Aphid gene expression following polerovirus acquisition is host species dependent

Upon acquisition of persistent circulative viruses such as poleroviruses, the virus particles transcytose through membrane barriers of aphids at the midgut and salivary glands via hemolymph. Such intricate interactions can influence aphid behavior and fitness and induce associated gene expression in viruliferous aphids. Differential gene expression can be evaluated by omics approaches such as transcriptomics. Previously conducted aphid transcriptome studies used only one host species as the source of virus inoculum. Viruses typically have alternate hosts. Hence, it is not clear how alternate hosts infected with the same virus isolate alter gene expression in viruliferous vectors. To address the question, this study conducted a transcriptome analysis of viruliferous aphids that acquired the virus from different host species. A polerovirus, cotton leafroll dwarf virus (CLRDV), which induced gene expression in the cotton aphid, Aphis gossypii Glover, was assessed using four alternate hosts, viz., cotton, hibiscus, okra, and prickly sida. Among a total of 2,942 differentially expressed genes (DEGs), 750, 310, 1,193, and 689 genes were identified in A. gossypii that acquired CLRDV from infected cotton, hibiscus, okra, and prickly sida, respectively, compared with non-viruliferous aphids that developed on non-infected hosts. A higher proportion of aphid genes were overexpressed than underexpressed following CLRDV acquisition from cotton, hibiscus, and prickly sida. In contrast, more aphid genes were underexpressed than overexpressed following CLRDV acquisition from okra plants. Only four common DEGs (heat shock protein, juvenile hormone acid O-methyltransferase, and two unannotated genes) were identified among viruliferous aphids from four alternate hosts. Gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations indicated that the acquisition of CLRDV induced DEGs in aphids associated with virus infection, signal transduction, immune systems, and fitness. However, these induced changes were not consistent across four alternate hosts. These data indicate that alternate hosts could differentially influence gene expression in aphids and presumably aphid behavior and fitness despite being infected with the same virus isolate.


Figure S4: Functional annotation of DEGs in A. gossypii that acquired CLRDV from infected hibiscus plants
A total 174 of the 310 DEGs in A. gossypii that acquired CLRDV from infected hibiscus were assigned functional groups under three classification systems: biological process (171 genes), molecular function (158 genes), and cellular component (158 genes).Forty-nine GO terms were assigned under the biological process category, of which only three terms (pigment metabolic process, metabolic process, and cell cycle) were significant (Additional file 1: Figure S3a, Additional file 2: Table S3).Twenty-seven GO terms were assigned under the molecular function category, only two (transferase activity and protein tag) of which were significant (Additional file 1: Figure S3b, Additional file 2: Table : S3).Twenty-two GO terms were identified in the cellular component category; none was significant (Additional file 1: Figure S3c, Additional file 2: Table S3).Overall, 707 of the 1193 DEGs in A. gossypii that acquired CLRDV from infected okra were assigned functional groups under three classification systems: biological process (691 genes), molecular function (645 genes), and cellular component (597 genes).Fifty-five GO terms were assigned under the biological process category, of which only three terms (metabolic process, grooming behavior, and aging) were significant (Additional file 1: Figure S4a, Additional file 2: Table S4).Forty-two GO terms were assigned under the molecular function category, only one (structure molecular activity) was significant (Additional file 1: Figure S4b, Additional file 2: Table S4).Thirty-seven GO terms were identified in the cellular component category, and one of those (extracellular region) was significant (Additional file 1: Figure S5c, Additional file 2: Table S4).

Figure S6: Functional annotation of DEGs in A. gossypii acquiring virus from CLRDV-infected prickly sida plants
Lastly, a total of 371 of the 689 DEGs in A. gossypii that acquired CLRDV from infected prickly sida were assigned functional groups under three classification systems: biological process (361 genes), molecular function (334 genes), and cellular component (321 genes).Fifty-two GO terms were assigned under the biological process category, of which only two terms (locomotion and protein folding) were significant (Additional file 1: Figure S5a, Additional file 2: Table S5).Thirty-seven GO terms were assigned under the molecular function category, only three (structure molecule activity, structural constituent of muscle, and transferase activity) of which were significant (Additional file 1: Figure S5b, Additional file 2: Table: S5).Twenty-eight GO terms were identified in the cellular component category, and two (cytochrome complex and basal part of cell) of those were significant (Additional file 1: Figure S5c, Additional file 2: Table S5).

Figure
Figure S1: Summary of RNA sequencing:

Figure S4 .
Figure S4.Scatterplots showing (a) biological process, (b) cellular component, and (c) molecular function gene ontology terms for DEGs in viruliferous A. gossypii adults that acquired CLRDV from infected hibiscus plant.Cluster representatives in a two-dimensional space were derived by applying multidimensional scaling to a matrix of the semantic similarities of the gene ontology terms.The bubble color indicates the p-value, and the size indicates the frequency of the GO term in the underlying GOA database.

Figure S5 :
Figure S5: Functional annotation of DEGs in A. gossypii that acquired CLRDV from infected okra plants

Figure S5 .
Figure S5.Scatterplots showing (a) biological process, (b) cellular component, and (c) molecular function gene ontology terms for for DEGs in viruliferous A. gossypii adults that acquired CLRDV from infected okra plant.Cluster representatives in a two-dimensional space were derived by applying multidimensional scaling to a matrix of the semantic similarities of the gene ontology terms.The bubble color indicates the p-value, and the size indicates the frequency of the GO term in the underlying GOA database.

Figure S6 .
Figure S6.Scatterplots showing (a) biological process, (b) cellular component, and (c) molecular function gene ontology terms for for DEGs in viruliferous A. gossypii adults that acquired CLRDV from infected prickly sida plant.Cluster representatives in a two-dimensional space were derived by applying multidimensional scaling to a matrix of the semantic similarities of the gene ontology terms.The bubble color indicates the p-value, and the size indicates the frequency of the GO term in the underlying GOA database.