Diverse Array of New Viral Sequences Identified in Worldwide Populations of the Asian Citrus Psyllid (Diaphorina citri) Using Viral Metagenomics

Abstract

The Asian citrus psyllid, Diaphorina citri, is the natural vector of the causal agent of Huanglongbing (HLB), or citrus greening disease. Together; HLB and D. citri represent a major threat to world citrus production. As there is no cure for HLB, insect vector management is considered one strategy to help control the disease, and D. citri viruses might be useful. In this study, we used a metagenomic approach to analyze viral sequences associated with the global population of D. citri. By sequencing small RNAs and the transcriptome coupled with bioinformatics analysis, we showed that the virus-like sequences of D. citri are diverse. We identified novel viral sequences belonging to the picornavirus superfamily, the Reoviridae, Parvoviridae, and Bunyaviridae families, and an unclassified positive-sense single-stranded RNA virus. Moreover, a Wolbachia prophage-related sequence was identified. This is the first comprehensive survey to assess the viral community from worldwide populations of an agricultural insect pest. Our results provide valuable information on new putative viruses, some of which may have the potential to be used as biocontrol agents. IMPORTANCEInsects have the most species of all animals, and are hosts to, and vectors of, a great variety of known and unknown viruses. Some of these most likely have the potential to be important fundamental and/or practical resources. In this study, we used highthroughput next-generation sequencing (NGS) technology and bioinformatics analysis to identify putative viruses associated with Diaphorina citri, the Asian citrus psyllid. D. citri is the vector of the bacterium causing Huanglongbing (HLB), currently the most serious threat to citrus worldwide. Here, we report several novel viral sequences associated with D. citri. Viruses are the most abundant microbes on our planet (1) and are found in all types of organisms. Insects are the largest and most diverse taxonomic class among animals, representing perhaps half of known animals, with more than one million species recognized worldwide (2). Insects are known to be hosts to viruses belonging to various viral taxa, including the Baculoviridae, Parvoviridae, Flaviviridae, Ascoviridae, Togaviridae, Bunyaviridae, and Rhabdoviridae (3). However, the number of currently described viral species infecting insects is relatively low compared to the number of viruses that have been discovered among prokaryotes, plants, and vertebrates. Furthermore, most of the insect viruses described to date have been discovered because of their pathogenic effects on their insect hosts or because they are pathogens of humans, other vertebrates, or economically important plants. Traditional viral detection methods that require prior knowledge of genome sequences may not be suitable for the discovery of new viruses and, in particular, viruses with a high level of genetic diversity. However, in the past decade, the development of high-throughput next-generation sequencing (NGS) technologies and bioinformatics applications has provided ne...

Unbiased RNA Shotgun Metagenomics in Social and Solitary Wild Bees Detects Associations with Eukaryote Parasites and New Viruses

“…This adds to the findings of Singh and co-authors who demonstrated the circulation of RNA viruses among bees through pollen-vectoring [22]. Another viral match included the RdRp of a tombusnodavirus related to the psyllid virus DcACV [56] and the honey bee CBPV. This was an unusual finding because these viruses lack a 3’ end polyA-tail [57] and are theoretically not retained by polyA+ mRNA enrichment.…”

Twenty five new viruses associated with the Drosophilidae (Diptera)

“…Kinkell virus, along with transcriptome sequences from the fly genera Bactrocera 62,66 and Ceratitis 63 , the beetle Colaphellus 67 , the thrip Frankliniella 68 , and the spider Latrodectus 69 , appears to define a major new clade that falls within or close to the Iflaviruses (Fig 2 D). Similarly, Corseley virus, which is almost identical to transcriptome sequences from D. pseudoananassae 70 and is related to transcriptome sequences from the bug genus Lygus 71 and the beetle genus Anoplophora 72 , appears to define an entirely new group of viruses distantly related to Tombusviridae and the recently-described Diaphorina citri associated C virus 73 (which is itself closely related to the newly identified Tartou virus of S. deflexa; Fig 2 E).…”

“…Fifteen of remaining 23 putative viruses in the present study are extremely closely related to known insect viruses or virus-like sequences from insect transcriptomes (Fig 1, Fig 2), and/or are present at such high levels (greater than 10% of host COI in the cases of Muthill virus and Eridge virus), that is seems likely that the associated drosophilid is indeed the host. 73 , Tartou virus and Corseley virus from the Drosophilidae, and transcripts from various invertebrates. All three groups appear to represent common and widespread infections of invertebrates that warrant taxonomic recognition.…”

The microbiome of pest insects: it is not just bacteria

“… Culture‐independent techniques have captured how microbial community composition in insects varies largely in time and space‐in response to diet, geography, season, and developmental stage (Hu et al., ; Wilhelm et al., ; Chaplinska et al., ; Lv et al., ; Vacchini et al, ; Bascuñán et al., ). The relevance of these parameters might vary according to the microbial groups, with environmental factors being more important for bacteria and fungi than in shaping the viral communities (Nouri et al., ). How do these variations in microbiome composition affect the interplay among these members of the microbiome, and how does that affect pest insects?…”