Fig. 7

A selection of differentially expressed bacterial putative operons in higher abundance in roots of contaminated trees (and discussed in the text). Bacterial contigs were first identified within the assembly as best annotated with a single bacterial protein. To find multiple potential coding regions within bacterial polycistronic sequences, we used TransDecoder software (https://transdecoder.github.io/) [3] with default parameters. A final hand annotation step was included to remove a minor number of overlapping uncharacterised ORFs. Precedence of transcriptional unit structure (putative operons) was verified in all cases against the database of prokaryotic operons (DOOR [48]) unless otherwise stated. The in-house contig label is presented with the structure of the putative operon annotated using E. coli nomenclature. The three putative operons c60225_g2_i5, c60225_g2_i7 and c60225_g2_i8 all include the transposable element insH9, similar read coverage may falsely conjoin up- and downstream DE sequence combinations around the common insert. A full list of bacterial DE putative operons (transcriptional units) including expression data, functional description (if available), gene ontology terms (if available) and secondary annotation (if available) is provided in Additional file 10