Biology subjects

Ronai, I.

Publications and source records attributed to Ronai, I..

12 recordsLinked to original sources

bioRxiv2026

Optimizing genome assembly, chromosome synteny, and genetic variant discovery from Oxford Nanopore sequences of Dermacentor reticulatus ticks

Generating high-quality genome assemblies for small animals with large genomes is complex due to their small body size, DNA contamination, and repetitive elements. Ticks exemplify these complexities, while also being a global health threat to humans, domestic animals, and wildlife. Advances in long-read sequencing platforms now make it feasible to obtain large amounts of raw sequence data from individual specimens, but challenges remain. Key genome workflow challenges include error correction, assembly, transposable element annotation, and chromosome assignment and synteny. Here we examine three individual Dermacentor reticulatus ticks using deep Oxford Nanopore sequencing. Comparing and contrasting bioinformatic tools for raw read and assembly manipulation allows us to identify the parameters that provide a high-quality haploid genome assembly among 38 assemblies. We find Dorado error corrected raw read data from approximately two flow cells are needed, but limiting assembly coverage to 40x produces the highest quality assemblies. Then we examined the effects of optimal workflow parameters on downstream analyses of gene synteny and manual transposable element annotation of the three tick assemblies in comparison to an independent assembly of a fourth D. reticulatus individual from a different country. Gene synteny analysis allows chromosome assignment of scaffolds and transposable element identification was improved markedly with manual curation. Finally, we compared the genetic variation of D. reticulatus across two populations and found similar genetic diversity. Our study provides a clear workflow to obtain high-quality assemblies from Oxford Nanopore sequences and genetic characterization of a species with a large, complex, and repetitive genome.

genomics↗

bioRxiv2025

Tick Genome Assemblies: Overcoming biological limitations through advances in sequencing and assembly

Ticks are blood-feeding arthropods with approximately 1,000 species, however, only 24 species currently have a genome assembly. These genome assemblies are important resources to advance tick biology and control of tick-associated diseases. Generating tick genome assemblies is challenging due to their small body size (low DNA input), DNA contamination (from microbiota and host bloodmeals), large genome size (on average 2.4 Gbp for hard ticks), and abundant transposable elements (at least 68% of the assembly for Ixodes species). Advances in sequencing technologies have driven an increasing number of tick assemblies from 2011 to 2025. We characterize and assess the 54 tick genome assemblies within public genome databases using QUAST-LG and BUSCO compleasm. Then we evaluate the impact of biological source material and sequencing platforms on these tick genome assemblies. From the 54 tick assemblies, we identify 34 high-quality assemblies from 21 species that are suitable for downstream analyses. We recommend future tick genome assemblies use long-read sequencing platforms and Hi-C scaffolding to improve genomic resources for these unique blood-feeding parasites.

genomics↗

bioRxiv2025

Evolutionary innovation through fusion of sequences from across the tree of life

Novel genes arise through multiple mechanisms, including gene duplication, gene fusion and horizontal gene transfer (HGT). While HGT has increasingly been documented in animals, the post-transfer evolutionary fate of horizontally-acquired genes is less well understood. We hypothesized that fusion with endogenous sequences in animal genomes might generate what we call "HGT-chimeras": genes with regions of non-metazoan and metazoan descent in the same open reading frame. To test this hypothesis, we developed a molecular phylogenetics pipeline that enables the identification of HGT-chimeras. We applied our pipeline to 319 high-quality annotated arthropod genomes and uncovered a high-confidence set of 274 HGT-chimeras corresponding to 104 independent origination events across diverse arthropods. HGT-chimeras contain intervals acquired from across the tree of life, and many likely originated via a gene duplication-based mechanism. To assess whether HGT-chimeras might be functionally important, we performed RT-PCR and Sanger sequencing of tissues from 20 arthropod species predicted to harbor HGT-chimeras in their genome. We found evidence for the expression of contiguous chimeric mRNAs for 36 of 41 tested HGT-chimeras across 18 of 20 different tested species. We also found evidence that HGT chimeras evolve under purifying selection and have acquired potentially functional domain architectures, consistent with the hypothesis that these genes are in active use and may participate in diverse biological processes. These results illuminate an underappreciated combinatorial mechanism underlying the origin of novel genes across the largest animal phylum, and suggest that interdomain sequence fusion can play important roles in animal biology and evolution. SignificanceEvolution forges novelty through the repurposing of available parts. Can recently acquired parts, previously foreign to an organism, be similarly repurposed? Applying a rigorous methodology to 319 genomes from arthropods, the largest phylum of animals, we uncover 104 novel genes that arose from the fusion of animal genes with fragments acquired via horizontal gene transfer from bacteria, viruses, fungi, and plants. RNA-Seq and RT-PCR across multiple species show that many of these novel genes are expressed as mRNAs. Many show signatures of evolutionary conservation and coherent domain architectures, suggesting that these chimeric genes may play important roles in diverse biological processes. These results reveal an understudied path to evolutionary innovation via "bricolage" of genes from across the tree of life.

evolutionary biology↗

bioRxiv2024

Duplex PCR assay to determine sex and mating status of Ixodes scapularis (Acari: Ixodidae), vector of the Lyme disease pathogen

Ticks are a major health threat to humans and other animals, through direct damage, toxicoses, and transmission of pathogens. An estimated half a million people are treated annually in the United States of America for Lyme disease, a disease caused by the bite of a black-legged tick (Ixodes scapularis Say) infected with the bacterial pathogen Borrelia burgdorferi. This tick species also transmits another six human-disease causing pathogens, for which vaccines are currently unavailable. While I. scapularis are sexually dimorphic at the adult life stage, the DNA sequence differences between male and female I. scapularis that could be used as a sex-specific marker have not yet been established. We determine the sex-specific DNA sequences for I. scapularis (male heterogametic system with XY), using whole-genome resequencing and restriction site-associated DNA sequencing. Then we identify a male-specific marker that we use as the foundation of a molecular sex identification method (duplex PCR) to differentiate the sex of an I. scapularis tick. In addition, we provide evidence that this molecular sexing method can establish the mating status of adult females that have been mated and inseminated with male-determining sperm. Our molecular tool allows the characterization of mating and sex-specific biology across development for I. scapularis, a major pathogen vector, which is crucial for a better understanding of their biology and controlling tick populations.

genomics↗

bioRxiv2024

The repetitive genome of the Ixodes ricinus tick reveals transposable elements have driven genome evolution in ticks

Ticks are obligate blood-feeding parasites associated with a huge diversity of diseases globally. The hard tick Ixodes ricinus is the key vector of Lyme borreliosis and tick-borne encephalitis in Western Eurasia. Ixodes ticks have large and repetitive genomes that are not yet well characterized. Here we generate two high-quality I. ricinus genome assemblies, with haploid genome sizes of approximately 2.15 Gbp. We find transposable elements comprise at least 69% of the two I. ricinus genomes, amongst the highest proportions found in animals. The transposable elements in ticks are highly diverse and novel, so we constructed a repeat library for ticks using our I. ricinus genomes and the genome of I. scapularis, another major tick vector of Lyme borreliosis. To understand the impact of transposable elements on tick genomes we compared their accumulation in the two Ixodes sister species. We find transposable elements in these two species to be drivers of genome evolution in ticks. The I. ricinus genome assemblies and our tick repeat library will be valuable resources for biological insights into this important ectoparasite. Our findings highlight that further research into the impact of transposable elements on the genomes of blood-feeding parasites is required.

genomics↗

bioRxiv2022

A long non-coding RNA is a key factor in the evolution of insect eusociality

Insect sociality is a major evolutionary transition based on the suppression of worker reproduction in favor of the reproductive monopoly of the queen. In the honey bee (Apis mellifera) model organism, the development of the two female caste phenotypes, queen and worker, is triggered by differences in their larval diets. However, the mechanistic details underlying their respective developmental trajectories, as well as the maintenance of sterility in the adult workers, are still not fully understood. Here we show that the long non-coding RNA lncov1 interacts with the Tudor staphylococcus nuclease (Tudor-SN) protein to form a regulatory module that promotes apoptosis in the ovaries of worker larvae. In adult workers, the lncov1/Tudor-SN module responds positively to environmental cues that suppress reproductive capacity. As lncov1 is considerably conserved in the Apidae, we propose that, by promoting worker sterility, the lncov1/Tudor-SN module has likely played critical roles in the social evolution of bees.

evolutionary biology↗

bioRxiv2021

DNA methylation is not a driver of gene expression reprogramming in young honey bee workers

Intragenic DNA methylation, also called gene body methylation, is an evolutionarily-conserved epigenetic mechanism in animals and plants. In social insects, gene body methylation is thought to contribute to behavioral plasticity, for example between foragers and nurse workers, by modulating gene expression. However, recent studies have suggested that the majority of DNA methylation is sequence-specific, and therefore cannot act as a flexible mediator between environmental cues and gene expression. To address this paradox, we examined whole-genome methylation patterns in the brains and ovaries of young honey bee workers that had been subjected to divergent social contexts: the presence or absence of the queen. Although these social contexts are known to bring about extreme changes in behavioral and reproductive traits through differential gene expression, we found no significant differences between the methylomes of workers from queenright and queenless colonies. In contrast, thousands of regions were differentially methylated between colonies, and these differences were not associated with differential gene expression in a subset of genes examined. Methylation patterns were highly similar between brain and ovary tissues and only differed in nine regions. These results strongly indicate that DNA methylation is not a driver of differential gene expression between tissues or behavioral morphs. Finally, despite the lack of difference in methylation patterns, queen presence affected the expression of all four DNA methyltransferase genes, suggesting that these enzymes have roles beyond DNA methylation. Therefore, the functional role of DNA methylation in social insect genomes remains an open question.

genomics↗

bioRxiv2021

Regulation of oogenesis in the queen honey bee (Apis mellifera)

In the honey bee (Apis mellifera), queen and worker castes originate from identical genetic templates but develop into different phenotypes. Queens lay up to 2,000 eggs daily whereas workers are sterile in the queens presence. Periodically queens stop laying; during swarming, when resources are scarce in winter and when they are confined to a cage by beekeepers. We used confocal microscopy and gene expression assays to investigate the control of oogenesis in honey bee queen ovaries. We show that queens use different combination of checkpoints to regulate oogenesis compared to honey bee workers and other insect species. However, both queen and worker castes use the same programmed cell death pathways to terminate oocyte development at their caste-specific checkpoints. Our results also suggest that the termination of oogenesis in queens is driven by nutritional stress. Thus, queens may regulate oogenesis via the same regulatory pathways that were utilised by ancestral solitary species but have adjusted physiological checkpoints to suit their highly-derived life history. Summary statementHoney bee queens regulate oogenesis using a different combination of checkpoints to workers, but both castes use the same molecular pathways.

developmental biology↗

bioRxiv2020

Irreversible sterility of workers and high-volume egg production by queens in the stingless bee Tetragonula carbonaria

Social insect reproduction is characterised by a division of labour. Typically, the queen is the sole reproductive female in the colony and the female workers are non-reproductive. However, in the majority of social insect species the workers are only facultatively sterile and remain capable of laying eggs under some conditions, such as when the queen dies. The Australian stingless bee Tetragonula carbonaria is noteworthy as workers never lay eggs, even if a colony loses its queen. Here we describe the reproductive anatomy of T. carbonaria workers (deactivated ovaries), virgin queens (semi-activated ovaries), and mated queens (activated ovaries). T. carbonaria mated queens have high-volume egg production compared to other female insects as each of their eight ovarioles (filaments of the ovary) produces approximately 40 eggs per day. We then conduct the first experimental test of absolute worker sterility in the social insects. Using a controlled microcolony environment, we investigate whether the reproductive capacity of adult workers can be rescued by manipulating the workers social environment (separating them from a queen) and diet (feeding them unrestricted highly nutritious honey bee royal jelly), both conditions which cause ovary activation in bee species where workers are facultatively sterile. The ovaries of T. carbonaria workers that are queenless and fed royal jelly remain non-functional, indicating they are irreversibly sterile and that ovary degeneration is fixed prior to adulthood. We suggest that T. carbonaria might have evolved absolute worker sterility because colonies under natural conditions are unlikely to ever be queenless.

evolutionary biology↗

bioRxiv2020

Queen pheromone modulates the expression of epigenetic modifier genes in the brain of honey bee workers

Pheromones are used by many insects to mediate social interactions. In the highly eusocial honeybee (Apis mellifera) queen mandibular pheromone (QMP) is involved in the regulation of reproduction and behaviour of workers. The molecular mechanisms by which QMP acts are largely unknown. Here we investigate how genes responsible for epigenetic modifications to DNA, RNA and histones respond to the presence of QMP. We show that several of these genes are upregulated in the honeybee brain when workers are exposed to QMP. This provides a plausible mechanism by which pheromone signalling may influence gene expression in the brain of honeybee workers. We propose that pheromonal communication systems, such as those used by social insects, evolved to respond to environmental signals by making use of existing epigenomic machineries.

ecology↗

bioRxiv2019

Aversion of the invasive Asian longhorned tick to the white-footed mouse, the dominant reservoir of tick-borne pathogens in the United States

The Asian longhorned tick (Haemaphysalis longicornis) was reported for the first time in the United States of America in 2017 and has now spread across 12 states. The potential of this invasive tick vector to transmit pathogens will be determined through its association to native hosts, such as the white-footed mouse (Peromyscus leucopus) which is the primary reservoir for the causative agent of Lyme disease (Borrelia burgdorferi) and other zoonotic pathogens. We placed larval H. longicornis on P. leucopus, 65% of the larvae (n = 40) moved off the host within a short period of time and none engorged. In contrast, larval black-legged ticks (Ixodes scapularis) did not move from where they were placed in the ear of the mouse. We then conducted a laboratory behavioural assay to assess the interaction of H. longicornis with the hair of potential mammalian host species in the United States of America. H. longicornis larvae were less likely to enter the hair zone of P. leucopus and humans compared to the hair of domestic cats, domestic dogs, and white-tailed deer. Our study identifies a tick-host hair interaction behaviour, which can be quantified in a laboratory assay to predict tick-host associations and provides insights into how ticks select a host.

zoology↗

bioRxiv2019

Vitellogenin expression in the ovaries of adult honeybee workers provides insights into the evolution of reproductive and social traits

Social insects are notable for having two female castes that exhibit extreme differences in their reproductive capacity. The molecular basis of these differences is largely unknown. A protein that likely plays a key role in these differences is Vitellogenin (Vg), a powerful antioxidant and insulin-signalling regulator. Here we investigate how Royal Jelly (the major food of honeybee queens) and queen pheromone (a major regulator of worker fertility), affects the longevity and reproductive status of honey bee workers, the expression of Vg, its receptor VgR and associated regulatory proteins. We find that Vg is expressed in the ovaries of workers and that workers fed a queen diet of Royal Jelly have increased Vg expression in the ovaries. Surprisingly, we find that Vg expression is not associated with worker ovary activation. Our findings provide further support for the reproductive ground plan hypothesis as Vg has acquired non-reproductive functions in honeybee workers.

evolutionary biology↗