Aphids are emerging as model organisms for both basic and applied research. Of the 5,000 estimated species, only three aphids have published whole genome sequences: the pea aphid Acyrthosiphon pisum, the Russian wheat aphid, Diuraphis noxia, and the green peach aphid, Myzus persicae. We present the whole genome sequence of a fourth aphid, the soybean aphid (Aphis glycines), which is an extreme specialist and an important invasive pest of soybean (Glycine max). The availability of genomic resources is important to establish effective and sustainable pest control, as well as to expand our understanding of aphid evolution. We generated a 302.9 Mbp draft genome assembly for Ap. glycines using a hybrid sequencing approach. This assembly shows high completeness with 19,182 predicted genes, 92% of known Ap. glycines transcripts mapping to contigs, and substantial continuity with a scaffold N of 174,505 bp. The assembly represents 95.5% of the predicted genome size of 317.1 Mbp based on flow cytometry. Ap. glycines contains the smallest known aphid genome to date, based on updated genome sizes for 19 aphid species. The repetitive DNA content of the Ap. glycines genome assembly (81.6 Mbp or 26.94% of the 302.9 Mbp assembly) shows a reduction in the number of classified transposable elements compared to Ac. pisum, and likely contributes to the small estimated genome size. We include comparative analyses of gene families related to host-specificity (cytochrome P450's and effectors), which may be important in Ap. glycines evolution. This Ap. glycines draft genome sequence will provide a resource for the study of aphid genome evolution, their interaction with host plants, and candidate genes for novel insect control methods.

Navel orangeworm, Amyelois transitella (Walker), is a primary pest of almonds, pistachios, and walnuts in California. These specialty tree nut crops are widely planted across the state and account for a significant share of total agricultural revenue, with 1.7 million combined acres generating a total farm-gate value of $8.9 billion. Larvae of A. transitella cause direct damage to the nut, burrowing into the kernel and contaminating it with frass and webbing, while adults are able to introduce fungi during oviposition that produce aflatoxin, a known human carcinogen that is heavily regulated both domestically and in key foreign markets. As such, there is little tolerance for A. transitella infestation, and most operations aim for <2% crop damage from this pest. Currently, integrated management of A. transitella involves a combination of orchard sanitation, well-timed insecticide sprays, timely harvest, and, most recently, mating disruption. Additional novel tools, such as sterile insect technique, are currently being explored. This species has a strong dispersal capacity, and given the extensive, and many times contiguous, acreage of tree nuts in California, long-term management will require the development of an effective area-wide management strategy. Tools, tactics, and conditions are in an ongoing state of change, and therefore pest management for this economically important species is a work in progress. Here, we discuss the biology, seasonal phenology, monitoring, and management of A. transitella across almonds, pistachios, and walnuts.

Host plant resistant (HPR) crop varieties offer control of many insect pest species. However, the evolution of virulent biotypes capable of overcoming plant resistance poses challenges for the implementation of HPR. Widespread planting of HPR crops further reduces HPR efficacy by increasing selection pressure on pests, favoring the rapid proliferation of virulence. An analogous situation occurs in managing insect resistance to transgenic Bt crops, where planting of susceptible refuges effectively delays the evolution and spread of Bt resistance. We investigated the applicability of susceptible refuges in HPR as a tactic to manage virulent biotypes, using the soybean aphid (Aphis glycines Matsumura) as a model system. The virulent biotype 3 and avirulent biotype 1 were reared in greenhouse microcosms using a variety of refuge size, HPR gene, and biotype mixture treatments, allowing us to discern how the presence of a refuge alters the relative fitness and movement of biotypes both by themselves and in competition. The virulent biotype had greater relative fitness in 10 of 12 tested microcosms, with the greatest advantage observed in refuge-free microcosms. In microcosms with a refuge, avirulent fitness increased significantly as these biotypes moved to and used refuge plants. When the two biotypes were reared in the same microcosm, biotype 3's fitness increased significantly relative to when reared in isolation, while biotype 1's fitness was slightly, but not significantly, increased. Our findings suggested that while susceptible refuges would be incapable of reversing the proliferation of virulent biotypes, they could slow the spread of virulence by maintaining avirulence.

Adaptive evolution of pest insects in response to the introduction of resistant cultivars is well documented and commonly results in virulent (i.e., capable of feeding upon resistant cultivars) insect populations being labeled as distinct biotypes. Phenotypically defined, biotypes frequently remain evolutionarily indistinct, resulting in ineffective application of virulence control measures and shorter durability of resistant cultivars. Here, we utilize an evolutionary framework to discern the genetic relationship between biotypes of the soybean aphid (Aphis glycines, Matsumura). The soybean aphid is invasive in North America and is among the most destructive pests of commercial soybean on the continent. Attempts to breed host-plant-resistant soybean have been hampered by the emergence of virulent aphid biotypes that are unaffected by the plant's resistance mechanism(s). Comparative population genetic analysis of virulent and avirulent (i.e., unable to feed on resistant cultivars) biotypes found populations to be genetically indistinguishable across biotype and geographic distance, with high rates of interpopulation immigration and admixture. The lack of genetic distinction between biotypes coupled with elevated genotypic diversity within all populations suggested virulence has a nongenetic-based or includes a gene complex that is widely distributed throughout soybean aphid populations, which undergo regular dispersal and unimpeded sexual recombination.

The navel orangeworm, Amyleois transitella (Lepidoptera: Pyralidae), is a key pest of almonds and pistachios in California. Larvae directly feed on nuts, reducing quality and yield, and adults can introduce fungi that produce aflatoxins. The development of sterile insect technique (SIT) is currently being explored as a management tool for this pest. Large quantities of A. transitella are mass-reared, irradiated, and shipped to California from a USDA APHIS facility in Phoenix, AZ. Preliminary field releases of sterile A. transitella from this facility resulted in poor recovery of males in pheromone traps, raising concerns that mass-reared male A. transitella may not be responding to pheromone from virgin females. In this study, a wind tunnel was used to evaluate the response of both irradiated and non-irradiated mass-reared A. transitella males to crude pheromone extract from females, and their performance was compared to two strains of locally reared non-irradiated A. transitella. While initial responses associated with pheromone detection where similar between mass-reared and locally reared moths, a lower proportion of the mass-reared moths ultimately made contact with the pheromone source. Surprisingly, the addition of irradiation did not further decrease their performance. While mass-reared moths respond to pheromone, their ability to locate and make contact with the pheromone source appears to be impeded. The underlying mechanism remains unclear, but is likely related to damage incurred during the mass-rearing and shipping process.