Fig. 4
Taxonomy of fungal differential expression and secondary annotation. MA plots of de novo assembled transcriptome; y-axis represents fold change (FC, log2) between contaminated (+ive) to non-contaminated conditions (−ive), and the x-axis represents mean normalised (EdgeR) counts per million (log2 CPM). Contours representing relative DE contig density. a DE contigs annotated from fungi with Ascomycota (red) and Basidiomycota (blue), b DE Ascomycota contigs with genera annotating > 20 contigs highlighted and c DE Basidiomycota contigs with genera annotating > 20 contigs highlighted. d Secondary annotation of each DE fungal contig illustrating alternative, equally valid annotation [2] from other species (presented as genera for clarity). Genera with correspondences > 20 are presented and coloured by DE direction (more abundant in contaminated roots = black; more abundant in non-contaminated roots = gold). Agaricles phylogeny (an order of Agaricomycetes) is provided to visualise expression profiles against relatedness, with clade II (Pluteoid), IV (Marasmoid), V (Tricholomatoid) and VI (Agaricoid) structure (taken from Matheny et al. [86]). An interactive chord diagram and Krona graph to assist more comprehensive navigation of taxonomy and fungal secondary annotation are available at: https://github.com/gonzalezem/Tripartite_Metatranscriptomics_article. A full fungal DE contig list including expression information, annotation (1° and 2°) and gene ontology is provided in Additional file 6 whereas a full list of Basidiomycota DE contigs upregulated in roots of contaminated trees is provided in Additional file 7