Hybridization and the Spread of the Apple Maggot Fly, Rhagoletis pomonella (Diptera: Tephritidae), in the Northwestern United States

Hybridization may be an important process interjecting variation into insect populations enabling host plant shifts and the origin of new economic pests. Here, we examine whether hybridization between the native snowberry-infesting fruit fly Rhagoletis zephyria (Snow) and the introduced quarantine pest R. pomonella (Walsh) is occurring and may aid the spread of the latter into more arid commercial apple-growing regions of central Washington state, USA. Results for 19 microsatellites implied hybridization occurring at a rate of 1.44% per generation between the species. However, there was no evidence for increased hybridization in central Washington. Allele frequencies for seven microsatellites in R. pomonella were more ‘R. zephyria-like’ in central Washington, suggesting that genes conferring resistance to desiccation may be adaptively introgressing from R. zephyria. However, in only one case was the putatively introgressing allele from R. zephyria not found in R. pomonella in the eastern USA. Thus, many of the alleles changing in frequency may have been prestanding in the introduced R. pomonella population. The dynamics of hybridization are therefore complex and nuanced for R. pomonella, with various causes and factors, including introgression for a portion, but not all of the genome, potentially contributing to the pest insect\u27s spread

Hybridization and the Spread of the Apple Maggot Fly, Rhagoletis pomonella (Diptera: Tephritidae), in the Northwestern United States

Hybridization may be an important process interjecting variation into insect populations enabling host plant shifts and the origin of new economic pests. Here, we examine whether hybridization between the native snowberry-infesting fruit fly Rhagoletis zephyria (Snow) and the introduced quarantine pest R. pomonella (Walsh) is occurring and may aid the spread of the latter into more arid commercial apple-growing regions of central Washington state, USA. Results for 19 microsatellites implied hybridization occurring at a rate of 1.44% per generation between the species. However, there was no evidence for increased hybridization in central Washington. Allele frequencies for seven microsatellites in R. pomonella were more ‘R. zephyria-like’ in central Washington, suggesting that genes conferring resistance to desiccation may be adaptively introgressing from R. zephyria. However, in only one case was the putatively introgressing allele from R. zephyria not found in R. pomonella in the eastern USA. Thus, many of the alleles changing in frequency may have been prestanding in the introduced R. pomonella population. The dynamics of hybridization are therefore complex and nuanced for R. pomonella, with various causes and factors, including introgression for a portion, but not all of the genome, potentially contributing to the pest insect\u27s spread

The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species

The Mediterranean fruit fly (medfly), Ceratitis capitata, is a major destructive insect pest due to its broad host range, which includes hundreds of fruits and vegetables. It exhibits a unique ability to invade and adapt to ecological niches throughout tropical and subtropical regions of the world, though medfly infestations have been prevented and controlled by the sterile insect technique (SIT) as part of integrated pest management programs (IPMs). The genetic analysis and manipulation of medfly has been subject to intensive study in an effort to improve SIT efficacy and other aspects of IPM control

High quality genomic resources for stored product insects: Presentation

The expansion of genomic resources for stored product insects has largely been hampered by cost, time required for inbreeding, and technical issues that can arise during genome assembly from pooling multiple individuals together for DNA isolation and library preparation. However, newer library methods, such as 10X Chromium libraries, largely overcome these issues in that sufficient DNA can be recovered from a single individual for library prep and allelic variants are assembled as separate phase blocks, eliminating the need for inbreeding. Using 10X Chromium libraries coupled with 150 x 150 bp HiSeqX sequencing to a depth of at least 60X coverage, we are developing high quality draft genome assemblies for eight different stored product insect species, including Dermestidae (Trogoderma variabile, Trogoderma granarium, and Dermestes maculatus), Tenebrionidae (Tribolium confusum), Anobiidae (Lasioderma serricorne and Stegobium paniceum), Bostrichidae (Prostephanus truncatus), and Pyralidae (Plodia interpunctella). Overall, BUSCO (Benchmarking Using Single Copy Orthologs) scores exceeded 95% in all assemblies with few fragmented or duplicated genes, suggesting a high quality assembly of the gene space. Further, scaffold N50s exceeded 1 Mb in many cases and further improvements to these scaffolding metrics will be made using linkage maps and Hi-C libraries. Overall, this approach will yield high quality assemblies for eight different insects and could be used to quickly and efficiently generate draft assemblies of invasive or emerging stored product pests.The expansion of genomic resources for stored product insects has largely been hampered by cost, time required for inbreeding, and technical issues that can arise during genome assembly from pooling multiple individuals together for DNA isolation and library preparation. However, newer library methods, such as 10X Chromium libraries, largely overcome these issues in that sufficient DNA can be recovered from a single individual for library prep and allelic variants are assembled as separate phase blocks, eliminating the need for inbreeding. Using 10X Chromium libraries coupled with 150 x 150 bp HiSeqX sequencing to a depth of at least 60X coverage, we are developing high quality draft genome assemblies for eight different stored product insect species, including Dermestidae (Trogoderma variabile, Trogoderma granarium, and Dermestes maculatus), Tenebrionidae (Tribolium confusum), Anobiidae (Lasioderma serricorne and Stegobium paniceum), Bostrichidae (Prostephanus truncatus), and Pyralidae (Plodia interpunctella). Overall, BUSCO (Benchmarking Using Single Copy Orthologs) scores exceeded 95% in all assemblies with few fragmented or duplicated genes, suggesting a high quality assembly of the gene space. Further, scaffold N50s exceeded 1 Mb in many cases and further improvements to these scaffolding metrics will be made using linkage maps and Hi-C libraries. Overall, this approach will yield high quality assemblies for eight different insects and could be used to quickly and efficiently generate draft assemblies of invasive or emerging stored product pests

A New Diagnostic Resource for Ceratitis capitata Strain Identification Based on QTL Mapping

The Mediterranean fruit fly Ceratitis capitata (Wiedemann) is a destructive agricultural pest and the subject of exclusion efforts in many countries. Suppression and eradication of invasive populations to prevent its establishment is facilitated by the release of sterile males using the sterile insect technique (SIT). In SIT release areas, it is critical to accurately discriminate between released sterile males and wild individuals to detect extremely rare invasive individuals in areas inundated with millions of sterile male flies. Current methods for discrimination exist but are not always definitive, and a more reliable method is necessary. To address this, we developed a genotyping assay that can be used to discriminate between sterile males from the SIT strain and wild individuals. This was achieved by identifying single nucleotide polymorphisms (SNPs) linked to the maintained traits that facilitate male-only releases, white pupae (wp) and temperature-sensitive lethal (tsl), via QTL mapping. This resulted in the identification of one SNP that was in near-perfect linkage disequilibrium between genotype at this locus and the pupal color phenotype. Medfly from many SIT colonies and wild individuals from across its geographic range were genotyped for this locus, and results show its consistency in identifying SIT flies. In addition, linkage and QTL mapping of wp and tsl have larger impacts as they can serve as foundational tools to identify the genetic basis of traits that facilitate the separation of males from female flies, which can be used to develop SIT programs in related species

Whole Genome Sequencing of the Braconid Parasitoid Wasp Fopius arisanus, an Important Biocontrol Agent of Pest Tepritid Fruit Flies

The braconid wasp Fopius arisanus (Sonan) is an important biological control agent of tropical and subtropical pest fruit flies, including two important global pests, the Mediterranean fruit fly (Ceratitis capitata), and the oriental fruit fly (Bactrocera dorsalis). The goal of this study was to develop foundational genomic resources for this species to provide tools that can be used to answer questions exploring the multitrophic interactions between the host and parasitoid in this important research system. Here, we present a whole genome assembly of F. arisanus, derived from a pool of haploid offspring from a single unmated female. The genome is ∼154 Mb in size, with a N50 contig and scaffold size of 51,867 bp and 0.98 Mb, respectively. Utilizing existing RNA-Seq data for this species, as well as publicly available peptide sequences from related Hymenoptera, a high quality gene annotation set, which includes 10,991 protein coding genes, was generated. Prior to this assembly submission, no RefSeq proteins were present for this species. Parasitic wasps play an important role in a diverse ecosystem as well as a role in biological control of agricultural pests. This whole genome assembly and annotation data represents the first genome-scale assembly for this species or any closely related Opiine, and are publicly available in the National Center for Biotechnology Information Genome and RefSeq databases, providing a much needed genomic resource for this hymenopteran group

Table S1

Relative percentages of chemical compounds comprising the synthetic fruit volatile blends used in the study to test Rhagoletis pomonella fly behavior

The USDA-ARS Ag100pest initiative: High-quality genome assemblies for agricultural pest arthropod research

The phylum Arthropoda includes species crucial for ecosystem stability, soil health, crop production, and others that present obstacles to crop and animal agriculture. The United States Department of Agriculture’s Agricultural Research Service initiated the Ag100Pest Initiative to generate reference genome assemblies of arthropods that are (or may become) pests to agricultural production and global food security. We describe the project goals, process, status, and future. The first three years of the project were focused on species selection, specimen collection, and the construction of lab and bioinformatics pipelines for the efficient production of assemblies at scale. Contig-level assemblies of 47 species are presented, all of which were generated from single specimens. Lessons learned and optimizations leading to the current pipeline are discussed. The project name implies a target of 100 species, but the efficiencies gained during the project have supported an expansion of the original goal and a total of 158 species are currently in the pipeline. We anticipate that the processes described in the paper will help other arthropod research groups or other consortia considering genome assembly at scale

Data from: A field test for host fruit odour discrimination and avoidance behaviour for Rhagoletis pomonella flies in the western United States

Prezygotic isolation due to habitat choice is important to many models of speciation-with-gene-flow. Habitat choice is usually thought to occur through positive preferences of organisms for particular environments. However, avoidance of non-natal environments may also play a role in choice and have repercussions for postzygotic isolation that preference does not. The recent host shift of Rhagoletis pomonella (Diptera: Tephritidae) from downy hawthorn, Crataegus mollis, to introduced apple, Malus domestica, in the eastern U.S. is a model for speciation-with-gene flow. However, the fly is also present in the western U.S. where it was likely introduced via infested apples < 60 years ago. R. pomonella now attacks two additional hawthorns in the West, the native C. douglasii (black hawthorn) and the introduced C. monogyna (English ornamental hawthorn). Flight tunnel tests have shown that western apple-, C. douglasii-, and C. monogyna-origin flies all positively orient to fruit volatile blends of their respective natal hosts in flight tunnel assays. Here, we show that these laboratory differences translate to nature through field trapping studies of flies in the state of Washington. Moreover, western R. pomonella display both positive orientation to their respective natal fruit volatiles and avoidance behaviour (negative orientation) to non-natal volatiles. Our results are consistent with the existence of behaviourally differentiated host races of R. pomonella in the West. In addition, the rapid evolution of avoidance behaviour appears to be a general phenomenon for R. pomonella during host shifts, as the eastern apple and downy hawthorn host races also are antagonized by non-natal fruit volatiles