Comparison of DNA-seq and RNA-seq in plant microbiome identification on rye – a case study

High-throughput sequencing of RNA is an indispensable tool in plant virology for virus detection and identification. However, the acquired dataset consists of more than just viral reads and traces of other pathogens can be detected in the data, like bacteria and fungi. Using RNA-seq for detection of more than just viral pathogens have been discussed in literature.
To test the reliability in detection of various microbes using only RNA-seq, this study presents the comparison of microorganisms detected in DNA-seq and RNA-seq analysis of the same samples. Five symptomatic and one asymptomatic (no visible symptoms) rye samples were collected from the field. DNA and RNA were extracted from the same plant material.