Shotgun microbiome analysis of two Schizaphis graminum biotypes with time with and without carried cereal yellow dwarf virus

Reads from a prior RNAseq study of gene expression in greenbug aphid (Schizaphis graminum (Rondani)) were used for shotgun metagenomic analysis in relation to two aphid biotypes, presence or absence of carried cereal yellow dwarf virus (CYDV), and five timepoints from zero to 20 days post-infestation. There were three biological replicates per condition. Reads were aligned with bwa mem to reference or representative genomes of 47000 bacterial, 1218 archaeal, 14165 viral, 571 fungal, and 94 protozoan taxa, plus greenbug and wheat, and each read was credited to the highest-scoring taxon. Read counts by taxon were imported into QIIME2 for statistical analysis and display. There were 105635 to 5938545 microbial reads per sample. The reads matched 3348 genera. The ratio of total microbial counts to total greenbug counts peaked at day 5 and declined 50% by day 20. Barplotted relative frequencies indicated two major communities, one enriched in Shigella and Escherichia, the other depleted in S..., An RNAseq study was conducted using whole Schizaphis graminum aphids without surface sterilization. Reads were mapped to reference genomes of Schizaphis graminum, its host Triticum aestivum (wheat), and all available reference or representative genomes of bacterial, archaeal, viral, fungal, and protozoan taxa available in NCBI as of 31 October 2023. It was necessary to divide these genomes among 61 separate databases and then merge the results of bwa mem runs because of the slowness of bwa indexing. A perl script, grouptaxa1211.pl, was written to collate closest hits in the resulting sam files. Other scripts were written to aggregate counts by taxon at different levels from species to phylum using files from NCBI taxonomy. The raw counts were subjected to DESeq2 to identify significantly responding taxa, since the data format was identical to the sister RNAseq data analyzed for aphid gene expression. The counts by taxon were also imported into QIIME2 for graphical presentation and ..., , # RNAseq read counts by microbial taxon from *Schizaphis graminum* with and without carried Cereal Yellow Dwarf Virus

[https://doi.org/10.5061/dryad.z08kprrp1](https://doi.org/10.5061/dryad.z08kprrp1)

## Description of the data and file structure

To see the contents of this tar.gz file, type 'gunzip gbmbiomeItodatadryad.tar.gz; tar -xvf gbmbiomeItodatadryad.tar' at the Unix command line. This tar file contains two kinds of data files: all\*counttable0502.txt and \*usedsamcountsbytaxon\*.txt. The former were aggregated from the latter. The former has the taxon name in the first column and counts for each combination of biotype, viral carrier status, and timepoint in subsequent columns. The header row gives the codes for these combinations: biotype (B or H), viral carrier status (nothing or RPV), timepoint (integers from 0 through 7), and replicate (1, 2, or 3). The latter kind has two parts: an initial list of GenBank accessions grouped by NCBI taxonomic identities (taxid), followed ...,