Shotgun metagenome analysis of two Schizaphis graminum biotypes over time with and without carried Cereal Yellow Dwarf Virus

Authors: Crane, Yan; Crane, Charles; Subramanyam, Subhashree; Schemerhorn, Brandon

Submitted to: Insects
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/21/2025
Publication Date: 5/23/2025
Citation: Crane, Y.M., Crane, C.F., Subramanyam, S.N., Schemerhorn, B.J. 2025. Shotgun metagenome analysis of two Schizaphis graminum biotypes over time with and without carried Cereal Yellow Dwarf Virus. Insects. https://doi.org/10.3390/insects16060554.
DOI: https://doi.org/10.3390/insects16060554

Interpretive Summary: Microbiomes and their impact on their host organism have become a hot research topic. In insects, a great deal of interest has been generated over the possibility that these organisms impact everything from resistance and susceptibility to vector pathogens, to their ability to overcome resistant crops. This interest sparks the possibility of targets for future insect control. An analysis of the microbiome of Greenbug was conducted using previous sequencing data from a study of gene-expression in the greenbug. We found thousands of potential genomes within the sequences suggesting that Greenbug may have potential targets for future biocontrol or even transgenic expression within their host (wheat, barley, sorghum, etc). The first step in these endeavors is to identify the genera present in the Greenbug. This study found 3,833 genera, some likely transferred from the wheat plant, but others are symbionts of Greenbug. This is the first report of this magnitude in the Greenbug.

Technical Abstract: A metagenomic analysis was conducted using shotgun reads from a prior time-course RNA-seq study of gene expression in greenbug (Schizaphis graminum (Rondani)). There were two biotypes, both with and without harbored Cereal Yellow Dwarf Virus (CYDV), and eight timepoints from zero to 20 days post infestation. There were three biological replicates per condition. The reads matched 3,833 genera. It appears that over time there were two major communities, one enriched in Shigella and Escherichia, the other depleted in Shigella and Escherichia but enriched in Acinetobacter and Gilbertella. The latter community prevailed on days 15 and 20 as the wheat host succumbed to aphid feeding. CYDV was not detected in any sample, but an aphid pathogen, Rhopalosiphum padi virus (RPV), was detected in 20 samples. Buchnera aphidicola, the standard intracellular endosymbiont of aphid bacteriocytes, was abundant in all samples. Two unrelated photosynthetic genera, Microcystis and Lamprocystis, were relatively abundant; the latter was positively correlated with Shigella.