Search for photosynthesis-related protein sites through chloroplast phylogenomics
Résumé
Since the late 90's, phylogeneticists have been interested in uncovering sites associated to phenotypes, across species. Several methods were developed to study them, including dn/ds methods or profile methods. Profile methods inform about the direction of the selection, and one of them -Pelican (Duchemin, 2023)-, allows us to detect proteic sites related to a phenotype of interest at the genome scale. In the context of my PhD, we will try to uncover genotype-phenotype associations in plants (Viridiplantae), a dificult kingdom to analyse because of multiple genome-wide duplications and multicopy gene families. As a first step, we decided to look for chloroplastic proteic sites related to the photosynthetic pathway (C3/C4/CAM), and present here our analysis and conclusion about our findings.
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