Skip to main content
Fig. 2 | Microbiome

Fig. 2

From: Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination

Fig. 2

Origin of differentially expressed contigs. MA plots (ac) 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). Plot a all contigs (including non-DE) and b DE contigs only; coloured by annotation including contours to represent contig density relative within each group. c Individual MA plots of differentially expressed (DE) contigs annotated from Viridiplantae, Fungi, Metazoa, Bacteria and Unknown (no known similar sequences) are included for clarity. Data patterning from contamination-driven shifts in the community are observable (a) prior to any annotation. An epsilon factor is added in place of zero abundance where contigs are present in only one condition to allow visualisation and abundance comparison (as fold change would be infinite); the presence or absence of contigs (due to contamination) is biologically informative. d All DE contigs represented within a Krona graph [47]; the proportion of each taxonomic grouping is defined by the number of distinct contigs, whereas the colour represents the relative abundance (transcripts per million, tpm) of transcripts in each taxon. An interactive Krona graph to assist navigation of DE contig annotation origin is available at: https://github.com/gonzalezem/Tripartite_Metatranscriptomics_article. A full contig list including expression information, annotation (1° and 2°) and gene ontology is provided in Additional file 4 whereas DE only contigs are provided in Additional file 9

Back to article page