Claude Rispe

Horizontal Gene Transfer (HGT) contributes to eukaryotic evolution, potentially bringing phenotypic novelties to the recipient organisms. Ticks pose a severe threat to human health as vectors of various pathogens, including viruses, bacteria and protozoa, while stably hosting endosymbiotic bacteria. As such, these obligate blood-feeding parasites have been and continue to be exposed to HGT from a broad range of donors. To determine whether bacterial-to-tick HGT has contributed to important tick traits, we surveyed Ixodes tick genomes for HGT events. We revealed duplications of the known bacteria-derived gene dae2 and discovered two novel cases of bacterial HGT, the most remarkable of which involves a bacterial peptidoglycan metabolic gene ( anmK ) acquired by the common ancestor of ticks. The acquisition of an intron demonstrates “eukaryotization” of anmK within tick genomes. Transcript profiling revealed that anmK expression is upregulated during blood feeding, peaking in female ovaries, a niche occupied by horizontally acquired endosymbionts. Biochemical analysis confirmed that, to some extent, recombinant AnmK retains kinase activity on its cognate substrate – the bacterial cell wall component 1,6-anhydro-N-acetylmuramic acid. Immunolocalization showed that the enzyme is predominantly localized towards outer layers of the vitellogenic oocytes. Silencing of anmK in different tick species compromised blood-feeding and reproduction, demonstrating that this domesticated bacterial enzyme underpins reproductive fitness across tick species. Our findings exemplify the ability of horizontally acquired genes to integrate into the host biology and thereby shape host life history.

Open aquaculture systems represent a strategic environment for the study of antibiotic resistance dynamics, given the interactions between bacteria from humans, animals and the environment. The genomic investigation of eight Pseudomonas isolated from rainbow trout in a previous study demonstrated that non-wild-type and resistance phenotypes to several antibiotics (oxytetracycline, sulphonamides and florfenicol) were predominantly attributable to the presence of related genes [ tet(Y) , sul2 and floR ]. Phylogenetic analyses revealed that several species of Pseudomonas iridis harboured these genes on mobile genetic elements, including integrative conjugative elements (ICE) on the chromosome or plasmids with a high degree of sequence similarity (>99%) between the genetic structures. Furthermore, comparisons between isolates with low and high MIC values to colistin showed mutations in the amino acid sequences of the PhoP/Q two-component system and a lack of the pmrA/B system. A wide diversity of known LPS-modifying genes involved in colistin resistance was also detected in resistant isolates. This study provided insights into the dynamics of antibiotic resistance in aquaculture systems. It demonstrated the presence of genes located on an ICE inserted into a chromosome or plasmid in P. iridis , which was isolated from healthy rainbow trout in different farms within the same watershed. Our study raises questions about the ability of environmental Pseudomonas bacteria to spread their antibiotic resistance genes to other bacterial species that are of interest in terms of human or animal surveillance.

Open aquaculture systems represent a strategic environment for the study of antibiotic resistance dynamics given the interactions between bacteria from humans, animals and the environment. The genomic investigation of eight Pseudomonas isolated from rainbow trout in a previous study demonstrated that non-wild-type and resistance phenotypes to several antibiotics (oxytetracycline, sulphonamides, florfenicol) were predominantly attributable to the presence of related genes (tet(Y), sul2 and floR). Phylogenetic analyses revealed that several the species Pseudomonas iridis harboured these genes on mobile genetic elements, including integrative conjugative elements on the chromosome or plasmids with a high degree of sequence similarity (>99%) between the genetic structures. Furthermore, comparisons between isolates with low and high MIC values to colistin showed mutations amino acid sequences of the PhoP/Q two-component system and a lack of the pmrA/B system. A wide diversity of known lipopolysaccharide-modifying genes involved in colistin resistance were also detected in resistant isolates. This study provided insights into the dynamics of antibiotic resistance in aquaculture systems. It demonstrated the presence of genes located on an integrative conjugative element (ICE) inserted into a chromosome or plasmid in Pseudomonas iridis, which was isolated from healthy rainbow trout in different farms within the same watershed. Our study raises questions about the ability of environmental Pseudomonas bacteria to spread their antibiotic resistance genes to other bacterial species that are of interest in terms of human or animal surveillance

Open aquaculture systems represent a strategic environment for the study of antibiotic resistance dynamics given the interactions between bacteria from humans, animals and the environment. The genomic investigation of eight Pseudomonas isolated from rainbow trout in a previous study demonstrated that non-wild-type and resistance phenotypes to several antibiotics (oxytetracycline, sulphonamides, florfenicol) were predominantly attributable to the presence of related genes (tet(Y), sul2 and floR). Phylogenetic analyses revealed that several multiple species of Pseudomonas harboured these genes on mobile genetic elements, including integrative conjugative elements or plasmids with a high degree of sequence similarity (>99%) between the genetic structures. Furthermore, this study identified an arnCADTEF operon in the three colistin-resistant isolates, which could explain the observed phenotypes with moderate to high minimum inhibitory concentrations (ranging from 16 µg/mL to more than 1,024 µg/mL). This study provided insights into the putative antibiotic resistance dynamics in aquaculture systems, demonstrating the presence of shared genes in diverse mobile genetic elements (plasmid, integrative conjugative elements) within the Pseudomonas genus, which were harboured by rainbow trout reared in different farms within the same watershed. Given the limited number of isolates analysed, our study raises questions about the frequency of these genetic events in these environments.

Ticks, hematophagous Acari, pose a significant threat by transmitting various pathogens to their vertebrate hosts during feeding. Despite advances in tick genomics, high-quality genomes were lacking until recently, particularly in the genus Ixodes, which includes the main vectors of Lyme disease. Here, we present the genome sequences of four tick species, derived from a single female individual, with a particular focus on the European species Ixodes ricinus, achieving a chromosome-level assembly. Additionally, draft assemblies were generated for the three other Ixodes species, I. persulcatus, I. pacificus, and I. hexagonus. The quality of the four genomes and extensive annotation of several important gene families have allowed us to study the evolution of gene repertoires at the level of the genus Ixodes and of the tick group. We have determined gene families that have undergone major amplifications during the evolution of ticks, while an expression atlas obtained for I. ricinus reveals striking patterns of specialization both between and within gene families. Notably, several gene family amplifications are associated with a proliferation of single-exon genes—most strikingly for fatty acid elongases and sulfotransferases. The integration of our data with existing genomes establishes a solid framework for the study of gene evolution, improving our understanding of tick biology. In addition, our work lays the foundations for applied research and innovative control targeting these organisms.

Ticks, hematophagous acari, pose a significant threat by transmitting various pathogens to their vertebrate hosts during feeding. Despite advances in tick genomics, high-quality genomes were lacking until recently, particularly in the genus Ixodes , which includes the main vectors of Lyme disease. Here, we present the complete genome sequences of four tick species, derived from a single female individual, with a particular focus on the European species Ixodes ricinus , achieving a chromosome-level assembly. Additionally, draft assemblies were generated for the three other Ixodes species, I. persulcatus, I. pacificus and I. hexagonus . The quality of the four genomes and extensive annotation of several important gene families have allowed us to study the evolution of gene repertoires at the level of the genus Ixodes and of the tick group. We have determined gene families that have undergone major amplifications during the evolution of ticks, while an expression atlas obtained for I. ricinus reveals striking patterns of specialization both between and within gene families. Notably, several gene family amplifications are associated with a proliferation of single-exon genes. The integration of our data with existing genomes establishes a solid framework for the study of gene evolution, improving our understanding of tick biology. In addition, our work lays the foundations for applied research and innovative control targeting these organisms.

Background: Ticks represent a major health issue for humans and domesticated animals. Exploring the expression landscape of the tick’s central nervous system (CNS), known as the synganglion, would be an important step in understanding tick physiology and in managing tick-borne diseases, but studies on that topic are still relatively scarce. Neuron-specific genes like the cys-loop ligand-gated ion channels (cys-loop LGICs, or cysLGICs) are important pharmacological targets of acaricides. To date their sequence have not been well catalogued for ticks, and their phylogeny has not been fully studied. Results: We carried out the sequencing of transcriptomes of the I. ricinus synganglion, for adult ticks in different conditions (unfed males, unfed females, and partially-fed females). The de novo assembly of these transcriptomes allowed us to obtain a large collection of cys-loop LGICs sequences. A reference meta-transcriptome based on synganglion and whole body transcriptomes was then produced, showing high completeness and allowing differential expression analyses between synganglion and whole body. Many of the genes upregulated in the synganglion were associated with neurotransmission and/or localized in neurons or the synaptic membrane. As the first step of a functional study of cysLGICs, we cloned the predicted sequence of the resistance to dieldrin (RDL) subunit homolog, and functionally reconstituted the first GABA-gated receptor of Ixodes ricinus. A phylogenetic study was performed for the nicotinic acetylcholine receptors (nAChRs) and other cys-loop LGICs respectively, revealing tick-specific expansions of some types of receptors (especially for Histamine-like subunits and GluCls). Conclusions: We established a large catalogue of genes preferentially expressed in the tick CNS, including the cysLGICs. We discovered tick-specific gene family expansion of some types of cysLGIC receptors, and a case of intragenic duplication, suggesting a complex pattern of gene expression among different copies or different alternative transcripts of tick neuro-receptors.

Ticks represent a major health issue for humans and domesticated animals. Assessing the expression patterns of the tick’s central nervous system, known as the synganglion, is an important step in understanding tick physiology and in managing tick-borne diseases. Neuron-specific genes like the cys-loop ligand-gated ion channels (cys-loop LGICs) are important pharmacological targets of acaricides. Here, we carried out the sequencing of transcriptomes of the I. ricinus synganglion, for adult ticks in different conditions (unfed males, unfed females, and partially-fed females). The de novo assembly of these transcriptomes allowed us to obtain a large collection of cys-loop LGICs sequences. A reference meta-transcriptome based on synganglion and whole body transcriptomes was then produced, showing high completeness and allowing differential expression analyses between synganglion and whole body. Many of the genes upregulated in the synganglion were related to biological processes or functions associated with neurotransmission and located in neurones or the synaptic membrane, including most of the cys-loop LGICs. As a first step of a functional study of cysLGICs, we cloned the predicted sequence of the resistance to dieldrin (RDL) subunit homologue, and functionally reconstituted the first GABA-gated receptor of Ixodes ricinus using a hetrologous expression approach. A phylogenetic study was performed for the nicotinic acetylcholine receptors (nAChRs) and for other cys-loop LGICs respectively, showing tick-specific expansions of some types of receptors (Histamine-gated, GluCls).

We studied a group of tick-associated viruses with characteristics of members of the family Iflaviridae, a family of viruses frequently found in arthropods. Our aim was to gain insight into the evolutionary dynamics of this group of viruses, which may be linked to the biology of ticks. We explored assembled RNA-Seq data sets for different species of ticks. We identified members of five different iflavirus species, four of them novel, and discovered nine new genome sequences, including variants. Five variants represented a virus species associated with Ixodes ricinus. Unexpectedly, a sequence found in the Ixodes scapularis cell line ISE6 was nearly identical to the sequences of I. ricinus variants, suggesting a contamination of this cell line by I. ricinus material. Analysing patterns of substitutions between these variants, we detected a strong excess of synonymous mutations, suggesting evolution under strong positive selection. The phylogenies of the viruses and of their tick hosts were not congruent, suggesting recurrent host changes across tick genera during their evolution. Overall, our work constitutes a step in the understanding of the interactions between this family of viruses and ticks.