Mining Public Data to Investigate the Virome of Neglected Pollinators and Other Floral Visitors

Abstract

This study reports the virome investigation of pollinator species and other floral visitors associated with plants from the south of Bahia: Aphis aurantii, Atrichopogon sp., Dasyhelea sp., Forcipomyia taiwana, and Trigona ventralis hoozana. Studying viruses in insects associated with economically important crops is vital to understand transmission dynamics and manage viral diseases that pose as threats for global food security. Using literature mining and public RNA next-generation sequencing data deposited in the NCBI SRA database, we identified potential vectors associated with Malvaceae plant species and characterized the microbial communities resident in these insects. Bacteria and Eukarya dominated the metagenomic analyses of all taxon groups. We also found sequences showing similarity to elements from several viral families, including Bunyavirales, Chuviridae, Iflaviridae, Narnaviridae, Orthomyxoviridae, Rhabdoviridae, Totiviridae, and Xinmoviridae. Phylogenetic analyses indicated the existence of at least 16 new viruses distributed among A. aurantii (3), Atrichopogon sp. (4), Dasyhelea sp. (3), and F. taiwana (6). No novel viruses were found for T. ventralis hoozana. For F. taiwana, the available libraries also allowed us to suggest possible vertical transmission, while for A. aurantii we followed the infection profile along the insect development. Our results highlight the importance of studying the virome of insect species associated with crop pollination, as they may play a crucial role in the transmission of viruses to economically important plants, such as those of the genus Theobroma, or they will reduce the pollination process. This information may be valuable in developing strategies to mitigate the spread of viruses and protect the global industry.

Keywords: Malvaceae; insects; pollinators; virome.

Figure 1

Overview of public data on plants and associated insects. (A) Insect species often associated with plant pollination and other plant-visiting insects referred to in the literature search. (B) Transcriptome assembly statistics for each library referring to insects associated with plants For each library, the value on the right column indicates N50, while the white box represents the mean and the diamond is related to the median value of the transcripts assembled. Black dots represent viral transcripts selected for further characterization.

Figure 2

Metagenomics analysis of plant-visiting insects. The global microbiome at kingdom (A,D,G,J,M) and family (B,E,H,K,N) levels. Diversity of viral families identified in each insect (C,F,I,L,O).

Figure 3

Characterization of viral sequences identified in Aphis aurantii samples. (A) Phylogenetics analyses of sequences related to members of Riboviria. The best model according to the Akaike information criterion (AIC) was VT + F. (B) Phylogeny of transcript showing similarity to members of the family Iflaviridae. The best model according to the Akaike information criterion (AIC) was BLOSSUM62 + F.

Figure 4

Characterization of viral sequences identified in Atrichopogon sp. samples. (A) Phylogenetics analyses of sequences related to members of the order Bunyavirales. The best model according to the Akaike information criterion (AIC) was VT + F. (B) Phylogeny of transcript showing similarity to members of the family Chuviridae. The best model according to the Akaike information criterion (AIC) was VT + F.

Figure 5

Characterization of viral sequences identified in Dasyhelea sp. samples. (A) Phylogenetics analyses of sequences related to members of the family Totiviridae. The best model according to the Akaike information criterion (AIC) was BLOSSUM62 + F. (B) Phylogeny of transcript showing similarity to members of the family Xinmoviridae. The best model according to the Akaike information criterion (AIC) was VT + F.

Figure 6

Characterization of viral sequences identified in samples of Forcipomyia taiwana. (A) Phylogenetics analyses of sequences related to members of the families Narnaviridae and Ourmiaviridae. The best model according to the Akaike information criterion (AIC) was BLOSSUM62 + F. (B) Phylogeny of transcript showing similarity to members of the family Orthomyxoviridae. The best model according to the Akaike information criterion (AIC) was BLOSSUM62 + F.

Figure 7

Assessment of the transcriptional activity of virus-derived sequences. Abundance of transcripts was normalized by Transcripts Per Million (TPM).