Differential gene expression between viruliferous and non-viruliferous Schizaphis graminum (Rondani)

Authors: Crane, Yan Ma; Crane, Charles; Schemerhorn, Brandi

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/30/2023
Publication Date: 11/15/2023
Citation: Crane, Y.M., Crane, C.F., Schemerhorn, B.J. 2023. Differential gene expression between viruliferous and non-viruliferous Schizaphis graminum (Rondani). PLOS ONE. 18(11):e0294013. https://doi.org/10.1371/journal.pone.0294013.
DOI: https://doi.org/10.1371/journal.pone.0294013

Interpretive Summary: Cereal Yellow-Dwarf Virus is a worldwide virus disease of our most important crops, including, wheat, rice and maize. The virus is transmitted by aphids, including greenbug. Experiments were conducted that sampled from two biotypes of greenbugs both with and without carrying the virus at several timepoints. This sequence data was analyzed and it shows that there is not a large-scale change in gene expression, but suggests that part of the aphid immune response is not present and has been lost during evolution. This work contributes to the continued knowledge of the cereal yellow dwarf virus cycle between aphid, virus and plant.

Technical Abstract: An experiment was performed to measure the effect of Cereal Yellow-Dwarf Virus, strain CYDV-RPV, on gene expression in its’ insect vector, greenbug (Schizaphis graminum (Rondani)). RNA was sampled from populations of two biotypes, both with and without carried CYDV-RPV, at 0, 1, 2, 3, 5, 10, 15 and 20 days from the introduction of greenbugs to uninfected wheat cv. ‘Newton’. Illumina paired-end sequencing produced 1,840,820,000,000 raw reads that yielded 1,000,089,950,000 clean reads, which were aligned to genome assemblies of Schizaphis graminum and Melanaphis sacchari Zehntner with bowtie2 and counted with R function featureCount. The reads were also aligned with bowtie2 to a set of 49 microbial genomes and counted by organism with a custom script. Differential expression was analyzed with DESeq2, and heatmap graphics of counts per million mapped reads were prepared with R function aspectHeatmap. A core set of 127 genes differed significantly at p < 0.01 between virus-free and viruliferous greenbugs when all timepoints were considered; many of these were DNA-binding transcription factors or retrotransposon-like proteins. There were 4488 genes that differed between the two biotypes when considering all timepoints. Counts varied much more erratically among individual pairs of timepoint and carrier status. There was little trend to comparisons between consecutive timepoints within carrier status, although counts changed less going into day 20. Aviruliferous biotype H exhibited a large shift in gene expression between days 3 and 5 and did not return to its previous state thereafter. The diverse microbiome was dominated by a coliform bacterium similar to Escherichia coli and the general aphid endosymbiont Buchnera aphidicola. The coliform counts collapsed between days 10 and 15, particularly on plants developing virus symptoms. Nutrition appeared to outweigh immunity in the response to acquired virus.