Cassava begomovirus species diversity changes during plant vegetative cycles.

Cassava is a root crop important for global food security and the third biggest source of calories on the African continent. Cassava production is threatened by Cassava mosaic disease (CMD), which is caused by a complex of single-stranded DNA viruses (family: Geminiviridae, genus: Begomovirus) that are transmitted by the sweet potato whitefly (Bemisia tabaci). Understanding the dynamics of different cassava mosaic begomovirus (CMB) species through time is important for contextualizing disease trends. Cassava plants with CMD symptoms were sampled in Lake Victoria and coastal regions of Kenya before transfer to a greenhouse setting and regular propagation. The field-collected and greenhouse samples were sequenced using Illumina short-read sequencing and analyzed on the Galaxy platform. In the field-collected samples, African cassava mosaic virus (ACMV), East African cassava mosaic virus (EACMV), East African cassava mosaic Kenya virus (EACMKV), and East African cassava mosaic virus-Uganda variant (EACMV-Ug) were detected in samples from the Lake Victoria region, while EACMV and East African mosaic Zanzibar virus (EACMZV) were found in the coastal region. Many of the field-collected samples had mixed infections of EACMV and another begomovirus. After 3 years of regrowth in the greenhouse, only EACMV-like viruses were detected in all samples. The results suggest that in these samples, EACMV becomes the dominant virus through vegetative propagation in a greenhouse. This differed from whitefly transmission results. Cassava plants were inoculated with ACMV and another EACMV-like virus, East African cassava mosaic Cameroon virus (EACMCV). Only ACMV was transmitted by whiteflies from these plants to recipient plants, as indicated by sequencing reads and copy number data. These results suggest that whitefly transmission and vegetative transmission lead to different outcomes for ACMV and EACMV-like viruses.

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.

Patterns of genetic divergence among populations of Aedes aegypti L. (Diptera: Culicidae) in the southeastern USA.

BACKGROUND: The yellow fever mosquito, Aedes aegypti is a public health concern in the USA, especially in the wake of emergent diseases such as Zika and chikungunya. Aedes aegypti populations dwindled after the invasion of Aedes albopictus in the 1980s and many populations were extirpated. However, in some areas Ae. aegypti persisted in small populations and there are reports of recent resurgences of Ae. aegypti in Florida, Louisiana, Nevada and California. We assessed the population genetic structure of Ae. aegypti in Florida and Georgia, which has concomitant consequences related to mosquito dispersal, pesticide resistance and vectorial capacity. METHODS: We collected Ae. aegypti across Florida and in Georgia using ovitraps. We hatched the eggs and reared them to adults, and after sacrifice we extracted their DNA. We then probed each individual for variation in 6 microsatellite markers, which we used to address population genetic characteristics. RESULTS: We collected Ae. aegypti and genotyped seven Florida populations and one Georgia population using microsatellite markers. We found evidence of isolation by distance model of gene flow supported by driving distance among cities within Florida and two theoretic genetic clusters. CONCLUSIONS: Significant genetic structure between some populations with substantial gene flow between geographically distant cities suggests regional genetic structuring of Ae. aegypti in Florida. This study provides information on the genetic exchange between populations of Ae. aegypti in the southeastern USA and suggests potential routes of spread of this species.

Rapid evolution and the genomic consequences of selection against interspecific mating.

While few species introduced into a new environment become invasive, those that do provide critical information on ecological mechanisms that determine invasions success and the evolutionary responses that follow invasion. Aedes albopictus (the Asian tiger mosquito) was introduced into the naturalized range of Aedes aegypti (the yellow fever mosquito) in the United States in the mid-1980s, resulting in the displacement of A. aegypti in much of the south-eastern United States. The rapid displacement was likely due to the superior competitive ability of A. albopictus as larvae and asymmetric mating interference competition, in which male A. albopictus mate with and sterilize A. aegypti females, a process called "satyrization." The goal of this study was to examine the genomic responses of a resident species to an invasive species in which the mechanism of character displacement is understood. We used double-digest restriction enzyme DNA sequencing (ddRADseq) to analyse outlier loci between selected and control lines of laboratory-reared A. aegypti females from two populations (Tucson, AZ and Key West, Florida, USA), and individual females classified as either "resisted" or "mated with" A. albopictus males via mating trials of wild-derived females from four populations in Florida. We found significant outlier loci in comparing selected and control lines and between mated and nonmated A. aegypti females in the laboratory and wild-derived populations, respectively. We found overlap in specific outlier loci between different source populations that support consistent genomic signatures of selection within A. aegypti. Our results point to regions of the A. aegypti genome and potential candidate genes that may be involved in mating behaviour, and specifically in avoiding interspecific mating choices.

Efficacy of Chlorantraniliprole in Controlling Structural Infestations of the Eastern Subterranean Termite in the USA.

Subterranean termites are the most economically important structural pests in the USA, and the eastern subterranean termite, Reticulitermes flavipes (Kollar) (Dictyoptera: Rhinotermitidae) is the most widely distributed species. Soil treatment with a liquid termiticide is a widely used method for controlling subterranean termites in structures. We assessed the efficacy of a nonrepellent termiticide, Altriset® (active ingredient: chlorantraniliprole), in controlling structural infestations of R. flavipes in Texas, North Carolina, and Ohio and determined the post-treatment fate of termite colonies in and around the structures. In all three states, microsatellite markers indicated that only one R. flavipes colony was infesting each structure. A single chlorantraniliprole treatment provided effective structural protection as there was no further evidence of termite activity in and on the majority of structures from approximately 1 month to 2 years post-treatment when the study concluded. Additionally, the treatment appeared to either severely reduce the infesting colony's footprint at monitors in the landscape or eliminate colony members from these monitors. A supplemental spot-treatment was conducted at one house each in Texas and North Carolina at 5 and 6 months post-treatment, respectively; no termites were observed thereafter in these structures and associated landscaping. The number of colonies found exclusively in the landscape (not attacking the structure) varied among the states, with the largest number of colonies in Texas (0-4) and North Carolina (0-5) as compared to 0-1 in Ohio, the most northern state.

Unrelated secondary reproductives in the neotropical termite Silvestritermes euamignathus (Isoptera: Termitidae).

A termite colony is usually founded by a pair of alates, the primary reproductives, which produce all the nestmates. In some species, secondary reproductives appear to either replace the primaries or supplement colony reproduction. In termites, secondary reproductives are generally ergatoids derived from workers or nymphoids derived from nymphs. Silvestritermes euamignathus is a termite species that forms multiple nymphoid reproductives, and to date it was hypothesized that these secondary reproductives were the progeny of the primary founding reproductives. We developed markers for 12 microsatellite loci and used COI mitochondrial DNA (mtDNA) to genotype 59 nymphoid neotenics found in a colony of S. euamignathus to test this hypothesis. Our results showed that nymphoids of S. euamignathus are not all siblings. The microsatellite analysis suggests that the secondary reproductives derived from a minimum of four different pairs of reproductives belonging to at least two different matrilines. This is the first record of non-sibling secondary reproductives occupying the same nest in a higher termite. These unrelated reproductives might be the result of either pleometrotic colony foundation or colony fusion.

Asexual queen succession in the subterranean termite Reticulitermes virginicus.

Termite colonies are founded by a pair of primary reproductives. In many species, including subterranean termites (family Rhinotermitidae), the primary king and queen can be succeeded by neotenic reproductives that are produced from workers or nymphs within the colony. It is generally believed that these neotenics inbreed within the colony, sometimes for many generations. Here, we show that primary queens of the North American subterranean termite, Reticulitermes virginicus, are replaced by numerous parthenogenetically produced female neotenics. We collected functional female neotenics from five colonies of R. virginicus in North Carolina and Texas, USA. Genetic analysis at eight microsatellite loci showed that 91-100% of the neotenics present within a colony were homozygous at all loci, indicating that they were produced through automictic parthenogenesis with terminal fusion. In contrast, workers, soldiers and alates were almost exclusively sexually produced by mating between the female neotenics and a single king. This is the second termite species shown to undergo asexual queen succession, a system first described in the Japanese species, Reticulitermes speratus. Thus, the conditional use of sexual and asexual reproduction to produce members of different castes may be widespread within Reticulitermes and possibly other subterranean termites.

Queen succession through asexual reproduction in termites.

The evolution and maintenance of sexual reproduction may involve important tradeoffs because asexual reproduction can double an individual's contribution to the gene pool but reduces diversity. Moreover, in social insects the maintenance of genetic diversity among workers may be important for colony growth and survival. We identified a previously unknown termite breeding system in which both parthenogenesis and sexual reproduction are conditionally used. Queens produce their replacements asexually but use normal sexual reproduction to produce other colony members. These findings show how eusociality can lead to extraordinary reproductive systems and provide important insights into the advantages and disadvantages of sex.