Abstract:
The tomato potato psyllid (TPP, Bactericera cockerelli Šulc) is a pest that causes significant economic loss to the tomato and potato industries. Insecticide applications, sometimes fortnightly, are currently used for TPP control. This raises concerns that TPP may develop insecticide resistance despite the use of different chemistries. Insect viruses (e.g. Nucleopolyhedroviruses and Granuloviruses) have been used to control insect pests as they are nontoxic to humans, livestock, most beneficial insects, plants and the environment. To investigate the possibility of insect viruses for control of TPP, a thorough understanding of the viruses associated with this pest is required. The aim of this study was to investigate the viral component of the TPP microbiome using DNA and RNA sequencing. TPP DNA metagenomic sequences were classified using Kraken. The sequences classified as viral were then verified by both BWA mapping and de novo assembly. The bioinformatics analysis of TPP DNA metagenome reveals that both the Honduras and New Zealand TPP DNA samples had similar virus diversity profiles. However, most classified viruses were not confirmed by BWA mapping and de novo assembly. The Wolbachia prophage (WO prophage) had a high mapping coverage within the Honduras-derived TPP metagenomes but a low mapping coverage with Hawke’s Bay (New Zealand) TPP metagenomes, suggesting that the WO prophage may be present in Honduras TPP but not TPP from the North Island of New Zealand. A diverse array of viral sequences were identified from TPP RNA metagenomes by both BLASTn and Kraken. The potato leafroll virus (PLRV), family Luteoviridae, had a BWA mapping coverage of 13.3% from field TPP metagenomic sequences. Mapping of the putative PLRV de novo assembled contigs revealed only 18.1% coverage to a reference viral genome. Nevertheless, neither BWA mapping, nor de novo assembly revealed the presence of the PLRV in the metagenomic samples from an iso-female TPP laboratory colony. Why a portion of the PLRV genome appears to be present in field TPP and not in colony TPP, is unknown but does suggest a differential pattern of potential virus diversity and distribution between field TPP and colony TPP. Furthermore, this study has developed an effective and efficient method of extracting and amplifying dsRNA from TPP nucleic acid extracts. This is the first survey to assess the viral component of the TPP microbiome. A range of bioinfomatic and molecular methods have been used to assess both the DNA and RNA components of the TPP metagenome. These methods can be used for future studies on viruses associated with TPP.