POSTERS: Pathogen detection, quantification and diagnosis
Metagenome sequence calculator for effective pathogen detection
Andres Espindola - Oklahoma State University. Kitty Cardwell- Oklahoma State University, Joshua Habiger- Oklahoma State University
Nucleic acid based analysis is a prevalent technology for plant disease diagnoses, particularly using amplification and primers designed on a unique sequence, primarily from the ITS region. Future diagnostic technology will turn to whole metagenome sequencing, without isolation or amplification, using in silico searches for any number of pathogen-specific unique nucleic acid signatures. A host-pathogen metagenome, comprised of full sequence data of the host and resident pathogen(s), then can be described in probabilistic terms, based upon relative abundance and size of the pathogen genome within the metagenome. Abundance of pathogen within a host tissue can be a gradient from high titer (highly symptomatic tissue) to low titer (pre-symptomatic infection). Generalizing pathogen genome size: viroids range from 0.2-0.5Knt, viruses from 10-100Knt, bacteria from 3Mnt-5Mnt, and fungi from 30 to 100Mnt. The ratio of (high to low abundance) pathogen sequence to host sequence can be calculated to inform the diagnostician how deep to sequence in order to positively detect the pathogen sequence within the metagenome. In this poster, we demonstrate how many sequenced reads are required in a metagenome in order to positively detect pathogen sequence with high probability, based on host genome size, pathogen genome size, and expected abundance of the pathogen within the host tissue.