Inferring the presence of aflatoxin-producing Aspergillus flavus strains using RNA sequencing and electronic probes as a transcriptomic screening tool

Andres S. Espindola; William Schneider; Kitty F. Cardwell; Yisel Carrillo; Peter R. Hoyt; Stephen M. Marek; Hassan Melouk; Carla D. Garzon

Using RNA sequencing and relative quantification of active genes is ideal to infer the 291 viability of plant pathogens. The use of EDNA transcriptomics to infer the production of 292 aflatoxin is a first attempt to introduce a novel strategy by using new sequencing 293 technologies to identify viable plant pathogens. The use of e-probes that are designed 294 on up-regulated genes incorporates an advantage to EDNA transcriptomics over other 295 tools that use RNA sequencing to assess gene expression [37] . The advantage of 296 EDNA transcriptomics over other methods of transcript frequency inference and 297 calculation is that the time-consuming map against the reference genome is not 298 necessary. Instead, we align the sample reads to the highly specific e-probes, which are 299 designed for known up-regulated genes. Directing the analysis to genes that are known 300 to be up-regulated reduces the analysis time tremendously since a mapping against a 301 whole genome is no longer necessary. Where needed total nucleic acids (DNA and 302 RNA) can be extracted from the sample of interest to perform both pathogen detection 303 and gene activity. 304 . CC-BY 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/365254 doi: bioRxiv preprint