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

• DOI: 10.1371/journal.pone.0198575
• Publication Date: 2018-10-16T17:36:58Z
• Authors: Andres S. Espindola; William Schneider; Kitty F. Cardwell; Yisel Carrillo; Peter R. Hoyt; Stephen M. Marek; Hassan A. Melouk; Carla D. Garzon
• Keywords: 0301 basic medicine; 2. Zero hunger; 0303 health sciences; Science; Q; Genes, Fungal; R; Biosynthetic Pathways; 03 medical and health sciences; Aflatoxins; Gene Expression Regulation, Fungal; Medicine; Aspergillosis; Humans; Transcriptome; Research Article; Aspergillus flavus

AbstractE-probe Diagnostic for Nucleic acid Analysis (EDNA) is a bioinformatic tool originally developed to detect plant pathogens in metagenomic databases. However, enhancements made to EDNA increased its capacity to conduct hypothesis directed detection of specific gene targets present in transcriptomic databases. To target specific pathogenicity factors used by the pathogen to infect its host or other targets of interest, e-probes need to be developed for transcripts related to that function. In this study, EDNA transcriptomics (EDNAtran) was developed to detect the expression of genes related to aflatoxin production at the transcriptomic level. E-probes were designed from genes up-regulated duringA.flavusaflatoxin production. EDNAtran detected gene transcripts related to aflatoxin production in a transcriptomic database from corn, where aflatoxin was produced. The results were significantly different from e-probes being used in the transcriptomic database where aflatoxin was not produced (atoxigenic AF36 strain and toxigenic AF70 in Potato Dextrose Broth).