Biology subjects

Rota Stabelli, O.

Publications and source records attributed to Rota Stabelli, O..

4 recordsLinked to original sources

bioRxiv2025

Rodent Origins and Human-Mediated Evolutionary Dynamics of PRRSV

Porcine reproductive and respiratory syndrome virus (PRRSV) is among the most economically damaging swine pathogens worldwide, yet its evolutionary origins and the forces driving its diversification remain unclear. Using complete arterivirus genomes, we applied an integrative, high-resolution phylogenomic framework that combined time-calibrated evolutionary inference with recombination- and introgression-aware analyses. This approach resolved the divergence history of PRRSV and uncovered a cryptic mosaic genome and reticulation shaped by recurrent recombination and interspecies viral gene flow. We show that North American and European lineages diverged in the late 19th century - long before the emergence of disease on either continent and that their closest relatives are rodent arteriviruses, indicating a rodent ancestry. Genome-wide scans further reveal that PRRSV evolution is driven by adaptive changes in the glycoprotein ORF3, whereas the replicase genes remain a conserved genomic backbone. Demographic reconstructions suggest that the intensification of pig farming in the mid-20th century-imposed transmission bottlenecks that amplified genetic drift and accelerated the fixation of advantageous variants. Together, these findings rewrite the evolutionary timeline of PRRSV and provide a framework for understanding how human practices shape the emergence and spread of viral pathogens across animal and human health.

evolutionary biology↗

bioRxiv2024

The high quality Chinese white truffle genome and novel fossil-calibrated estimate of Pezizomycetes divergence reveal the tempo and mode of true truffles genome evolution

The genus Tuber (family: Tuberaceae) includes the most economically valuable ectomycorrhizal (ECM), truffle-forming fungi. Previous genomic analyses revealed that massive transposable element (TE) proliferation represents a convergent genomic feature of mycorrhizal fungi, including Tuberaceae. Repetitive sequences are one of the major drivers of genome evolution shaping its architecture and regulatory networks. In this context, Tuberaceae represent an important model system to study their genomic impact; however, the family lacks high-quality assemblies. Here, we tested the interplay between TEs and Tuberaceae genome evolution by producing a highly contiguous assembly for the endangered Chinese truffle Tuber panzhihuanense, along with a novel timeline for Tuberaceae diversification and comprehensive comparative genomic analyses. We found that concurrently with a Paleogene diversification of the family, pre-existing Chromoviridae-related Gypsy clades independently expand in different truffle lineages leading to increased genome size and high gene family turnover rates, but without resulting in highly scrambled genomes. Additionally, we found an enrichment of ECM-induced gene families among ancestral duplication events. Finally, we explored the repetitive structure of nuclear ribosomal DNA (rDNA) loci for the first time in the clade. We found that most of the 45S rDNA paralogues are undergoing concerted evolution, though an isolated divergent locus raises concerns about potential issues for metabarcoding and biodiversity assessments. Our study provides a fundamental genomic resource for future research on truffle genomics and showcases a clear example on how establishment and self-perpetuating expansion of heterochromatin can drive massive genome size variation due to activity of selfish genetic elements.

evolutionary biology↗

bioRxiv2019

The Glossina Genome Cluster: Comparative Genomic Analysis of the Vectors of African Trypanosomes

BackgroundTsetse flies (Glossina sp.) are the sole vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood specific diet by both sexes and obligate bacterial symbiosis. This work describes comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans (G.m. morsitans), G. pallidipes, G. austeni), Palpalis (G. palpalis, G. fuscipes) and Fusca (G. brevipalpis) which represent different habitats, host preferences and vectorial capacity. ResultsGenomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossina relative to Drosophila melanogaster shows reduced structural conservation across the sex-linked X chromosome. Sex linked scaffolds show increased rates of female specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse specific genes are enriched in protease, odorant binding and helicase activities. Lactation associated genes are conserved across all Glossina species while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other characterized insects. Vision associated Rhodopsin genes show conservation of motion detection/tracking functions and significant variance in the Rhodopsin detecting colors in the blue wavelength ranges. ConclusionsExpanded genomic discoveries reveal the genetics underlying Glossina biology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies.

genomics↗

bioRxiv2018

Genomic analysis of European Drosophila melanogaster populations on a dense spatial scale reveals longitudinal population structure and continent-wide selection

Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatio-temporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterise variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.

evolutionary biology↗