Biology subjects

Darby, A. C.

Publications and source records attributed to Darby, A. C..

At least 19 recordsLinked to original sources

bioRxiv2026

A near-complete chromosome from a bacterial pathogen integrated into the genome of its arthropod vector

Lateral gene transfer (LGT) from organellar to eukaryotic genomes is ubiquitous, resulting in the presence of widespread nuclear mitochondrial DNA segments (NUMTs) and/or plastid gene transfers. While LGT from bacterial associates of eukaryotes is generally less common, many arthropod genomes are littered with LGT originating from Wolbachia (order Rickettsiales) - a vertically transmitted, obligate intracellular symbiont of invertebrates. This contrasts with Rickettsia, a related genus including many important human pathogens, which has not been shown to promulgate LGT within its arthropod vectors. Here, we present the 8.6 Gb genome of a cell line derived from A. variegatum (the tropical bont tick), which is the primary vector of Rickettsia africae (agent of African tick-bite fever). In addition to numerous NUMTs and diverse families of transposable elements, an almost-complete chromosome of R. africae origin was identified in the cell line genome, localised to the putative sex chromosome. Sequencing of field-collected A. variegatum confirmed the presence of this large LGT in wild ticks, although the absence of transferred genes from the R. africae plasmid provided a means to differentiate LGT from genuine rickettsial infections. These findings highlight the imperative to consider the possibility of LGT when screening vectors for pathogens by PCR.

genomics↗

bioRxiv2026

Chromosome assembly for the Black bean aphid Aphis fabae

The black bean aphid, Aphis fabae is a crop pest and vector of insect-transmitted pathogens, comprising closely related sub-species with overlapping host ranges. In other Aphis species, over-expression of specific detoxification genes has been linked to insecticide tolerance. We present two chromosome-scale assemblies for a clonal A. fabae line, representing two phased haplotypes, generated using HiFi and Hi-C sequencing technologies. A comprehensive genome annotation, built with PacBio Iso-Seq data, was used to investigate genes underlying insecticide tolerance. Both genomes are comprised of four chromosomal blocks (haplotype 1: 427 Mb; haplotype 2: 396 Mb) with high BUSCO completeness (98.7%). Comparative genomics revealed an expansion of UDP-glycosyltransferases, whose expression is linked to insecticide detoxification in other Aphis species. These high-quality references provide a foundation for studying A. fabae sub-species and a genomic resource for investigating insecticide tolerance across the Aphis genus. Author summaryHere we have provided a comprehensive assembly and annotation for further study into the Black bean aphid, Aphis fabae, using up to date long-range sequencing technologies. The final assemblies for both haplotypes are chromosome length and consist of 4 main chromosome blocks, consistent with the literature. The A. fabae genome was found to contain an increase in copy number of UDP-glycosyltransferases, which have previously been linked to insecticide resistance. The work here will be a resource to those studying insecticide tolerance in crop pests, as well as the differences between A. fabae sub-species.

genomics↗

bioRxiv2025

Mosquito Viromes in England and Wales Reveal Hidden Arbovirus Signals and Limited Ecological Structuring

Outbreaks of mosquito-borne viruses are increasing in temperate regions, with West Nile and Usutu viruses now established in wide regions across Europe, and both detected in the UK. Current surveillance strategies focus on targeted approaches which are well suited for monitoring established threats but limited in their ability to detect recently described or neglected viruses. High throughput sequencing (HTS) provides an unbiased alternative, allowing simultaneous identification of well-recognised and overlooked arboviruses, alongside insect-specific viruses (ISVs) that may modulate vector competence of the insects transmitting these pathogens. This study presents the first comprehensive virome survey of Culex mosquitoes in the UK, analysing populations collected from 93 sites across England and Wales through HTS and a systematic virus discovery pipeline. Across these sites, 41 distinct viral taxa were identified, including 11 novel species. Most viruses were rare or confined to a few sites, with only three detected in more than one third of sites, suggesting the absence of a broad conserved virome across populations. Within this diversity, three arbovirus-related lineages were detected: Hedwig virus (Peribunyaviridae), Umatilla virus (Sedoreoviridae), and Atherstone virus (Peribunyaviridae), the former two representing the first detections in the UK. These putative arboviruses were embedded in viral communities that showed minimal structuring by coarse land type but a modest decline in richness with latitude across rural sites, consistent with diversity gradients observed in other microbial systems. Together, these findings provide the first national-scale baseline of Culex mosquito-associated viral diversity in the UK, and demonstrate the value of metagenomic approaches in arbovirus preparedness.

microbiology↗

bioRxiv2025

Hybrid short- and long-read assembly of an experimentally evolved Sodalis glossinidius strain SgGmmC1*

Bacterial symbionts of insects undergo dramatic genome reduction during their evolutionary transition from free-living to host-dependent lifestyles, but the dynamics of this process remain poorly understood due to the difficulty of observing these processes in real-time. Sodalis glossinidius, a facultative endosymbiont of tsetse flies, provides an exceptional opportunity to study this transition experimentally: Unlike highly specialised obligate symbionts, S. glossinidius can be cultured in vitro and retains a large genome (4 Mbp) with extensive pseudogene content (49%), suggesting a recent evolutionary transition. Here, we present a comparative genomic analysis of S. glossinidius strains isolated from laboratory colony-derived Glossina morsitans morsitans, comparing one after ten years of serial passaging in laboratory culture (SgGmmC1*) to a counterpart isolated at the same time (SgGmmB4). Hybrid genome assembly using Oxford Nanopore and Illumina technologies produced a high-quality 4.29 Mbp genome comprising one circular chromosome and four plasmids similar. Comparative analysis revealed a significant deletion (17,209 bp) containing 31 genes, including (involved in thiamine biosynthesis) and genes encoding sulfur transporters. Additionally, we identified multiple small-scale mutations (8 deletions, 39 insertions, 10 SNPs) resulting in frameshifts in genes including a hemolysin precursor (shlA). Our findings demonstrate that, under stable laboratory conditions without the selective pressures of the host environment, S. glossinidius continues to undergo genome degradation. The loss of thiM supports previous hypotheses of complementary metabolic pathways between S. glossinidius and the primary symbiont Wigglesworthia glossinidia for thiamine biosynthesis. This study provides insights into the evolutionary trajectory of facultative symbionts and has implications for paratransgenic approaches using S. glossinidius for trypanosome control. DATA SUMMARYRaw Nanopore and MiSeq reads are available in the European Nucleotide Archive under Project PRJEB32321 (Read accessions: ERX3321202 and ERX3321201 respectively). A full GBK formatted annotation of SgGmmC1* has been deposited in Figshare at https://doi.org/10.17866/rd.salford.8052437.v1. IMPACT STATEMENTIn this study we provide new insights into the ongoing genome degradation of Sodalis glossinidius, a facultative endosymbiont of tsetse flies implicated in their ability to transmit trypanosomiasis, during prolonged laboratory culture. Through high-quality comparative genomics we reveal significant gene loss and mutational changes, including disruption of pathways involved in nutrient biosynthesis. These findings enhance our understanding of symbiont genome evolution and inform the development of S. glossinidius as a potential tool for paratransgenic strategies in controlling trypanosome transmission.

genomics↗

bioRxiv2025

Emergence Risks from Within? Metagenomic Analysis of Mosquito Viromes from Two Zoos Reveals Mosquito-associated Orthobunyaviruses in the UK

In regions naive to mosquito-borne threats, risk assessments often prioritise incursion events, particularly those driven by climate change and host movement. However, these same factors may also facilitate the emergence of viruses already circulating in local vector populations. The use of metagenomics to assess mosquito viromes has expanded in recent decades, enabling the detection of both arboviruses and insect-specific viruses (ISVs), and helping to fill gaps in our understanding of virus circulation. In particular, zoological collections are potential interfaces for virus transmission between mosquitoes, animals, and humans, making them valuable sentinel sites for surveillance. Although mosquito virome studies have been conducted globally, UK mosquito populations remain comparatively understudied. To address this gap, we investigated the viromes of two key mosquito species, Culex pipiens s.l. and Culiseta annulata, through metagenomic sequencing of specimens collected at two UK zoos between 2021 and 2022. A total of 4,042 mosquitoes underwent sequencing across 44 pools, leading to the identification of 26 viral genomes, including nine novel species spanning RNA and DNA virus families. Viral distribution patterns revealed viruses shared across all pools, supporting the possibility of a conserved virome between mosquito species. Notably, two novel Orthobunyavirus species (Family Peribunyaviridae), Atherstone and Deva viruses, were detected. These represent the first documented mosquito-associated orthobunyaviruses in the UK, a genus that includes several known pathogens. Classification using the machine-learning tool MosViR suggests Atherstone virus, present at both zoos, is a putative arbovirus warranting further investigation. Supporting this is the presence of a non-structural protein S (NSs), a known virulence factor in orthobunyaviruses. In contrast, Deva virus had no NSs ORF and was not predicted to be an arbovirus. These findings improve our understanding of UK mosquito viruses, indicate possible risks to people or animals from orthobunyaviruses, and highlight the role of metagenomic surveillance in detecting emerging viral threats.

genomics↗

bioRxiv2024

Cappable-Seq reveals the transcriptional landscape of stress responses in the bacterial endosymbiont Wolbachia

Bacterial endosymbionts are highly prevalent among invertebrate animals, in which they can confer fitness benefits such as pathogen defence and/or act as reproductive manipulators, inducing phenotypes including cytoplasmic incompatibility (CI). For the alpha-proteobacterium Wolbachia, its wide distribution among macroparasites and disease-transmitting arthropods coupled with mutualistic roles, reduction of vector competence, and CI have found recent applications in the control of several vector-borne tropical diseases. However, in common with other bacterial endosymbionts, which often lose regulatory elements during genomic erosion, the degree to which Wolbachia can respond to environmental or pharmacological stressors is poorly understood. Here, we apply Cappable-Seq methodology to achieve unprecedented depth and resolution of transcriptional start sites (TSS) in two Wolbachia strains (wMelPop-CLA and wAlbB) that have been used to transinfect mosquitoes for arbovirus control. We exposed Wolbachia in mosquito cell lines to temperature stress (both strains) or antibiotics (wAlbB only) and observed that all classes of TSS (including antisense) exhibited differential regulation, some of which were associated with mobile elements and may control ncRNA expression. Cappable-Seq also resolved the organisation of the bicistronic cifA/cifB operon that is responsible for inducing CI in Wolbachia hosts and shows great promise for revealing regulation of symbiont functions in whole invertebrates.

microbiology↗

bioRxiv2023

Genomic insights into clonal diversity in UK populations of the Potato aphid, Macrosiphum euphorbiae

The potato aphid Macrosiphum euphorbiae is one of many polyphagous crop pests involved in the transmission of insect-vectored pathogens. While their North American counterparts reproduce via cyclical parthenogenesis, UK populations of M. euphorbiae appear to persist asexually, resulting in the maintenance of several genotypes, with some demonstrating genotype-specific traits; this includes innate resistance to parasitism from the hymenopterous parasitoid wasp Aphidius ervi. The genetic and molecular basis for genotype-specific traits is often unknown. Here we present a chromosome scale assembly for a parasitoid-resistant clonal line of M. euphorbiae and provide insights into the genotypic composition and distribution of UK potato aphid populations using microsatellite and whole-genome sequencing (WGS) techniques, focusing on geographically separated potato crops within two distinct areas of the UK (Merseyside and Tayside). We show that the genome consists of five chromosomal blocks, has a total size of 560 Mbp and is highly complete based on BUSCO (C: 95.6%). The sampled potato aphid populations were dominated by two genotypes, one of which is absent from commercial farm settings, suggesting either an intolerance to farming practices, such as insecticide use, or a broader host range. We suggest some putative gene functions using WGS data to explain the observed frequency of aphid genotypes. WGS data highlighted the asexual clonal lifestyle of M. euphorbiae genotypes in the UK, resolving individuals to a higher resolution than using microsatellite data. The work presented here will provide useful information for integrated pest management of potato aphids, elaborating on the relationship between genotype diversity and functional traits such as parasitism and insecticide resistance, and host plant use, as well as providing more resources for further comparative genomics studies within the Aphididae.

genomics↗

bioRxiv2023

Genome dynamics across the evolutionary transition to endosymbiosis

Endosymbiosis - where a microbe lives and replicates within a host - is an important contributor to organismal function that has accelerated evolutionary innovations and catalysed the evolution of complex life. The evolutionary processes associated with transitions to endosymbiosis, however, are poorly understood. Here, we use comparative genomics of the genus Arsenophonus to reveal the complex processes that occur on evolution of an endosymbiotic lifestyle. We compared the genomes of 38 strains spanning diverse lifestyles from environmentally acquired infections to obligate inter-dependent endosymbionts. We observed recent endosymbionts had larger genome sizes than closely related environmentally acquired strains, consistent with evolutionary innovation and rapid gain of new function. Increased genome size was a consequence of prophage and plasmid acquisition including a cargo of type III effectors, and concomitant loss of CRISPR-Cas genome defence systems enabling mobile genetic element expansion. Persistent endosymbiosis was also associated with loss of type VI secretion, likely reflecting reduced microbe-microbe competition. Thereafter, the transition to stable endosymbiosis and vertical inheritance was associated with the expected relaxation of purifying selection, pseudogenisation of genes and reduction of metabolism, leading to genome reduction. However, reduced %GC that is typically considered a progressive linear process was observed only in obligate interdependent endosymbionts. We argue that a combination of the need for rapid horizontal gene transfer-mediated evolutionary innovation together with reduced phage predation in endosymbiotic niches drives loss of genome defence systems and rapid genome expansion upon adoption of endosymbiosis. These remodelling processes precede the reductive evolution traditionally associated with adaptation to endosymbiosis.

genomics↗

bioRxiv2023

Metagenomics of culture isolates and insect tissue illuminate the evolution of Wolbachia, Rickettsia and Bartonella symbionts in Ctenocephalides spp. fleas

While fleas are often perceived simply as a biting nuisance and cause of allergic dermatitis, they represent important disease vectors worldwide, especially for bacterial zoonoses such as plague (transmitted by rodent fleas) and some of the rickettsioses and bartonelloses. The cosmopolitan cat (Ctenocephalides felis) and dog (C. canis) fleas, as well as C. orientis (restricted to tropical and subtropical Asia), breed in human dwellings and are vectors of cat-scratch fever (caused by Bartonella spp.) and Rickettsia spp. of the so-called "transitional group". The latter includes R. felis (agent of flea-borne spotted fever) and R. asembonensis, an emerging pathogen. The relatively depauperate flea microbiome can also contain arthropod-specific endosymbionts, including a diverse range of Wolbachia strains. Here, we present circularized genome assemblies for two C. orientis-associated pathogens (Bartonella clarridgeiae and R. asembonensis) from Malaysia, a novel Wolbachia strain (wCori), and the C. orientis mitochondrion; all obtained by direct metagenomic sequencing of flea tissues. Moreover, we isolated two Wolbachia strains from Malaysian C. felis into tick cell culture and recovered circularized genome assemblies for both, one of which (wCfeF) is newly sequenced. We demonstrate that the three Wolbachia strains are representatives of different major clades ("supergroups"), two of which appear to be flea-specific. These Wolbachia genomes exhibit unique combinations of features associated with reproductive parasitism or mutualism, including prophage WO, cytoplasmic incompatibility factors, and the biotin operon of obligate intracellular microbes. The first circularized assembly for R. asembonensis includes a plasmid with a markedly different structure and gene content compared to the published plasmid; moreover, this novel plasmid was also detected in cat flea metagenomes from the US. Analysis of loci under positive selection in the transitional group revealed genes involved in host-pathogen interactions that may facilitate host switching. Finally, the first B. clarridgeiae genome from Asia exhibited largescale genome stability compared to isolates from other continents, except for SNPs in regions predicted to mediate interactions with the vertebrate host. These findings highlight the paucity of data on the genomic diversity of Ctenocephalides-associated bacteria and raise questions regarding how interactions between members of the flea microbiome might influence vector competence. Impact statementWhile fleas are vectors for several globally-distributed bacterial zoonoses, including plague, murine typhus, cat-scratch fever, and flea-borne spotted fever, data on the genomic diversity of the etiological agents of these diseases and other members of the flea microbiome are scant. Here, we focused on Ctenocephalides spp. fleas associated with dogs and cats in Malaysia, a region where flea microbiome data are particularly sparse. Using a combination of direct metagenomic sequencing of flea tissues coupled with culture isolation and sequencing of infected cell lines, we obtained the first genomes for a cat-scratch agent (Bartonella clarridgeiae) and an emerging human pathogen (Rickettsia asembonensis) from Asia, as well as genomes for three different Wolbachia endosymbiont strains and the first mitochondrial genome for Ctenocephalides orientis. The pathogen genomes reveal evidence of selection in genes involved in host-pathogen interactions and in the case of R. asembonensis, a novel plasmid genome was obtained. Two of the Wolbachia genomes are entirely novel and exhibit highly unusual combinations of features associated with potential reproductive manipulations and mutualistic roles. Our findings highlight major gaps in our understanding of flea microbiome diversity worldwide, with implications for the emergence of bacterial pathogens transmitted by these ubiquitous ectoparasites associated with human dwellings. Data summarySequencing reads and genome assemblies produced in study have been deposited in NCBI Genbank under BioProject accession PRJNA909216. Accession numbers for symbiont genomes: wCfeF (CP116767), wCfeJ (CP116768), wCori (CP116769), Rickettsia asembonensis str. Perak (CP116496), pRAS02 (CP116495) and Bartonella clarridgeiae str. Perak (CP116497). Ctenocephalides orientis mitochondrial assembly was deposited with the accession number OQ383237. The authors confirm all supporting data, code and protocols have been provided within 86 the article or through supplementary data files.

genomics↗

bioRxiv2022

Emerging variants of canine enteric coronavirus associated with seasonal outbreaks of severe canine gastroenteric disease

Canine enteric coronavirus (CECoV) variants have an emerging role in severe outbreaks of canine gastroenteritis. Here we used syndromic health data from a sentinel network of UK veterinary practices to identify an outbreak of severe canine gastroenteritis. Affected dogs frequently presented with vomiting, diarrhoea and inappetence. Data from sentinel diagnostic laboratories showed similar seasonal increases in CECoV diagnosis. Membrane glycoprotein (M) gene sequence analysis implied wide geographical circulation of a new CECoV variant. Whole genome sequencing suggested the main circulating 2022 variant was most closely related to one previously identified in 2020 with additional spike gene recombination; all variants were unrelated to CECoV-like viruses recently associated with human respiratory disease. Identifying factors that drive population-level evolution, and its implications for host protection and virulence, will be important to understand the emerging role of CECoV variants in canine and human health, and may act as a model for coronavirus population adaptation more widely.

genomics↗

bioRxiv2022

Timing and Delivery route effects of Cecal Microbiome transplants on Salmonella Typhimurium infections in Chickens

BackgroundExposure to microbes early in life has long-lasting effects on microbial community structure and function of the microbiome. However, in commercial poultry settings chicks are reared as a single-age cohort with no exposure to adult birds which can have profound effects on microbiota development and subsequent pathogen challenge. Microbiota manipulation is a proven and promising strategy to help reduce pathogen load and transmission within broiler flocks. ResultsManipulation of the microbiota between 4 and 72 hours of hatch markedly reduces faecal shedding and colonisation with the foodborne pathogen Salmonella enterica serovar Typhimurium (ST4/74). Administration route has minimal effect on the protection conferred with fewer birds in transplant groups shown to shed ST4/74 in the faeces compared to PBS-gavaged control birds. Analysis of the microbiome following transplantation demonstrated that the relative abundance of the anti-inflammatory bacterium Faecalibacterium prausnitzii was significantly higher in CMT groups compared to PBS controls. The presence of F. prausnitzii was also shown to increase in PBS-challenged birds compared to unchallenged birds potentially indicating a role of this bacterium in limiting Salmonella infections. ConclusionsThis study highlights the efficacy of using microbiome transplants as a means to reduce colonisation and shedding of Salmonella in chickens. Effective protection can be conferred during the first few days of a chicks life regardless of time point and traditional hatchery delivery systems are sufficient to alter the microbiome and transfer donor material. Early microbiota intervention in chickens is a promising route of pathogen control in broiler flocks in the fight to control food-borne outbreaks in the human population.

microbiology↗

bioRxiv2021

Large-scale comparative genomics unravels great genomic diversity across the Rickettsia and Ca. Megaira genera and identifies Torix group as an evolutionarily distinct clade.

Rickettsia are intracellular bacteria originally described as arthropod borne pathogens that are emerging as a diverse group of often biologically important, non-pathogenic symbionts of invertebrates and microeukaryotes. However, sparse genomic resources for symbiotic strains and for the sister genus (Candidatus Megaira) inhibit our understanding of Rickettsia evolution and biology. Here, we present the first closed genomes of Ca. Megaira from an alga (Mesostigma viride), and Torix Rickettsia from midge (Culicoides impunctatus) and bed bug (Cimex lectularius) hosts. Additionally, we sequenced and constructed draft genomes for Ca. Megaira from another alga (Carteria cerasiformis), Transitional group Rickettsia from tsetse fly (Glossina morsitans submorsitans), and Torix Rickettsia from a spider mite (Bryobia graminum). We further extract 22 draft genomes from arthropod genome sequencing projects, including 1 Adalia, 4 Transitional, 1 Spotted Fever, 7 Torix, 7 Belli and the first Rhyzobius and Meloidae Rickettsia group genomes. We used new and existing Rickettsia genomes to estimate the phylogeny and metabolic potential across groups and reveal transitions in genomic properties. These data reveal Torix as unique amongst currently described Rickettsia, with highly distinct and diverse accessory genomes. We confirm the presence of a third subclade of Torix, previously only known from gene marker sequences. Further, Torix share an intact pentose phosphate pathway with Ca. Megaira, not observed in other Rickettsia. Considering the distinctness and diversity of Torix, we propose that the group be named Candidatus Tisiphia. The wide host range of Ca. Tisiphia symbionts necessitates onward research to understand the biological and physiological bases of Ca. Tisiphia-host interactions. Importance statementMembers of the genus Rickettsia were originally identified as causative agents of mammalian vector-borne disease. In the last 25 years we have recognised that many Rickettsia are arthropod symbionts, and sit alongside a sister taxon, Ca. Megaira, which are symbiotic associates of microeukaryotes. The lack of genomic information for symbiotic strains affects our ability to determine the evolutionary relationships between strains and understand the biological underpinnings of the different symbioses. We clarify these relationships by assembling 26 genomes of Rickettsia from understudied groups, and the first two Ca. Megaira, from various insects and microeukaryotes. Of note, the accessory genome diversity and broad host range of Torix Rickettsia parallels all other Rickettsia combined. This diversity, alongside the breadth of host species, make the Torix clade an important hidden player in invertebrate biology and physiology. We argue this clade should be given its own genus status, for which we propose Ca. Tisiphia.

microbiology↗

bioRxiv2021

A gene expression panel for estimating age in males and females of the sleeping sickness vector Glossina morsitans

Many vector-borne diseases are controlled by methods that kill the insect vectors responsible for disease transmission. Recording the age structure of vector populations provides information on mortality rates and vectorial capacity, and should form part of the detailed monitoring that occurs in the wake of control programmes, yet tools for obtaining estimates of individual age remain limited. We investigate the potential of using markers of gene expression to predict age in tsetse flies, which are the vectors of deadly and economically damaging African trypanosomiases. We use RNAseq to identify candidate expression markers, and test these markers using qPCR in laboratory-reared Glossina morstians morsitans of known age. Measuring the expression of six genes was sufficient to obtain a prediction of age with root mean squared error of less than 8 days, while just two genes were sufficient to classify flies into age categories of [≤] 15 and >15 days old. Further testing of these markers in field-caught samples and in other species will determine the accuracy of these markers in the field.

ecology↗

bioRxiv2020

Diminutive, degraded but dissimilar: Wolbachia genomes from filarial nematodes do not conform to a single paradigm

Wolbachia are alpha-proteobacteria symbionts infecting a large range of arthropod species and two different families of nematodes. Interestingly, these endosymbionts are able to induce diverse phenotypes in their hosts: they are reproductive parasites within many arthropods, nutritional mutualists within some insects and obligate mutualists within their filarial nematode hosts. Defining Wolbachia "species" is controversial and so they are commonly classified into 16 different phylogenetic lineages, termed supergroups, named A to S. However, available genomic data remains limited and not representative of the full Wolbachia diversity; indeed, of the 24 complete genomes and 55 draft genomes of Wolbachia available to date, 84% belong to supergroups A and B, exclusively composed of Wolbachia from arthropods. For the current study, we took advantage of a recently developed DNA enrichment method to produce four complete genomes and two draft genomes of Wolbachia from filarial nematodes. Two complete genomes, wCtub and wDcau, are the smallest Wolbachia genomes sequenced to date (863,988bp and 863,427bp, respectively), as well as the first genomes representing supergroup J. These genomes confirm the validity of this supergroup, a controversial clade due to weaknesses of the multi-locus system typing (MLST) approach. We also produced the first draft Wolbachia genome from a supergroup F filarial nematode representative (wMhie), two genomes from supergroup D (wLsig and wLbra) and the complete genome of wDimm from supergroup C. Our new data confirm the paradigm of smaller Wolbachia genomes from filarial nematodes containing low levels of transposable elements and the absence of intact bacteriophage sequences, unlike many Wolbachia from arthropods, where both are more abundant. However, we observe differences among the Wolbachia genomes from filarial nematodes: no global co-evolutionary pattern, strong synteny between supergroup C and supergroup J Wolbachia, and more transposable elements observed in supergroup D Wolbachia compared to the other supergroups. Metabolic pathway analysis indicates several highly conserved pathways (haem and nucleotide biosynthesis for example) as opposed to more variable pathways, such as vitamin B biosynthesis, which might be specific to certain host-symbiont associations. Overall, there appears to be no single Wolbachia- filarial nematode pattern of co-evolution or symbiotic relationship. Graphical abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY RepositoriesData generated are available in GenBank: BioProject PRJNA593581; BioSample SAMN13482485 for wLsig, Wolbachia endosymbiont of Litomosoides sigmodontis (genome: CP046577); Biosample SAMN15190311 for the nematode host Litomosoides sigmodontis (genome: JABVXW000000000); BioSample SAMN13482488 for wDimm, Wolbachia endosymbiont of Dirofilaria (D.) immitis (genome: CP046578); Biosample SAMN15190314 for the nematode host Dirofilaria (D.) immitis (genome: JABVXT000000000); BioSample SAMN13482046 for wCtub, Wolbachia endosymbiont of Cruorifilaria tuberocauda (genome: CP046579); Biosample SAMN15190313 for the nematode host Cruorifilaria tuberocauda (genome: JABVXU000000000); BioSample SAMN13482057 for wDcau, Wolbachia endosymbiont of Dipetalonema caudispina (genome: CP046580); Biosample SAMN15190312 for the nematode host Dipetalonema caudispina (genome: JABVXV000000000); BioSample SAMN13482459 for wLbra, Wolbachia endosymbiont of Litomosoides brasiliensis (genome: WQM000000000); Biosample SAMN15190311 for the nematode host Litomosoides brasiliensis (genome: JABVXW000000000); BioSample SAMN13482487 for wMhie, Wolbachia endosymbiont of Madathamugadia hiepei (genome: WQMP00000000); Biosample SAMN15190315 for the nematode host Madathamugadia hiepei (genome: JABVXS000000000). The raw data are available in GenBank as Sequence Read Archive (SRA): SRR10903008 to SRR10903010; SRR10902913 to SRR10902914; SRR10900508 to SRR10900511; SRR10898805 to SRR10898806. Data summaryThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. Eleven Supplementary tables and two supplementary files are available with the online version of this article. Impact StatementWolbachia are endosymbiotic bacteria infecting a large range of arthropod species and two different families of nematodes, characterized by causing diverse phenotypes in their hosts, ranging from reproductive parasitism to mutualism. While available Wolbachia genomic data are increasing, they are not representative of the full Wolbachia diversity; indeed, 84% of Wolbachia genomes available on the NCBI database to date belong to the two main studied clades (supergroups A and B, exclusively composed of Wolbachia from arthropods). The present study presents the assembly and analysis of four complete genomes and two draft genomes of Wolbachia from filarial nematodes. Our genomics comparisons confirm the paradigm that smaller Wolbachia genomes from filarial nematodes contain low levels of transposable elements and the absence of intact bacteriophage sequences, unlike many Wolbachia from arthropods. However, data show disparities among the Wolbachia genomes from filarial nematodes: no single pattern of co-evolution, stronger synteny between some clades (supergroups C and supergroup J) and more transposable elements in another clade (supergroup D). Metabolic pathway analysis indicates both highly conserved and more variable pathways, such as vitamin B biosynthesis, which might be specific to certain host-symbiont associations. Overall, there appears to be no single Wolbachia-filarial nematode pattern of symbiotic relationship.

genomics↗

bioRxiv2020

White pupae genes in the Tephritids Ceratitis capitata, Bactrocera dorsalis and Zeugodacus cucurbitae: a story of parallel mutations

Mass releases of sterilized male insects, in the frame of sterile insect technique programs, have helped suppress insect pest populations since the 1950s. In the major horticultural pests Bactrocera dorsalis, Ceratitis capitata, and Zeugodacus cucurbitae, a key phenotype white pupae (wp) has been used for decades to selectively remove females before releases, yet the gene responsible remained unknown. Here we use classical and modern genetic approaches to identify and functionally characterize causal wp− mutations in these distantly related fruit fly species. We find that the wp phenotype is produced by parallel mutations in a single, conserved gene. CRISPR/Cas9-mediated knockout of the wp gene leads to the rapid generation of novel white pupae strains in C. capitata and B. tryoni. The conserved phenotype and independent nature of the wp− mutations suggest that this technique can provide a generic approach to produce sexing strains in other major medical and agricultural insect pests.Competing Interest StatementThe authors have declared no competing interest.View Full Text

genetics↗

bioRxiv2019

Recovering individual haplotypes and a contiguous genome assembly from pooled long read sequencing of the diamondback moth (Lepidoptera: Plutellidae)

BackgroundRecent advances in genomics have addressed the challenge that divergent haplotypes pose to the reconstruction of haploid genomes. However for many organisms, the sequencing of either field-caught individuals or a pool of heterogeneous individuals is still the only practical option. Here we present methodological approaches to achieve three outcomes from pooled long read sequencing: the generation of a contiguous haploid reference sequence, the sequences of heterozygous haplotypes; and reconstructed genomic sequences of individuals related to the pooled material. ResultsPacBio long read sequencing, Dovetail Hi-C scaffolding and linkage map integration yielded a haploid chromosome-level assembly for the diamondback moth (Plutella xylostella), a global pest of Brassica crops, from a pool of related individuals. The final assembly consisted of 573 scaffolds, with a total assembly size of 343.6Mbp a scaffold N50 value of 11.3Mbp (limited by chromosome size) and a maximum scaffold size of 14.4Mbp. This assembly was then integrated with an existing RAD-seq linkage map, anchoring 95% of the assembled sequence to defined chromosomal positions. ConclusionsWe describe an approach to resolve divergent haplotype sequences and describe multiple validation approaches. We also reconstruct individual genomes from pooled long-reads, by applying a recently developed k-mer binning method.

genomics↗

bioRxiv2019

Functional genomics of a symbiotic community: shared traits in the olive fruit fly gut microbiota

The olive fruit fly Bactrocera oleae is a major pest of olives worldwide and houses a specialized gut microbiota dominated by the obligate symbiont \"Candidatus Erwinia dacicola\". Ca. E. dacicola is thought to supplement dietary nitrogen to the host, with only indirect evidence for this hypothesis so far. Here, we sought to investigate the contribution of the symbiosis to insect fitness and explore the ecology of the insect gut. For this purpose, we examined the composition of bacterial communities associated with Cretan olive fruit fly populations, and inspected several genome and transcriptome assemblies. We identified, and reconstructed the genome of, a novel component of the gut microbiota, Tatumella sp. TA1, which is stably associated with Mediterranean olive fruit fly populations. We also reconstructed a number of pathways related to nitrogen assimilation and interaction with the host. The results show that, despite variation in taxa composition of the gut microbial community, core functions related to the symbiosis are maintained. Functional redundancy between different microbial taxa was observed for genes allowing urea hydrolysis. The latter is encoded in the obligate symbiont genome by a conserved urease operon, likely acquired by horizontal gene transfer, based on phylogenetic evidence. A potential underlying mechanism is the action of mobile elements, especially abundant in the Ca. E. dacicola genome. This finding, along with the identification, in the studied genomes, of extracellular surface structure components that may mediate interactions within the gut community, suggest that ongoing and past genetic exchanges between microbes may have shaped the symbiosis.

evolutionary biology↗

bioRxiv2019

Honey bee trypanosomatid parasite dynamically changes the transcriptome during the infection of honey bee and modifies the host physiology

Although there are many honey bee pathogens/parasites, it is still not understood how they change their gene expression to adapt to the host environment or how the host simultaneously responds to pathogen/parasite infection by modifying its own gene expression. Such interactions must lead to changes in the physiological states of both host and parasite. To address this question, we studied a trypanosomatid, Lotmaria passim, which can be cultured in medium and inhabit the honey bee hindgut. We found that L. passim dynamically modifies the expression of mRNAs associated with protein translation and the electron transport chain to adapt to the anaerobic and nutritionally poor honey bee hindgut at early stages of infection, and to become dormant at late stages of infection. Meanwhile, several genes are continuously up- or down-regulated during infection, including GP63 as well as genes coding for host cell signaling pathway modulators (up-regulated), and those involved in detoxification of radical oxygen species as well as flagellar formation (down-regulated). L. passim infection only slightly increases honey bee mortality and does not affect the number of microorganisms in the gut microbiota; but it induces honey bee innate immune response. Upon infection, the host appears to be in poor nutritional status, indicated by the increase in the levels of mRNAs for take-out and facilitated trehalose transporter and the decrease of vitellogenin mRNA level. Simultaneous gene expression profiling of L. passim and honey bee during infection provided insight into how both parasite and host modify their gene expressions. This study presents one of the best models to understand host-parasite interactions at the molecular and cellular levels in honey bee.

microbiology↗