Eukayotic genome evolution

The group « Eukaryotic Genomes Evolution » has been part of the UMR 7138 since its creation (1st Jan. 2003) under the name « genetics and evolution ». Our research is about the molecular evolution of genomes.

Different subjects are under investigation:

  • Transposable elements and genome evolution:

Evolutionary strategies of the different transposable elements (TEs): copia, gypsy and tyrosine recombinase retrotransposons

Role of TEs on chromosomal rearrangements and speciation

Role of TEs in gene transfer in Eukaryotes

Response of TEs to environmental change

  • Evolutionary forces and genome evolution

Dynamics of microsatellites in coding sequences

New neutrality test

What constraints the order of mutations?

Effect of human impacts on populations of Cervus elaphus in the île-de-France

Last publications

Evolution of coding microsatellites in primate genomes. Genome Biology and Evolution (2013).

LTR-retrotransposons in R. exoculata and other crustaceans: the outstanding success of GalEa-like Copia elements. PLOS ONE (2013)

Expression patterns suggest that despite considerable functional redundancy galectin-4 and -6 play distinct roles in normal and damaged mouse digestive tract. Journal of Histochemistry & Cytochemistry (2013)

More...

  • Transposable elements and genome evolution.

Transposable elements are an important part of eukaryotic genomes. Due to their number of copies and their mobility, they can generate genetic diversity and are widely involved in the evolution of genomes. These elements are interesting in two levels: first these sequences had with an evolutionary success; second they have an impact on genomes.

By studying the different super-families of transposable elements in eukaryotic genomes, we look for different evolutionary strategies to explain their evolutionary success. At a shorter time scale, we are interested in the response of transposable to environmental changes, using annelids or crustaceans as models.

Finally, we investigate the role of transposable elements in chromosomal rearrangements of Antarctic fishes of the genus Trematomus.

  • Evolutionary forces and genome evolution

The different sequences that form a genome are subject to evolutionary forces such as mutation, drift and selection. These forces shape the eukaryotic genomes. We are interested in measuring their impact mainly in the genes, focusing firstly on the microsatellite sequences, and secondly on the epistatic interactions between locus. This leads us to develop new tests for testing the neutral reference model, mutation-drift equilibrium.

Highlights

  • Transposable elements and genome evolution.

We have shown that DIRS1 elements had a major evolutionary success contrary to what has been described previously. Furthermore, we have shown that transposable elements from gypsy and copia super-families had different evolutionary strategies. In particular, the copia elements from the GalEa family have an evolutionary success in metazoans due to a strategy that we called “domino's day spreading”.

  • Evolutionary forces and genome evolution

By analyzing the genomes of four primates (humans, chimpanzees, orangutans, and macaques), we have shown that tandem repeats (SSRs) in coding sequences showed a two times higher substitution rate than other coding sequences. Moreover, we observe that although numerous coding SSRs are created and lost by substitutions in the different lineages of primates, their numbers remain constant. Thus, we have estimated the fitness cost of mono-SSRs and shown that it increases with the number of repeated unit.

Future directions

  • Transposable elements and genome evolution.

The evolutionary strategy of GalEa elements is successful in metazoans when this family of elements is missing in plants. By analyzing other phylum, we want to determine the phylogenetic limit of this success. The “domino’s day” strategy involves periods with bursts of transposition. We wish to highlight the environmental factors that may induce such bursts.

  • Evolutionary forces and genome evolution

In Genome scale, epistasis is the interaction between two loci. This may result from the existence of physical interactions within a single molecule or between different molecules. It may also result from “logical” interactions because they belong to the same (metabolic, control ...) network. If we focus on selected polymorphism, the order in which advantageous mutations can be fixed may be constraint by this epistasis. We want to understand changes in cascade and characterize the rules that govern them.

Publications

Evolution of coding microsatellites in primate genomes. Genome Biology and Evolution (2013).

LTR-retrotransposons in R. exoculata and other crustaceans: the outstanding success of GalEa-like Copia elements. PLOS ONE (2013)

Expression patterns suggest that despite considerable functional redundancy galectin-4 and -6 play distinct roles in normal and damaged mouse digestive tract. Journal of Histochemistry & Cytochemistry (2013)