Biology subjects

Nardi, T.

Publications and source records attributed to Nardi, T..

5 recordsLinked to original sources

bioRxiv2025

Genome-resolved expansion of Nucleocytoviricota and Mirusviricota reveals new diversity, functional potential, and biotechnological applications

Nucleocytoplasmic large DNA viruses (NCLDV) of the phyla Nucleocytoviricota and viruses of the newly proposed Duplodnaviria phylum, Mirusviricota, exhibit taxonomic richness which continues to expand due to metagenomic sequencing of Earths biomes. Giant viruses contain complex genomes encoding genes of both viral and cellular origin, representing a reservoir of unexplored biological functions with potential implications for ecology, evolution, and biotechnology. Here, we present the largest curated database of giant virus metagenome-assembled genomes (GVMAGs V2), comprising 8,508 species-level clusters inferred from 18,727 genomes, originating from marine, freshwater, anthropogenic and terrestrial environments, a six-fold increase from the previous giant virus phylogenetic frameworks. Phylogenomics and relative evolutionary distance analysis revealed 712 novel genera, 13 previously unknown viral families and a new proposed order, tentatively named Mycodnavirales. We improved gene calling of 12% of giant virus genomes by accounting for alternative and custom genetic codes, enabling more accurate identification of protein-coding genes. Database mining uncovered endogenous viral elements in a broad spectrum of eukaryotes, spanning algae, fungi, and parasitic protists highlighting that giant virus integration is both widespread and evolutionarily persistent. Orthologous clustering of 2.5 million proteins identified 135,998 orthogroups representing comprehensive metabolic capabilities, such as enrichment of genes involved in aromatic compound degradation (commonly associated with bioremediation) in Algavirales genomes. Furthermore, we detected widespread biosynthetic gene clusters underpinning antimicrobial activity and antibiotic resistance, suggesting roles of giant viruses in host defense and in the dissemination of antibiotic resistance genes. Conversely, 67% of orthogroups have unknown functions, underscoring a substantial unexplored potential. This comprehensive publicly available database provides a critical resource for the giant virus research community and a foundation for uncovering virus-host interactions, exploring viral evolution, and identifying reservoirs for novel enzymes with the potential to advance biotechnological applications.

microbiology↗

bioRxiv2023

Comparative genomics reveals the emergence of an outbreak-associated Cryptosporidium parvum population in Europe and its spread to the USA

The zoonotic parasite Cryptosporidium parvum is a global cause of gastrointestinal disease in humans and ruminants. Sequence analysis of the highly polymorphic gp60 gene enabled the classification of C. parvum isolates into multiple groups (e.g. IIa, IIc, Id) and a large number of subtypes. In Europe, subtype IIaA15G2R1 is largely predominant and has been associated with many water-and food-borne outbreaks. In this study, we generated new whole genome sequence (WGS) data from 123 human-and ruminant-derived isolates collected in 13 European countries and included other available WGS data from Europe, Egypt, China and the USA (n=72) in the largest comparative genomics study to date. We applied rigorous filters to exclude mixed infections and analysed a dataset from 141 isolates from the zoonotic groups IIa (n=119) and IId (n=22). Based on 28,047 high quality, biallelic genomic SNPs, we identified three distinct and strongly supported populations: isolates from China (IId) and Egypt (IIa and IId) formed population 1, a minority of European isolates (IIa and IId) formed population 2, while the majority of European (IIa, including all IIaA15G2R1 isolates) and all isolates from the USA (IIa) clustered in population 3. Based on analyses of the population structure, population genetics and recombination, we show that population 3 has recently emerged and expanded throughout Europe to then, possibly from the UK, reach the USA where it also expanded. In addition, genetic exchanges between different populations led to the formation of mosaic genomes. The reason(s) for the successful spread of population 3 remained elusive, although genes under selective pressure uniquely in this population were identified.

genomics↗

bioRxiv2022

Host association and intracellularity evolved multiple times independently in the Rickettsiales

The order Rickettsiales (Alphaproteobacteria) encompasses multiple diverse lineages of host-associated bacteria, including pathogens, reproductive manipulators, and mutualists. In order to understand how intracellularity and host association originated in this order, and whether they are ancestral or convergently evolved characteristics, we built an unprecedentedly large and phylogenetically-balanced dataset that includes de novo sequenced genomes and an accurate selection of published genomic and metagenomic assemblies. We performed detailed functional reconstructions that clearly indicated "late" and parallel evolution of obligate host-association and intracellularity in different Rickettsiales lineages. According to the depicted scenario, multiple independent series of horizontal acquisitions of transporters led to the progressive loss of biosynthesis of nucleotides, amino acids and other metabolites, producing distinct conditions of host-dependence. Coherently, each clade experienced a different pattern of evolution of the ancestral arsenal of interaction apparatuses, including development of specialised effectors involved in the lineage-specific mechanisms of host cell adhesion/invasion and intracellularity.

microbiology↗

bioRxiv2021

A dual endosymbiosis drives nutritional adaptation to hematophagy in the invasive tick Hyalomma marginatum

Many animals are dependent on microbial partners that provide essential nutrients lacking from their diet. Ticks, whose diet consists exclusively on vertebrate blood, rely on maternally inherited bacterial symbionts to supply B vitamins. While previously studied tick species consistently harbor a single lineage of those nutritional symbionts, we evidence here that the invasive tick Hyalomma marginatum harbors a unique dual-partner nutritional system between an ancestral symbiont, Francisella, and a more recently acquired symbiont, Midichloria. Using metagenomics, we show that Francisella exhibits extensive genome erosion that endangers the nutritional symbiotic interactions: Its genome includes folate and riboflavin biosynthesis pathways but deprived functional biotin biosynthesis on account of massive pseudogenization. Co-symbiosis compensates this deficiency since the Midichloria genome encompasses an intact biotin operon, which was primarily acquired via lateral gene transfer from unrelated intracellular bacteria commonly infecting arthropods. Thus, in H. marginatum, a mosaic of co-evolved symbionts incorporating gene combinations of distant phylogenetic origins emerged to prevent the collapse of an ancestral nutritional symbiosis. Such dual endosymbiosis was never reported in other blood feeders but was recently documented in agricultural pests feeding on plant sap, suggesting that it may be a key mechanism for advanced adaptation of arthropods to specialized diets.

evolutionary biology↗

bioRxiv2020

Sequence of a Coxiella endosymbiont of the tick Amblyomma nuttalli suggests a pattern of convergent genome reduction in the Coxiella genus

Ticks require bacterial symbionts for the provision of necessary compounds that are absent in their hematophagous diet. Such symbionts are frequently vertically transmitted and, most commonly, belong to the Coxiella genus, which also includes the human pathogen Coxiella burnetii. This genus can be divided in four main clades, presenting partial but incomplete co-cladogenesis with the tick hosts. Here we report the genome sequence of a novel Coxiella, endosymbiont of the African tick Amblyomma nuttalli, and the ensuing comparative analyses. Its size ([~]1 Mb) is intermediate between symbionts of Rhipicephalus species and other Amblyomma species. Phylogenetic analyses show that the novel sequence is the first genome of the B clade, the only one for which no genomes were previously available. Accordingly, it allows to draw an enhanced scenario of the evolution of the genus, one of parallel genome reduction of different endosymbiont lineages, which are now at different stages of reduction from a more versatile ancestor. Gene content comparison allows to infer that the ancestor could be reminiscent of Coxiella burnetii. Interestingly, the convergent loss of mismatch repair could have been a major driver of such reductive evolution. Predicted metabolic profiles are rather homogenous among Coxiella endosymbionts, in particular vitamin biosynthesis, consistently with a host-supportive role. Concurrently, similarities among Coxiella endosymbionts according to host genus and despite phylogenetic unrelatedness hint at possible host-dependent effects. Significance statementThe genus Coxiella includes the pathogen Coxiella burnetii and widespread nutritional mutualists in ticks. Current knowledge on their evolution is hampered by the limited genomic resources available. Here we provide the first genome sequence of a Coxiella endosymbiont of clade B, the only clade for which none was available. These data allow to infer an evolutionary scenario of parallel genome reduction among Coxiella endosymbionts, with similar constraints, leading to selective retention of biosynthetic pathways beneficial for the host. The combined predicted functional capabilities of the symbionts appear to be a subset of those of C. burnetii. Accordingly, this pathogen could be closer to an ancestral state of the endosymbionts, rather than being derived from an endosymbiotic ancestor, as previously hypothesized.

genomics↗