Work Package 1: Rates and patterns of molecular evolution of bacterial symbionts (outgoing phase: Udem, Montreal Canada)
We conducted phylogenomic analyses on Buchnera (the primary symbiont of aphids) and Serratia symbiotica (one of the lineages that complements Buchnera in the Cinara genus) and inferred codiversification scenarios using reconciliation analyses. These analyses show that Serratia has been acquired and lost several times during the diversification of Cinara. Fossil calibrations of both the phylogenies of Serratia and Buchnerashow that both bacterial lineages have very similar substitution rates. These results suggest that they experience similar demographic events. Our results also show that the genome shrinkage experienced by Serratia symbiotica upon its integration as an obligate symbiont is very fast.
Similar analyses were conducted on the association between Erwinia and Buchnera aphidicola in specific clade of Cinara. These confirmed that Erwinia has cospeciated with its aphid hosts in this clade and experienced very similar substitution rates to Buchnera.
In order to investigate the process of genome shrinkage at a finer evolutionary scale, we also investigated intraspecifc variations in the endosymbiont genomes of two study systems: the association between Cinara strobi and its two endosymbionts (Buchnera and Serratia) and the association between Cinara pseudotaxifoliae and its two symbionts (Buchnera and Erwinia). In both systems, coding regions evolve at very similar rates in both Buchnera and its obligate associates, with few non synonymous substitutions which confirms that these genomes are under purifying selection. Deletions occur in non-coding regions (pseudogenes and intergenic regions) in both Serratia and Erwinia. In Serratia small deletions occur through replication slippage in homopolymers. In Erwinia, deletions occur mostly in more complex microsatellite repeat motifs. These results give an overview of the process of genomic erosion at a recent evolutionary scale.
Work package 2 : Role of bacterial associations in aphid evolutionary transitions
The annotation of Erwinia genomes showed that these bacteria carry a new metabolic function: Erwinia can synthetize Thiamin, while this B vitamin cannot be synthetized by any known Buchnera or the Serratia that are known to complement Buchnera in other aphids. The aphids hosting this symbiont are the only ones that feed on Larix and Pseudotsuga, this suggest that Erwinia acquisition could have played a key role in the colonisation of these conifer genera.
On the other hand, the ongoing annotation of Serratia genomes associated with Cinara, suggests that all Serratia (old and more recently acquired) fill the same metabolic functions, complementing Buchnera. The acquisition of a new serratia seems to be neutral for the aphids.
Through phylogenetic analyses of 16 phage genomes (APSE associated with Hamiltonella), we show that recombination has occurred repeatedly among phage. AWealso found acquisition of new genes in the toxin cassette. These variations are probably associated with the variable protective phenotypes these phages confer to their insect hosts.
