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The parasitoid wasp Venturia canescens is an important biological control agent of stored products moth pests and serves as a model to study the function and evolution of domesticated endogenous viruses (DEVs). The DEVs discovered in V. canescens are known as virus-like particles (VcVLPs), which are produced using nudivirus-derived components and incorporate wasp-derived virulence proteins instead of packaged nucleic acids. Previous studies of virus-derived components in the V. canescens genome identified 53 nudivirus-like genes organized in six gene clusters and several viral pseudogenes, but how VcVLP genes are organized among wasp chromosomes following their integration in the ancestral wasp genome is largely unknown. Here, we present a chromosomal scale genome of V. canescens consisting of 11 chromosomes and 56 unplaced small scaffolds. The genome size is 290.8 Mbp with a N50 scaffold size of 24.99 Mbp. A high-quality gene set including 11,831 protein-coding genes were produced using RNA-Seq data as well as publicly available peptide sequences from related Hymenoptera. A manual annotation of genes of viral origin produced 61 intact and 19 pseudogenized nudivirus-derived genes. The genome assembly revealed that two previously identified clusters were joined into a single cluster and a total of 5 gene clusters comprising of 60 intact nudivirus-derived genes were located in three chromosomes. In contrast, pseudogenes are dispersed among 8 chromosomes with only 4 pseudogenes associated with nudivirus gene clusters. The architecture of genes encoding VcVLP components suggests it originates from a recent virus acquisition and there is a link between the processes of dispersal and pseudogenization. This high-quality genome assembly and annotation represents the first chromosome-scale assembly for parasitoid wasps associated with VLPs, and is publicly available in the National Center for Biotechnology Information Genome and RefSeq databases, providing a valuable resource for future studies of DEVs in parasitoid wasps.

 

Abstract Biological introductions are unintended “natural experiments” that provide unique insights into evolutionary processes. Invasive phytophagous insects are of particular interest to evolutionary biologists studying adaptation, as introductions often require rapid adaptation to novel host plants. However, adaptive potential of invasive populations may be limited by reduced genetic diversity—a problem known as the “genetic paradox of invasions”. One potential solution to this paradox is if there are multiple invasive waves that bolster genetic variation in invasive populations. Evaluating this hypothesis requires characterizing genetic variation and population structure in the invaded range. To this end, we assemble a reference genome and describe patterns of genetic variation in the introduced white pine sawfly, Diprion similis. This species was introduced to North America in 1914, where it has rapidly colonized the thin-needled eastern white pine (Pinus strobus), making it an ideal invasion system for studying adaptation to novel environments. To evaluate evidence of multiple introductions, we generated whole-genome resequencing data for 64 D. similis females sampled across the North American range. Both model-based and model-free clustering analyses supported a single population for North American D. similis. Within this population, we found evidence of isolation-by-distance and a pattern of declining heterozygosity with distance from the hypothesized introduction site. Together, these results support a single-introduction event. We consider implications of these findings for the genetic paradox of invasion and discuss priorities for future research in D. similis, a promising model system for invasion biology. 

The small hive beetle (SHB), Aethina tumida, has emerged as a worldwide threat to honey bees in the past two decades. These beetles harvest nest resources, feed on larval bees, and ultimately spoil nest resources with gelatinous slime together with the fungal symbiont Kodamaea ohmeri.

Here, we present the first chromosome-level genome assembly for the SHB. With a 99.1% representation of conserved (BUSCO) arthropod genes, this resource enables the study of chemosensory, digestive, and detoxification traits critical for SHB success and possible control. We use this annotated assembly to characterize features of SHB sex chromosomes and a female-skewed primary sex ratio. We also found chromosome fusion and a lower recombination rate in sex chromosomes than in autosomes.

Genome-enabled insights will clarify the traits that allowed this beetle to exploit hive resources successfully and will be critical for determining the causes of observed sex ratio asymmetries.

 

The Oriental fruit flyBactrocera dorsalis(Hendel), a global pest that can decimate regional fruit industries and elicit international quarantines, has been the subject of considerable taxonomic confusion. Previous phylogenetic work revealed thatB. dorsalisis part of a monophyletic clade containing 12 species. We present restriction site‐associated DNA sequencing (RAD‐seq) genomic data for 2,292 specimens, which unequivocally supports the delimitation of two new species, here described asBactrocera borneoensissp. n.Doorenweerd & San Jose andB. incognitasp. n.Doorenweerd & San Jose. We additionally obtained 1,985 Cytochrome C oxidase I (COI) sequences for a subset of the specimens to see which species can be diagnosed with this mtDNA marker and conclude thatB. dorsalis,B. incognita,B. carambolaeDrew & Hancock,B. raiensisDrew & Hancock,B. occipitalis(Bezzi) andB. kandiensisDrew & Hancock cannot be identified reliably using COI due to introgression—but the newly described speciesB. borneoensiscan be identified using COI. The supposed innocuous speciesB. raiensisdistribution is underestimated in Asia and Africa.Bactrocera kandiensisCOI genotypes occur in African flies, but RAD‐seq data confirm that these areB. dorsaliswith introgressedB. kandiensisCOI. The phylogenomic dataset brings new light to the extent of theB. dorsalis s.l.clade and the morphological and molecular confusion based on COI. This will have ramifications for ecological data—including host and distribution ranges—associated withB. dorsalis s.l.clade species, pest identification protocols and our understanding of the economic importance of the various species in the clade.

 

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. 

Abstract Taro (Colocasia esculenta) is a food staple widely cultivated in the humid tropics of Asia, Africa, Pacific and the Caribbean. One of the greatest threats to taro production is Taro Leaf Blight caused by the oomycete pathogen Phytophthora colocasiae. Here we describe a de novo taro genome assembly and use it to analyze sequence data from a Taro Leaf Blight resistant mapping population. The genome was assembled from linked-read sequences (10x Genomics; ∼60x coverage) and gap-filled and scaffolded with contigs assembled from Oxford Nanopore Technology long-reads and linkage map results. The haploid assembly was 2.45 Gb total, with a maximum contig length of 38 Mb and scaffold N50 of 317,420 bp. A comparison of family-level (Araceae) genome features reveals the repeat content of taro to be 82%, >3.5x greater than in great duckweed (Spirodela polyrhiza), 23%. Both genomes recovered a similar percent of Benchmarking Universal Single-copy Orthologs, 80% and 84%, based on a 3,236 gene database for monocot plants. A greater number of nucleotide-binding leucine-rich repeat disease resistance genes were present in genomes of taro than the duckweed, ∼391 vs. ∼70 (∼182 and ∼46 complete). The mapping population data revealed 16 major linkage groups with 520 markers, and 10 quantitative trait loci (QTL) significantly associated with Taro Leaf Blight disease resistance. The genome sequence of taro enhances our understanding of resistance to TLB, and provides markers that may accelerate breeding programs. This genome project may provide a template for developing genomic resources in other understudied plant species. 

The Fusarium solani species complex (FSSC) is a clade of environmentally ubiquitous fungi that includes plant, animal, and insect associates. Here, we report the draft genome sequence of the undescribed species FSSC 6 (isolate MYA-4552), housed in the gut of the wood-boring cerambycid beetle Anoplophora glabripennis .