Pest status, molecular evolution, and epigenetic factors derived from the genome assembly of Frankliniella fusca, a thysanopteran phytovirus vector.

BACKGROUND: The tobacco thrips (Frankliniella fusca Hinds; family Thripidae; order Thysanoptera) is an important pest that can transmit viruses such as the tomato spotted wilt orthotospovirus to numerous economically important agricultural row crops and vegetables. The structural and functional genomics within the order Thysanoptera has only begun to be explored. Within the > 7000 known thysanopteran species, the melon thrips (Thrips palmi Karny) and the western flower thrips (Frankliniella occidentalis Pergrande) are the only two thysanopteran species with assembled genomes. RESULTS: A genome of F. fusca was assembled by long-read sequencing of DNA from an inbred line. The final assembly size was 370 Mb with a single copy ortholog completeness of ~ 99% with respect to Insecta. The annotated genome of F. fusca was compared with the genome of its congener, F. occidentalis. Results revealed many instances of lineage-specific differences in gene content. Analyses of sequence divergence between the two Frankliniella species' genomes revealed substitution patterns consistent with positive selection in ~ 5% of the protein-coding genes with 1:1 orthologs. Further, gene content related to its pest status, such as xenobiotic detoxification and response to an ambisense-tripartite RNA virus (orthotospovirus) infection was compared with F. occidentalis. Several F. fusca genes related to virus infection possessed signatures of positive selection. Estimation of CpG depletion, a mutational consequence of DNA methylation, revealed that F. fusca genes that were downregulated and alternatively spliced in response to virus infection were preferentially targeted by DNA methylation. As in many other insects, DNA methylation was enriched in exons in Frankliniella, but gene copies with homology to DNA methyltransferase 3 were numerous and fragmented. This phenomenon seems to be relatively unique to thrips among other insect groups. CONCLUSIONS: The F. fusca genome assembly provides an important resource for comparative genomic analyses of thysanopterans. This genomic foundation allows for insights into molecular evolution, gene regulation, and loci important to agricultural pest status.

Prospective Alternate Hosts of an Emerging Polerovirus in Cotton Landscapes in the Southeastern United States.

The identification of alternate hosts that can act as virus inoculum sources and vector reservoirs in the landscape is critical to understanding virus epidemics. Cotton leafroll dwarf virus (CLRDV) is a serious pathogen in cotton production and is transmitted by the cotton/melon aphid, Aphis gossypii, in a persistent, circulative, and non-propagative manner. CLRDV was first reported in the United States in Alabama in 2017, and thereafter in several cotton-producing states. CLRDV has since established itself in the southeastern United States. The role of alternate hosts in CLRDV establishment is not clear. Fourteen common plant species in the landscape, including crops, weeds, and ornamentals (cotton, hollyhock, marshmallow, country mallow, abutilon, arrowleaf sida, okra, hibiscus, squash, chickpea, evening primrose, henbit, Palmer amaranth, and prickly sida) were tested as potential alternate hosts of CLRDV along with an experimental host (Nicotiana benthamiana) via aphid-mediated transmission assays. CLRDV was detected following inoculation in hibiscus, okra, N. benthamiana, Palmer amaranth, and prickly sida by RT-PCR, but not in the others. CLRDV accumulation determined by RT-qPCR was the highest in N. benthamiana compared with cotton and other hosts. However, aphids feeding on CLRDV-infected prickly sida, hibiscus, and okra alone were able to acquire CLRDV and back-transmit it to non-infected cotton seedlings. Additionally, some of the alternate CLRDV hosts supported aphid development on par with cotton. However, in a few instances, aphid fitness was reduced when compared with cotton. Overall, this study demonstrated that plant hosts in the agricultural landscape can serve as CLRDV inoculum sources and as aphid reservoirs and could possibly play a role in the reoccurring epidemics of CLRDV in the southeastern United States.

Microbiome profiling of the onion thrips, Thrips tabaci Lindeman (Thysanoptera: Thripidae).

The gut microbial community structure of adult Thrips tabaci collected from 10 different agro-climatically diverse locations of India was characterized by using the Illumina MiSeq platform to amplify the V3 region of the 16S rRNA gene of bacteria present in the sampled insects. Analyses were performed to study the bacterial communities associated with Thrips tabaci in India. The complete bacterial metagenome of T. tabaci was comprised of 1662 OTUs of which 62.25% belong to known and 37.7% of unidentified/unknown bacteria. These OTUs constituted 21 bacterial phyla of 276 identified genera. Phylum Proteobacteria was predominant, followed by Actinobacteria, Firmicutes, Bacteroidetes and Cyanobacteria. Additionally, the occurrence of the reproductive endosymbiont, Wolbachia was detected at two locations (0.56%) of the total known OTUs. There is high variation in diversity and species richness among the different locations. Alpha-diversity metrics indicated the higher gut bacterial diversity at Bangalore and lowest at Rahuri whereas higher bacterial species richness at T. tabaci samples from Imphal and lowest at Jhalawar. Beta diversity analyses comparing bacterial communities between the samples showed distinct differences in bacterial community composition of T. tabaci samples from different locations. This paper also constitutes the first record of detailed bacterial communities associated with T. tabaci. The location-wise variation in microbial metagenome profile of T. tabaci suggests that bacterial diversity might be governed by its population genetic structure, environment and habitat.

Monitoring Seasonal Distribution of Thrips Vectors of Soybean Vein Necrosis Virus in Alabama Soybeans.

Soybean vein necrosis virus (SVNV), a new virus in the genus Orthotospovirus, has been found in all soybean-growing regions in the United States and Ontario, Canada. Soybean thrips, Neohydatothrips variabilis (Beach) (Thysanoptera: Thripidae), tobacco thrips, Frankliniella fusca (Hinds) (Thysanoptera: Thripidae), and eastern flower thrips, Frankliniella tritici (Fitch) (Thysanoptera: Thripidae) are reported vectors of this virus, but there are no reports on their distribution in Alabama. A monitoring study was conducted in 2015 and 2016 to determine thrips species composition and abundance in Alabama soybean agroecosystems. Thrips were monitored weekly by collecting them on yellow sticky traps and soybean plant parts including foliage and reproductive structures. All three reported vectors of SVNV were identified in Alabama, with N. variabilis and F. tritici as the predominant species, while F. fusca was not consistently collected from soybean plants. Four additional thrips species were collected, of which Echinothrips americanus (Morgan) (Thysanoptera: Thripidae) was commonly found on soybean at all three locations. Results presented in this study provide new information about seasonal thrips species abundance in soybean agroecosystems in Alabama, and is an important first step to understanding thrips vector species of epidemiological importance in the Southern United States.

Insecticide Resistance Signals Negative Consequences of Widespread Neonicotinoid Use on Multiple Field Crops in the U.S. Cotton Belt.

The intensification of industrial agriculture has been enabled by improved crop varieties, genetically engineered crops, fertilizers, and pesticides. Over the past 15 years, neonicotinoid seed treatments have been adopted worldwide and are used on a large proportion of U.S. field crops. Although neonicotinoids are used widely, little is known about how large-scale deployment affects pest populations over long periods. Here, we report a positive relationship between the deployment of neonicotinoid seed-dressings on multiple crops and the emergence of insecticide resistance in tobacco thrips (Frankliniella fusca), a polyphagous insect herbivore that is an important pest of seedling cotton but not soybean or maize. Using a geospatial approach, we studied the relationship between neonicotinoid resistance measured in 301 F. fusca populations to landscape-scale crop production patterns across nine states in the southeastern U.S. cotton production region, in which soybean, maize and cotton are the dominant crops. Our research linked the spatiotemporal abundance of cotton and soybean production to neonicotinoid resistance in F. fusca that is leading to a dramatic increase in insecticide use in cotton. Results demonstrate that cross-crop resistance selection has important effects on pests and, in turn, drives pesticide use and increases environmental impacts associated with their use.

Frankliniella fusca resistance to neonicotinoid insecticides: an emerging challenge for cotton pest management in the eastern United States.

BACKGROUND: Over the past two decades, neonicotinoid seed treatments have become the primary method to manage tobacco thrips, Frankliniella fusca Hinds, on seedling cotton. Because this insect is highly polyphagous and the window of insecticide exposure is short, neonicotinoid resistance was expected to pose a minimal risk. However, reports of higher than expected F. fusca seedling damage in seed-treated cotton fields throughout the Mid-South and Southeast US production regions suggested neonicotinoid resistance had developed. To document this change, F. fusca populations from 86 different locations in the eastern United States were assayed in 2014 and 2015 for imidacloprid and thiamethoxam resistance to determine the extent of the issue in the region. RESULTS: Approximately 57 and 65% of the F. fusca populations surveyed had reduced imidacloprid and thiamethoxam sensitivity respectively. Survivorship in diagnostic bioassays was significantly different at both the state and regional scales. Multiple-dose bioassays conducted on 37 of the populations documented up to 55- and 39-fold resistance ratios for imidacloprid and thiamethoxam respectively. CONCLUSION: Estimates of neonicotinoid resistance indicate an emerging issue for management of F. fusca in the eastern United States. Significant variation in survivorship within states and regions indicated that finer-scale surveys were needed to determine factors (genetic, insecticide use) driving resistance evolution. © 2016 Society of Chemical Industry.

Thrips tabaci population genetic structure and polyploidy in relation to competency as a vector of tomato spotted wilt virus.

Knowledge of population-level genetic differences can help explain variation among populations of insect vectors in their role in the epidemiology of specific viruses. Variation in competency to transmit Tomato spotted wilt virus (TSWV) that exists among populations of Thrips tabaci has been associated with the presence of cryptic species that exhibit different modes of reproduction and host ranges. However, recent findings suggest that vector competency of T. tabaci at any given location depends on the thrips and virus populations that are present. This study characterizes the population genetic structure of T. tabaci collected from four locations in North Carolina and examines the relationship between population genetic structure and variation in TSWV transmission by T. tabaci. Mitochondrial COI sequence analysis revealed the presence of two genetically distinct groups with one characterized by thelytokous, parthenogenetic reproduction and the other by arrhenotokous, sexual reproduction. Using a set of 11 microsatellite markers that we developed to investigate T. tabaci population genetic structure, we identified 17 clonal groups and found significant genetic structuring among the four NC populations that corresponded to the geographic locations where the populations were collected. Application of microsatellite markers also led to the discovery of polyploidy in this species. All four populations contained tetraploid individuals, and three contained both diploid and tetraploid individuals. Analysis of variation in transmission ofTSWV among isofemale lines initiated with individuals used in this study revealed that 'clone assignment,' 'virus isolate' and their interaction significantly influenced vector competency. These results highlight the importance of interactions between specific T. tabaci clonal types and specific TSWV isolates underlying transmission of TSWV by T. tabaci.