Biology subjects

Rossier, V.

Publications and source records attributed to Rossier, V..

7 recordsLinked to original sources

bioRxiv2026

Temporal, spatial, and parasitic drivers of microbial variation in European honey bees

Although the roles of host-associated microbiomes in animal health are increasingly recognised, the factors influencing their variation remain understudied. The relatively simple microbiome of honey bees is a relevant system to address this gap. In particular, the relationship between variations in microbiome composition and the ectoparasite Varroa destructor, the main threat to honey bee health worldwide, is poorly established. In this study, we used metagenomic and statistical analyses of 1442 European honey bee colonies to investigate the relationships between the honey bee microbiome, temporality, location, V. destructor load, and behavioural response to its infestation by the host. While season, year, and location were identified as the main drivers of microbiome variation, V. destructor load emerged as a significant factor associated with microbiome variation. Notably, we identify several pathogens and opportunists that correlated positively with V. destructor load, while the core symbiont Bombilactobacillus correlated negatively. This is compatible with a shift in the microbiome toward dysbiosis, which may be driven by or promote V. destructor parasitism. By contrast, we found only limited evidence of an association between the microbiome and resistance behaviours of the host against this parasite. While the study cannot establish causal relationships, we present the largest metagenomic analysis of honey bee microbiomes to date, providing robust, generalisable evidence about the factors driving variation in the microbiome composition of this ecologically and economically important pollinator. These findings may serve as additional markers in selective breeding programs targeting V. destructor resistance, which could ultimately improve honey bee health.

microbiology↗

bioRxiv2023

Matreex: compact and interactive visualisation of large gene families provides evidence for loss of intraflagellar transport in a myxozoan

Studying gene family evolution strongly benefits from insightful visualisations. However, the evergrowing number of sequenced genomes is leading to increasingly larger gene families, which challenges existing gene tree visualisations. Indeed, most of them present users with a dilemma: display complete but intractable gene trees, or collapse subtrees, thereby hiding their childrens information. Here, we introduce Matreex, a new dynamic tool to scale-up the visualisation of gene families. Matreexs key idea is to use "phylogenetic" profiles, which are dense representations of gene repertoires, to minimise the information loss when collapsing subtrees. We illustrate Matreex usefulness with three biological applications. First, we demonstrate on the MutS family the power of combining gene trees and phylogenetic profiles to delve into precise evolutionary analyses of large multi-copy gene families. Secondly, by displaying 22 intraflagellar transport gene families across 622 species cumulating 5500 representatives, we show how Matreex can be used to automate large-scale analyses of gene presence-absence. Notably, we report for the first time the complete loss of intraflagellar transport in the myxozoan Thelohanellus kitauei. Finally, using the textbook example of visual opsins, we show Matreexs potential to create easily interpretable figures for teaching and outreach. Matreex is available from the Python Package Index (pip install matreex) with the source code and documentation available at https://github.com/DessimozLab/matreex.

evolutionary biology↗

bioRxiv2022

Multifaceted quality assessment of gene repertoire annotation with OMArk

Assessing the quality of protein-coding gene repertoires is critical in an era of increasingly abundant genome sequences for a diversity of species. State-of-the-art genome annotation assessment tools measure the completeness of a gene repertoire, but are blind to other types of errors, such as gene over-prediction or contamination. We developed OMArk, a software relying on fast, alignment-free sequence comparisons between a query proteome and precomputed gene families across the tree of life. OMArk assesses not only the completeness, but also the consistency of the gene repertoire as a whole relative to closely related species. It also reports likely contamination events. We validated OMArk with simulated data, then performed an analysis of the 1805 UniProt Eukaryotic Reference Proteomes, illustrating its usefulness for comparing and prioritizing proteomes based on their quality measures. In particular, we found strong evidence of contamination in 59 proteomes, and identified error propagation in avian gene annotation resulting from the use of a fragmented zebra finch proteome as reference. OMArk is available on GitHub (https://github.com/DessimozLab/OMArk), as a Python package on PyPi, and as an interactive online tool at https://omark.omabrowser.org/.

bioinformatics↗

bioRxiv2020

Convergent consequences of parthenogenesis on stick insect genomes

The shift from sexual reproduction to parthenogenesis has occurred repeatedly in animals, but how the loss of sex affects genome evolution remains poorly understood. We generated de novo reference genomes for five independently evolved parthenogenetic species in the stick insect genus Timema and their closest sexual relatives. Using these references in combination with population genomic data, we show that parthenogenesis results in an extreme reduction of heterozygosity, and often leads to genetically uniform populations. We also find evidence for less effective positive selection in parthenogenetic species, supporting the view that sex is ubiquitous in natural populations because it facilitates fast rates of adaptation. Contrary to studies of non-recombining genome portions in sexual species, genomes of parthenogenetic species do not accumulate transposable elements (TEs), likely because successful parthenogens derive from sexual ancestors with inactive TEs. Because we are able to conduct replicated comparisons across five species pairs, our study reveals, for the first time, how animal genomes evolve in the absence of sex in natural populations, providing empirical support for the negative consequences of parthenogenetic reproduction as predicted by theory.

evolutionary biology↗

bioRxiv2020

OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches

Assigning new sequences to known protein families and subfamilies is a prerequisite for many functional, comparative and evolutionary genomics analyses. Such assignment is commonly achieved by looking for the closest sequence in a reference database, using a method such as BLAST. However, ignoring the gene phylogeny can be misleading because a query sequence does not necessarily belong to the same subfamily as its closest sequence. For example, a hemoglobin which branched out prior to the hemoglobin alpha/beta duplication could be closest to a hemoglobin alpha or beta sequence, whereas it is neither. To overcome this problem, phylogeny-driven tools have emerged but rely on gene trees, whose inference is computationally expensive. Here, we first show that in multiple animal and plant datasets, 18 to 62% of assignments by closest sequence are misassigned, typically to an over-specific subfamily. Then, we introduce OMAmer, a novel alignment-free protein subfamily assignment method, which limits over-specific subfamily assignments and is suited to phylogenomic databases with thousands of genomes. OMAmer is based on an innovative method using evolutionarily-informed k-mers for alignment-free mapping to ancestral protein subfamilies. Whilst able to reject non-homologous family-level assignments, we show that OMAmer provides better and quicker subfamily-level assignments than approaches relying on the closest sequence, whether inferred exactly by Smith-Waterman or by the fast heuristic DIAMOND. OMAmer is available from the Python Package Index (as omamer), with the source code and a precomputed database available at https://github.com/DessimozLab/omamer.

bioinformatics↗

bioRxiv2017

First draft genome assembly of an iconic clownfish species (Amphiprion frenatus)

Clownfishes (or anemonefishes) form an iconic group of coral reef fishes, particularly known for their mutualistic interaction with sea anemones. They are characterized by particular life history traits, such as a complex social structure and mating system involving sequential hermaphroditism, coupled with an exceptionally long lifespan. Additionally, clownfishes are considered to be one of the rare group to have experienced an adaptive radiation in the marine environment.\n\nHere, we assembled and annotated the first genome of a clownfish species, the tomato clownfish (Amphiprion frenatus). We obtained a total of 17,801 assembled scaffolds, containing a total of 26,917 genes. The completeness of the assembly and annotation was satisfying, with 96.5% of the Actinopterygii BUSCOs (Benchmarking Universal Single-Copy Orthologs) being retrieved in A. frenatus assembly. The quality of the resulting assembly is comparable to other bony fish assemblies.\n\nThis resource is valuable for the advancing of studies of the particular life-history traits of clownfishes, as well as being useful for population genetic studies and the development of new phylogenetic markers. It will also open the way to comparative genomics. Indeed, future genomic comparison among closely related fishes may provide means to identify genes related to the unique adaptations to different sea anemone hosts, as well as better characterize the genomic signatures of an adaptive radiation.

genomics↗

bioRxiv2017

Evolutionary history of New World monkeys revealed by molecular and fossil data

New World monkeys (parvorder Platyrrhini) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, morphology, and behavior. Although the relationships among the almost 200 living species are relatively well understood, we lack robust estimates of the timing of origin, the ancestral morphology, and the evolution of the distribution of the clade. Here we integrate paleontological and molecular evidence to investigate the evolutionary dynamics of extinct and extant platyrrhines. We develop an analytical framework to infer ancestral states, the evolution of body mass, and changes in latitudinal ranges through time. Our results show that extant platyrrhines originated some 5-10 million years earlier than previously assumed, likely dating back to the Middle Eocene ([~] 43 million years ago, Ma). The estimated ancestral platyrrhine was strikingly small - weighing [~] 0.4 kg, as compared to the largest modern species over 10 kg - matching the size of their presumed Eocene North African ancestors. Small-sized callitrichines (marmosets and tamarins) retained a small body mass throughout their evolutionary history, thus challenging the hypothesis of phyletic dwarfism as an explanation to their adaptive traits. In contrast, a rapid change in body mass range took place as the three families diverged between the Late Oligocene and the Early Miocene. That period also marks a peak in diversity of fossil platyrrhines and is associated with their widest latitudinal range, expanding as far to the South as Patagonia. This geographic expansion is temporally coincident with a significant increase in platyrrhine population size inferred from genomic data, and with warm and humid climatic conditions linked to the Miocene Climatic Optimum and the lower elevation of the Andes. These results unveil the early evolution of an iconic group of monkeys and showcase the advantages of integrating fossil and molecular data for estimating evolutionary rates and trends.

evolutionary biology↗