Biology subjects

Coeur d'acier, A.

Publications and source records attributed to Coeur d'acier, A..

6 recordsLinked to original sources

bioRxiv2026

Coevolution and synchronized evolutionary rates in aphid dual endosymbiosis

Many insects rely on obligate bacterial endosymbionts for essential nutrients. However, long-term endosymbiosis drives genome erosion, frequently resulting in the acquisition of additional symbionts that complement or replace ancestral partners. In aphids, the primary nutritional symbiont Buchnera aphidicola can be supplemented by a co-obligate symbiont, most commonly Serratia symbiotica. The long-term evolutionary trajectory of this newly acquired symbiont and its impact on Buchnera remain unknown. Here, we assembled host mitochondrial and endosymbiont genomes from thirteen aphid species belonging to a clade in which Serratia has functioned as a co-obligate symbiont for approximately 25 million years. Phylogenomic analyses reveal that Serratia has undergone extensive genome reduction followed by strict codivergence with aphids and Buchnera. Bayesian molecular dating shows that substitution rates in Serratia and Buchnera are tightly correlated and fall within the range previously reported for Buchnera. Genome-wide analyses indicate pervasive purifying selection in both symbionts. Homologous host-provisioning genes retained in both symbionts did not exhibit elevated evolutionary rates. However, unlike other functional categories, their dN/dS values were not correlated between symbionts, suggesting that they no longer evolve under shared selective regimes, consistent with progressive metabolic specialization. Intraspecific patterns of polymorphism and phylogenies mirror macroevolutionary patterns across the clade. Fluorescence in situ hybridization shows that Serratia and Buchnera occupy distinct bacteriocytes, suggesting that similar demographic processes may contribute to their parallel evolution. Our findings demonstrate that, once integrated into an obligate partnership, newly acquired nutritional symbionts can converge on the long-term evolutionary dynamics of ancient obligate symbionts while undergoing functional specialization.

evolutionary biology↗

bioRxiv2024

Discordance between phylogenomic datasets in aphids: who is telling the truth?

Aphids (Hemiptera: Aphididae) are intensively studied due to their significance as pests and their captivating biological traits. Despite this considerable research interest, the evolutionary history of this insect family is poorly understood. Recent phylogenomic analyses have produced conflicting topologies, particularly at deep nodes, complicating our understanding of aphid trait evolution. In this work, we aimed to produce new data to unravel the backbone phylogeny of aphids. We sequenced partial and whole mitochondrial genomes from 87 species that were added to 31 published mitochondria. We additionally sequenced 42 nuclear loci across 95 aphid species and sourced 146 genes from 12 new and 61 published genomes from the primary aphid obligate endosymbiont, Buchnera aphidicola. We obtain data from these three sources for a subset of 51 aphid species, facilitating a comparative analysis of their phylogenetic signals. Our analyses confirm the monophyly of subfamilies, validating current taxonomic classifications, except for Eriosomatinae and Calaphidinae. However, relationships between subfamilies remain contentious in both mitochondrial and nuclear phylogenies. The topologies obtained with Buchnera appear fully resolved but exhibit some discordance with host phylogenies at deep evolutionary scales and conflict with views on the evolution of aphid morphology. We discuss alternative hypotheses for these discrepancies. Finally, the paucity of phylogenetic information at deep phylogenetic scales may stem from an initial rapid radiation. Though challenging to establish, this scenario may inherently hinder resolution in aphid phylogenetics.

evolutionary biology↗

bioRxiv2022

Co-obligate symbioses have repeatedly evolved across aphids, but partner identity and nutritional contributions vary across lineages

Aphids are a large family of phloem-sap feeders. They typically rely on a single bacterial endosymbiont, Buchnera aphidicola, to supply them with essential nutrients lacking in their diet. This association with Buchnera was described in model aphid species from the Aphidinae subfamily and has been assumed to be representative of most aphids. However, in two lineages, Buchnera has lost some essential symbiotic functions and is now complemented by additional symbionts. Though these cases break our view of aphids harbouring a single obligate endosymbiont, we know little about the extent, nature, and evolution of these associations across aphid subfamilies. Here, using metagenomics on 25 aphid species from nine subfamilies, re-assembly and re-annotation of 20 aphid symbionts previously sequenced, and 16S rRNA amplicon sequencing on 223 aphid samples (147 species from 12 subfamilies), we show that dual symbioses have evolved anew at least six times. We also show that these secondary co-obligate symbionts have typically evolved from facultative symbiotic taxa. Genome-based metabolic inference confirms interdependencies between Buchnera and its partners for the production of essential nutrients but shows contributions vary across pairs of co-obligate associates. Fluorescent in situ hybridisation microscopy shows a common bacteriocyte localisation of two newly acquired symbionts. Lastly, patterns of Buchnera genome evolution reveal that small losses affecting a few key genes can be the onset of these dual systems, while large gene losses can occur without any co-obligate symbiont acquisition. Hence, the Buchnera-aphid association, often thought of as exclusive, seems more flexible, with a few metabolic losses having recurrently promoted the establishment of a new co-obligate symbiotic partner.

genomics↗

bioRxiv2020

The protector within: Comparative genomics of APSE phages across aphids reveals rampant recombination and diverse toxin arsenals

Phages can fundamentally alter the physiology and metabolism of their hosts. While ubiquitous in the bacterial world, they have seldom been described among endosymbiotic bacteria. One notable exception in the APSE phage that is found associated with the gammaproteobacterial Hamiltonella defensa, hosted by several insect species. This secondary facultative endosymbiont is not necessary for the survival of its hosts but can infect certain individuals or even whole populations. Its infection in aphids is often associated with protection against parasitoid wasps. This protective phenotype has actually been linked to the infection of the symbiont strain with an APSE, which carries a toxin cassette that varies among so-called "types". In the present work, we seek to expand our understanding of the diversity of APSE phages as well as the relations of their Hamiltonella hosts. For this, we assembled and annotated the full genomes of 16 APSE phages infecting Hamiltonella symbionts across 10 insect species. Molecular and phylogenetic analyses suggest that recombination has occurred repeatedly among lineages. Comparative genomics of the phage genomes revealed two variable regions that are useful for phage typing. Additionally, we find that mobile elements could play a role in the acquisition of new genes in the toxin cassette. Altogether, we provide an unprecedented view of APSE diversity and their genome evolution across aphids. This genomic investigation will provide a valuable resource for the design and interpretation of experiments aiming at understanding the protective phenotype these phages confer to their insect hosts.

genomics↗

bioRxiv2019

Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids' di-symbiotic systems

Many insects with a nutrient-restricted diet depend on obligate mutualistic bacteria for the provisioning of essential nutrients lacking from their food source, namely essential amino acids and B vitamins. Most aphids (Hemiptera: Aphididae), whose diet consists of phloem, rely on the bacterial endosymbiont Buchnera for the supply of the aforementioned compounds. However, in some aphid lineages Buchnera have lost the capability of producing these nutrients and thus the symbiotic consortium has accommodated an extra bacterial partner to supplement Buchneras deficiencies. In this work, we explore the di-symbiotic nutritional endosymbiosis of a group of Cinara aphids which has been found to harbour both Buchnera and an Erwinia-related symbiont. Using fluorescence in situ hybridisation, we have located this symbiont to the bacteriome where it inhabits its own bacteriocytes. Through whole-genome sequencing of the endosymbionts of 9 species of Erwinia-associated Cinara aphids, we have found that Ewrinia genomes are highly syntenic and all show significant genome reduction. Additionally, Erwinia symbionts display phylogenetic congruency with Buchnera, suggesting long-term co-divergence. Most significantly, we found that not only is Erwinia capable of complementing Buchneras auxotrophies, but that the genes involved in the biosynthesis of two B vitamins have actually been horizontally acquired from a Sodalis-related bacterium. Finally, this B-vitamin biosynthetic genes have been further transferred to a new Hamiltonella co-obligate symbiont in a specific Cinara lineage, thus displaying a tri-symbiotic system. These results highlight the important role horizontal gene transfer plays in the establishment of new obligate nutritional symbionts.

genomics↗

bioRxiv2018

A Freeloader?: The Highly Eroded Yet Big-Genomed Serratia symbiotica symbiont of Cinara strobi

Genome reduction is pervasive among maternally-inherited bacterial endosymbionts. This genome reduction can eventually lead to serious deterioration of essential metabolic pathways, thus rendering an obligate endosymbiont unable to provide essential nutrients to its host. This loss of essential pathways can lead to either symbiont complementation (sharing of the nutrient production with a novel co-obligate symbiont) or symbiont replacement (complete takeover of nutrient production by the novel symbiont). However, the process by which these two evolutionary events happen remains somewhat enigmatic by the lack of examples of intermediate stages of this process. Cinara aphids (Hemiptera: Aphididae) typically harbour two obligate bacterial symbionts: Buchnera and Serratia symbiotica. However, the latter has been replaced by different bacterial taxa in specific lineages, and thus species within this aphid lineage could provide important clues into the process of symbiont replacement. In the present study, using 16S rRNA high-throughput amplicon sequencing, we determined that the aphid Cinara strobi harbours not two, but three fixed bacterial symbionts: Buchnera aphidicola, a Sodalis sp., and S. symbiotica. Through genome assembly and genome-based metabolic inference, we have found that only the first two symbionts (Buchnera and Sodalis) actually contribute to the hosts supply of essential nutrients while S. symbiotica has become unable to contribute towards this task. We found that S. symbiotica has a rather large and highly eroded genome which codes only for a few proteins and displays extensive pseudogenisation. Thus, we propose an ongoing symbiont replacement within C. strobi, in which a once competent\" S. symbiotica does no longer contribute towards the beneficial association. These results suggest that in dual symbiotic systems, when a substitute co-symbiont is available, genome deterioration can precede genome reduction and a symbiont can be maintained despite the apparent lack of benefit to its host.

genomics↗