainable Production of Beef Cattle

Location: Genetics and Animal Breeding

Title: Complete genome assemblies and methylome characterization in infectious diseases

item Smith, Timothy - Tim

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/28/2012
Publication Date: 1/12/2013
Citation: Smith, T.P. 2013. Complete genome assemblies and methylome characterization in infectious diseases [Abstract]. Plant & Animal Genome XXI Conference, January 12-16, 2013, San Diego, CA. Paper No. W483.

Interpretive Summary:

Technical Abstract: Understanding the genetic basis of infectious diseases is a critical component to effective treatments. Because of the rapid evolution of bacterial strains and frequent horizontal transfer of DNA between them, resequencing of new isolates against known reference strains often provides an incomplete picture of their genetic constitution. Therefore, de novo sequencing approaches and complete genomes are important to identify many forms of variation known to influence pathogenicity, including large-scale structural variations and the acquisition of new phage elements or plasmids. In the past, genome finishing has been cumbersome and expensive due to the lack of high-throughput, long-read sequencing techniques. We have applied long sequence reads from a single molecule, real-time (SMRT) sequencing platform in combination with short read sequencing technologies in a hybrid genome assembly wherein the short reads are used to error-correct the long reads which are then used for assembly. We have used this method to generate finished genomes for several strains of Biebersteinia trehalosi and Mannheimia haemolytica which cause Bovine Respiratory Disease Complex (BRDC) in cattle. In addition, the kinetic information from SMRT sequencing reads can be used to identify methylated bases. These epigenetic marks are known to influence gene expression, and in some cases directly influence pathogenic states. We have determined the genome-wide methylation status of different Biebersteinia and Mannheimia strains and find that the methylomes between different strains are distinct and can serve as an epigenetic fingerprint for the characterization of different strains.