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1. Genome Sequence of Fusarium Isolate MYA-4552 from the Midgut of Anoplophora glabripennis , an Invasive, Wood-Boring Beetle

   https://doi.org/10.1128/genomeA.00544-16  

   Herr, Joshua R.; Scully, Erin D.; Geib, Scott M.; Hoover, Kelli; Carlson, John E.; Geiser, David M. (July 2016, Genome Announcements)

   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 . 

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2. Heritable viral symbionts in the family Iflaviridae are widespread among aphids

   https://doi.org/10.1101/2025.02.03.636351  

   Rozo-Lopez, Paula; Torres, Vanesa; Torres, Joseph; Käfer, Simon; Parker, Benjamin J (February 2025, bioRxiv)

   A<sc>bstract</sc> Heritable microbes shape host phenotypes and are important drivers of evolution. While interactions between insects and bacterial symbionts have been extensively studied, the prevalence and consequences of insect-viral symbiosis are an open question. We show that viral symbionts in the familyIflaviridaeare widespread among aphids, an important model for research on bacterial symbiosis. We discovered multiple new species of iflaviruses that are maintained in asexual lines without apparent fitness costs and are transmitted vertically from mothers to offspring. Using field data and phylogenetic evidence, we further show that aphid iflaviruses likely move horizontally across species, but through laboratory experiments, we demonstrated that horizontal transfer among species infesting the same host plants does not persist throughout clonal lineages. Using quantitative PCR and immunohistochemistry, we discovered that viral infections localize in the host fat bodies and developing embryos. Surprisingly, we also found viral infections inside bacteria-housing cells called bacteriocytes, with a positive correlation between viral and bacterial symbiont density, indicating a mechanism for vertical transmission. Together, our work suggests that iflaviruses are an important but previously unrecognized piece of aphid symbiosis and sets the stage to use this model to answer new questions about host-microbe associations. I<sc>mportance</sc>In recent years, the rise of metatranscriptome sequencing has led to the rapid discovery of novel viral sequences in insects. However, few studies have carefully investigated the dynamics of insect-virus interactions to produce a general understanding of viral symbiosis. Aphids are a significant agricultural pest but also an important model for understanding the evolution of host-microbe interactions and the molecular basis of bacterial symbiosis. We show that heritable iflaviruses are an important but previously unrecognized part of the aphid heritable microbiome, with viral symbionts transmitted alongside bacteria from mothers to offspring, potentially via specialized bacteriocytes that house symbiotic microbes. Our findings have important implications for furthering the understanding of insect-microbe symbiosis and the potential for biocontrol of agriculturally relevant pest species. 

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3. Untangling an insect’s virome from its endogenous viral elements

   https://doi.org/10.1186/s12864-023-09737-z  

   Rozo-Lopez, Paula; Brewer, William; Käfer, Simon; Martin, McKayla M.; Parker, Benjamin J. (October 2023, BMC Genomics)

   Abstract BackgroundInsects are an important reservoir of viral biodiversity, but the vast majority of viruses associated with insects have not been discovered. Recent studies have employed high-throughput RNA sequencing, which has led to rapid advances in our understanding of insect viral diversity. However, insect genomes frequently contain transcribed endogenous viral elements (EVEs) with significant homology to exogenous viruses, complicating the use of RNAseq for viral discovery. MethodsIn this study, we used a multi-pronged sequencing approach to study the virome of an important agricultural pest and prolific vector of plant pathogens, the potato aphidMacrosiphum euphorbiae. We first used rRNA-depleted RNAseq to characterize the microbes found in individual insects. We then used PCR screening to measure the frequency of two heritable viruses in a local aphid population. Lastly, we generated a quality draft genome assembly forM. euphorbiaeusing Illumina-corrected Nanopore sequencing to identify transcriptionally active EVEs in the host genome. ResultsWe found reads from two insect-specific viruses (aFlavivirusand anAmbidensovirus) in our RNAseq data, as well as a parasitoid virus (Bracovirus), a plant pathogenic virus (Tombusvirus), and two phages (Acinetobacter and APSE). However, our genome assembly showed that part of the ‘virome’ of this insect can be attributed to EVEs in the host genome. ConclusionOur work shows that EVEs have led to the misidentification of aphid viruses from RNAseq data, and we argue that this is a widespread challenge for the study of viral diversity in insects. 

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4. Heritable viral symbionts in the family Iflaviridae are widespread among aphids

   https://doi.org/10.1128/aem.01606-25  

   Rozo-Lopez, Paula; Torres, Vanesa; Torres, Joseph; Drolet, Barbara S; Käfer, Simon; Parker, Benjamin J (November 2025, Applied and Environmental Microbiology)

   Rudi, Knut (Ed.)

   ABSTRACT Heritable microbes shape host phenotypes and serve as important drivers of evolution. While interactions between insects and bacterial symbionts have been extensively studied, the prevalence and evolution of insect-viral symbioses remain poorly understood. We discovered multiple new species of iflaviruses in aphids, an important model for research on symbiosis, and found these microbes to be widespread across aphid species. We show that iflaviruses are persistently maintained in asexual host lines without apparent fitness costs while being transmitted vertically from mothers to offspring. Using field data and phylogenetic evidence, we found that aphid iflaviruses move horizontally among host species, but laboratory experiments showed that horizontal transmission does not result in persistent infections. Using quantitative PCR and immunohistochemistry, we discovered that viral infections localize in the host fat bodies and developing embryos. Surprisingly, we also found viral infections inside bacteria-housing cells called bacteriocytes, along with a positive correlation between viral and bacterial symbiont density. Together, our work suggests that iflaviruses are widespread heritable symbionts in aphids. IMPORTANCEIn recent years, the rise of metatranscriptome sequencing has led to the rapid discovery of novel viral sequences in insects. However, few studies have carefully investigated the dynamics of insect-virus interactions to produce a general understanding of viral symbiosis. Aphids are an important model for understanding the evolution and molecular basis of symbiosis, but whether viruses are forming persistent symbiotic relationships with aphids remains unclear. Here, we show that heritable iflaviruses are a widespread but previously unrecognized part of the aphid heritable microbiome. Aphid iflaviruses are transmitted alongside bacteria from mothers to offspring, potentially via specialized bacteriocytes that house symbiotic microbes. Our findings suggest that aphids establish persistent relationships with iflaviruses and are likely coevolving with these viral symbionts. 

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5. Whole-genome sequence of the Cooley spruce gall adelgid, Adelges cooleyi (Hemiptera: Sternorrhyncha: Adelgidae)

   https://doi.org/10.1093/g3journal/jkad224  

   Dial, Dustin T; Weglarz, Kathryn M; Brunet, Bryan_M T; Havill, Nathan P; von_Dohlen, Carol D; Burke, Gaelen R (September 2023, G3: Genes, Genomes, Genetics)

   McIntyre, L (Ed.)

   Abstract The adelgids (Adelgidae) are a small family of sap-feeding insects, which, together with true aphids (Aphididae) and phylloxerans (Phylloxeridae), make up the infraorder Aphidomorpha. Some adelgid species are highly destructive to forest ecosystems such as Adelges tsugae, Adelges piceae, Adelges laricis, Pineus pini, and Pineus boerneri. Despite this, there are no high-quality genomic resources for adelgids, hindering advanced genomic analyses within Adelgidae and among Aphidomorpha. Here, we used PacBio continuous long-read and Illumina RNA-sequencing to construct a high-quality draft genome assembly for the Cooley spruce gall adelgid, Adelges cooleyi (Gillette), a gall-forming species endemic to North America. The assembled genome is 270.2 Mb in total size and has scaffold and contig N50 statistics of 14.87 and 7.18 Mb, respectively. There are 24,967 predicted coding sequences, and the assembly completeness is estimated at 98.1 and 99.6% with core BUSCO gene sets of Arthropoda and Hemiptera, respectively. Phylogenomic analysis using the A. cooleyi genome, 3 publicly available adelgid transcriptomes, 4 phylloxera transcriptomes, the Daktulosphaira vitifoliae (grape phylloxera) genome, 4 aphid genomes, and 2 outgroup coccoid genomes fully resolves adelgids and phylloxerans as sister taxa. The mitochondrial genome is 24 kb, among the largest in insects sampled to date, with 39.4% composed of noncoding regions. This genome assembly is currently the only genome-scale, annotated assembly for adelgids and will be a valuable resource for understanding the ecology and evolution of Aphidomorpha. 

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