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Oral: Novel Applications of Whole Genome Sequencing and Bioinformatics in Microbial Forensics and Agricultural Biosecurity


Whole genome analyses of all known populations of the Select Agent Rathayibacter toxicus
J. STACK (1), M. Arif (2), G. Busot (3), R. Mann (4), S. Liu (2), B. Rodoni (5) (1) Kansas State University, U.S.A.; (2) Kansas State University, U.S.A.; (3) Kansas State Univesrity, U.S.A.; (4) Victoria Department of Economic Development and Primary Indu

The U.S. Select Agent Rathayibacter toxicus is a gram positive bacterium with an ecologically complex life history. It has been responsible for the deaths of hundreds of thousands of animals; sheep and cattle in Australia and horses in South Africa. Prior population genetic analyses have identified at least five distinct genetic populations in Australia. To better understand this organism, whole genome sequences were generated (PacBio RS II), de novo assembled (HGAP3 assembly pipeline: Hierarchical Genome Assembly Process) and annotated for representative isolates from the five genetically distinct R. toxicus populations on four plant species from three geographic regions (Western Australia, South Australia and New South Wales). Illumina Miseq data for all five isolates was used to enhance the accuracy in assembly. Annotation pipelines, Bacterial Annotation System (BASys), Rapid Annotation using Subsystem Technology (RAST), and Integrated Microbial Genomes (IMG-JGI) were used for annotation. Genomes size ranged from 2.346 MB to 2.422 MB; the maximum nucleotide difference among genomes was 76,459 bp. The annotation projected total number of genes from 2491 to 2598. A total of 51 RNA genes were identified including, 45 tRNA CDS and 6 rRNA CDS in each genome. Genome structure and character among the five genetic populations will be discussed.