Section: New Results

Symbiont genome evolution and dynamics

The objective of this part of our work was to analyse genome rearrangements and dynamics. The results obtained were both algorithmic and biological.

In terms of algorithms, we developed a new method for repeat identification (Rime ) [12] , as well as an algorithm for finding the minimum number of three constrained versions of inversions that transform one given genome into another [25] . The constrained versions concerned symmetric, almost-symmetric and unitary inversions. The genome rearrangement algorithm is not exact: it is based on a greedy randomized search procedure to find such minimum number of constrained inversions.

The main set of biological results [4] , [14] concerned trypanosomatids of the genera Angomonas and Strigomonas that live in a mutualistic association characterised by extensive metabolic cooperation with obligate endosymbiotic Betaproteobacteria. In contrast to their counterparts lacking symbionts, such trypanosomatids exhibit lower nutritional requirements and are autotrophic for essential amino acids and vitamins. Phylogenetic analyses showed that the cooperation in the first case is complemented by multiple horizontal gene transfers, from bacterial lineages to trypanosomatids, that appear to have occurred several times in the course of evolution. In contrast, but for three exceptions, such transfers are absent as concerns vitamin biosynthesis.

The above work was made possible in part because of the sequencing and annotation of the genomes whose metabolic pathways could then be inferred. We participated in these for some of the genomes involved in the above study [17] .