Understanding the genetic determinism of phenotypic traits is of paramount importance to identify and understand the mechanisms that drive their evolution and, for instance, predict their evolution under environmental changes. This is, however, a challenging task because of their complex determinism; they are indeed controlled by a multitude of genetic and non-genetic factors (e.g. epigenetic factors, environmental effects…).
The development of next generation sequencing has just begun to shed light on the complexity of their genetic architecture and it appears that adaptation generally occurs by changes at a multitude of loci. One major issue with genome-wide approaches is that they usually focus on point mutations, whereas structural rearrangements have received limited attention. Yet, literature abounds of example of evolution through genomic rearrangements and in particular gene duplications. The rate of gene duplications per generation has been recently estimated as being of the same magnitude or even higher than the substitution rate. While the role of gene duplications on long-term evolution has been theorized decades ago, their role at a micro-evolutionary scale is more and more considered; gene duplications have been shown to be involved in numerous adaptions in all kingdoms of life.
In our group we investigate the role of gene duplication in adaptation from plant models. Coniferous species are particularly fitted to address these questions as their genomes exhibit a high fraction of gene duplications and they are known to be locally adapted despite large amounts of long-distance gene flow (making easier the detection of loci / genomic regions involved in local adaptation). The main project will be developed along three main axes.
The first one aims at identifying and describing the distribution of gene duplications in different coniferous species in order to compare their prevalence at both large and small phylogenetic scales. The comparison between species having similar distribution range (thus facing the same environmental gradient) would, for instance, allow studying convergent evolution through gene duplications.
The second axe aims at investigating the relationships between gene-dosage and RNA expression patterns. Intuitively, the first consequence of a gene duplication is an increase in gene-product, however RNA expression is known to be under strong stabilizing selection and post-duplication regulation processes can take place, for instance to constraint the total amount of protein produced. Finally, if involved in local adaptation, one would expect gene duplication frequencies (or copy number of a given gene) to vary according to environmental variation and/or to phenotypic variation.
The last part of the project aims at determining the role of gene duplications in the adaptation of coniferous species through common garden experiment and association studies. If the main project focus on gene duplications, the same questions stand for all kind of structural variant but one has always to start somewhere…
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