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Evolutionary Symbiomics

Lead: Siv Andersson (Uni Uppsala)

Rationale

Endosymbiotic relationships between bacteria and their animal hosts are widespread in nature. They have evolved from many different bacterial lineages. The extensive sequencing of endosymbiont genomes now sets the stage for large-scale comparative analyses to learn more about what underpins the success of these relationships. Important questions concern the genomic basis of convergence, diversification and innovation in lifestyle. Although it is well known that endosymbiont genomes evolve by reductive processes, the diversity of gene functions remaining after extensive gene loss from lineages independently adapted to similar lifestyles has not been explored. This WP provides an ideal data set for examining and comparing such reductive processes given the wide range of symbionts in the different research tasks from recently evolved endosymbionts with full, unreduced genomes to bacteria that established a symbiotic relationship several hundred million years ago and have genomes the size of organelle genomes. It is hypothesized that metabolic functions lost by the primary endosymbiont may be provided by the host, from secondary endosymbionts or from bacterial genes inserted into the host nuclear genome. Although a few examples of such complementation has been discovered, we still know very little about the limits of genome reduction and the mechanisms and selective constraints driving the emergence of rescue functions from other genomes.

Objectives

To test hypotheses about functional convergence, the objective of this work package is to compare functions and metabolic networks in flavobacterial and gammaproteobacterial insect endosymbionts with defined diet behaviours (Project_5) as well as of free-living and chemosynthetic bacteria of marine invertebrates (Project_3). Mechanisms of diversification and functional innovation at different stages in the adaptation process will be explored, ranging from recombination across co-infecting strains in reproductive parasites at early stages of endosymbioses (Project_1), to replacement and metabolic complementation in both recently evolved symbiotic consortia (Project_5) and dual endosymbiont systems in an advanced state of genome reduction (Project_4). Mechanisms and consequences of endosymbiont gene transfers to the host nuclear genome will be studied to learn more about the fate of transferred genes (Project_1). To explore the extreme limits of reductive evolution in one of the most ancient symbioses, the functions and metabolic interdependencies between microsporidian parasitic protists and their tiny remnant mitochondria (mitosomes) will be examined (Project_2). Finally, a curated database of symbiont genes will be developed to enable extensive diversity and biogeography analyses of symbiotic associations (Project_6).

Key methods

This work package synergistically builds upon a variety of complementary experimental and bioinformatic methods including sequencing (Project 1), proteomics, functional assays and fluorescence immuno-electron microscopy (Project 2). The bioinformatic analyses include the development of a curated symbiont database with sequence data and linked contextual data (Project 6), phylogenetic and phylogenomic inference (Projects 1, 2, 3, 4 and 5), assembly, gene prediction, annotation, comparative genomics (Project 1), metabolic inference (Projects 2, 3 and 5), statistical testing (Projects 3, 4 and 5) and simulations (Project 5).