Biology subjects

Davison, H. R.

Publications and source records attributed to Davison, H. R..

5 recordsLinked to original sources

bioRxiv2025

The promise of AlphaFold for gene structure annotation

BackgroundAs sequencing technology improves, more genomes become available. Most lack annotation, automated methods are error prone, and few genomes are ever manually curated due to time and cost. Protein structure prediction software may provide new angles for assessing and improving gene models without requiring experimental data. In this paper, we explore whether scores from protein structure prediction can aid in scoring gene model quality. We chose three species (Fusarium graminearum, Toxoplasma gondii, and Aspergillus fumigatus) from the VEuPathDB database which have collectively undergone more than 1000 manual curation events. We modelled translations of the gene models with AlphaFold 3, before and after curation, collecting various scores. Then we carried out structure searching of the PDB with Foldseek and sequence-based domain identification using InterProScan. We profiled the scores produced by these methods to identify those best for gene model assessment. ResultsAlphaFold 3 scores strongly favoured manually improved over pre-improvement models, supporting 75% of manually-curated changes in F. graminearum, 65% in T. gondii, and 84% in A. fumigatus (the lower percentage in T. gondii attributed to a high level of disorder). Further, combining scores across multiple tools (AlphaFold 3, Foldseek and InterProScan) provided additional improvements in model scoring. ConclusionOverall, the most discriminative scores combined outputs of AlphaFold 3 and Foldseek. Our results therefore highlight the potential of scores derived from deep learning-based protein structure prediction for scoring gene models in the absence of experimental data. Future work should focus on intrinsically disordered regions and developing integrated tools to apply this approach.

bioinformatics↗

bioRxiv2023

Hidden from plain sight: Novel Chlamydiota diversity emerging from screening genomic and metagenomic data.

Chlamydiota are an ancient and hyperdiverse Phylum of obligate intracellular bacteria. The best characterized representatives are pathogens or parasites of mammals, but it is thought that their most common hosts are microeukaryotes like Amoebozoa. The diversity in taxonomy, evolution, and function of non-pathogenic Chlamydiota are slowly being described. Here we use data mining techniques and genomic analysis to extend our current knowledge of Chlamydiota diversity and its hosts, in particular the Order Parachlamydiales. We extract one Rhabdochlamydiaceae and three Simkaniaceae genomes from NCBI Short Read Archive deposits of ciliate and algal genome sequencing projects. We then use these to identify a further 14 and 8 genomes respectively amongst existing, unidentified environmental assemblies. From these data we identify two novel clades with host associated data, for which we propose the names Candidatus Sacchlamydia (Family Rhabdochlamydiaceae) and Candidatus Amphrikania (Family Simkaniaceae), as well as a third new clade of environmental MAGs Candidatus Acheromydia (Family Rhabdochlamydiaceae). The extent of uncharacterized diversity within the Rhabdochlamydiaceae and Simkaniaceae is indicated by 16 of the 22 MAGs being evolutionarily distant from currently characterised genera. Within our limited data, we observe great predicted diversity in Parachlamydiales metabolism and evolution, including the potential for metabolic and defensive symbioses as well as pathogenicity. These data provide an imperative to link genomic diversity in metagenomics data to their associated eukaryotic host, and to develop onward understanding of the functional significance of symbiosis with this hyperdiverse clade. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=161 HEIGHT=200 SRC="FIGDIR/small/533158v2_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@fd4282org.highwire.dtl.DTLVardef@1199065org.highwire.dtl.DTLVardef@156f740org.highwire.dtl.DTLVardef@829eed_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

bioRxiv2023

'Candidatus Tisiphia' is a widespread Rickettsiaceae symbiont in the mosquito Anopheles plumbeus (Diptera: Culicidae)

Symbiotic bacteria alter host biology in numerous ways, including the ability to reproduce or vector disease. Deployment of symbiont control of vector borne disease has focused on Wolbachia interactions with Aedes and is hampered in Anopheles by a lack of compatible symbioses. Previous screening found the symbiont Ca. Tisiphia in Anopheles plumbeus, an aggressive biter and potential secondary vector of malaria parasites and West Nile virus. We screen An. plumbeus samples collected over a ten-year period across Germany and use climate databases to assess environmental influence on incidence. We find a 95% infection rate that does not fluctuate with broad environmental factors. Microscopy suggests the infection is maternally inherited based on strong localisation throughout the ovaries. Finally, we assemble a high-quality draft genome of Ca. Tisiphia to explore its phylogeny and potential metabolism. This strain is closely related to those found in Culicoides midges and shows similar patterns of metabolic potential. An. plumbeus provides a viable avenue of symbiosis research in anopheline mosquitoes, which to date have one other proven infection of a heritable symbiont. Additionally, it provides future opportunity to study the impacts of Ca. Tisiphia on natural and transinfected hosts, especially in relation to reproductive fitness and vector efficiency.

evolutionary biology↗

bioRxiv2022

Candidatus Megaira are diverse symbionts of algae and ciliates with the potential for defensive symbiosis

Symbiotic microbes from the genus Candidatus Megaira (Rickettsiales) are known to be common associates of algae and ciliates. However genomic resources for these bacteria are scarce, limiting our understanding of their diversity and biology. We therefore utilized SRA and metagenomic assemblies to explore the diversity of this genus. We successfully extracted four draft Ca. Megaira genomes including one complete scaffold for a Ca. Megaira and identified an additional 14 draft genomes from uncategorised environmental Metagenome-Assembled Genomes. We use this information to resolve the phylogeny for the hyper-diverse Ca. Megaira, with hosts broadly spanning ciliates, micro- and macro-algae, and find that the current single genus designation Ca. Megaira significantly underestimates their diversity. We also evaluate the metabolic potential and diversity of Ca. Megaira from this new genomic data and find no clear evidence of nutritional symbiosis. In contrast, we hypothesize a potential for defensive symbiosis in Ca. Megaira. Intriguingly, one symbiont genome revealed a proliferation of ORFs with ankyrin, tetratricopeptide and Leucine rich repeats like those observed in the genus Wolbachia where they are considered important for host-symbiont protein-protein interactions. Onward research should investigate the phenotypic interactions between Ca. Megaira and their various potential hosts, including the economically important Nemacystus decipiens, and target acquisition of genomic information to reflect the diversity of this massively variable group. Data SummaryGenomes assembled in this project have been deposited in bioproject PRJNA867165 Impact statementBacteria that live inside larger organisms commonly form symbiotic relationships that impact the hosts biology in fundamental ways, such as improving defences against natural enemies or altering host reproduction. Certain groups like ciliates and algae are known to host symbiotic bacteria commonly, but our knowledge of their symbionts evolution and function is limited. One such bacteria is Candidatus Megaira, a Rickettsiales that was first identified in ciliates, then later in algae. To improve the available data for this common but understudied group, we searched the genomes of potential hosts on online databases for Rickettsiales and assembled their genomes. We found 4 Ca. Megaira this way and then used these to find a further 14 genomes in environmental metagenomic data. Overall, we increased the number of known Ca. Megaira draft genomes from 2 to 20. These new genomes show us that Ca. Megaira is far more diverse than previously thought and that it is potentially involved in defensive symbioses. In addition, one genome shows striking resemblance to well characterized symbiont, Wolbachia, in encoding many proteins predicted to interact directly with host proteins. The genomes we have identified and examined here provide baseline resources for future work investigating the real-world interactions between the hyper diverse Ca. Megaira and its various potential hosts, like the economically important Nemacystus decipiens.

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↗