S01 - Session P3 - The influence of gene duplication mechanisms on evolution in the Rosaceae

Authors: Martin Leduc *

Genetic diversity can arise through different means . One of them is gene duplication where a region containing one or more genes will be duplicated inside the genome. This event may allow selective pressure to be relaxed on one of the duplicated regions and thus permit divergence. Different mechanisms for gene duplication have been discovered, including whole genome duplication, segmental duplication and tandem duplication. Every duplication mechanism has different characteristics for the resulting duplicated region . Some only duplicate the exonic sequences, whereas some duplicate the whole gene sequence alongside the promoter . Hence, these differences might affect the retention rate and evolution of the duplicated gene. In this study, we investigate if the duplication mechanisms influence the evolution of the duplicated gene with an emphasis on selective pressure and transposable elements environment . The analysis resulted in the development of a pipeline which combines different tools to: i) detects duplicated genes; ii) infer their duplication mechanism; and iii) analyse duplicates evolution divergence . Duplicated genes are detected using Orthofinder 1 , where sequence similarity serves as a proxy for homology. Duplication mechanisms are inferred through i ‑ADHoRe 2 which helps us yield segmental and tandem duplicates specifically . The evolution divergence analysis is made by comparing s elective pressure and the transposable elements environment between duplicates depending on duplication mechanisms . The pipeline was used on seven species from the Rosaceae family with high quality sequenced genomes comprising 4 diploïds, 2 diploïd with recent WGD, and 1 octoploïd . We demonstrate how this pipeline succeeded in detecting para logs using a multi-species and orthogroups- based approach on top of using genomic context to infer duplication mechanisms. The analysis showed that duplication mechanisms influence the selective pressure and the transposable elements environment. It also revealed that duplicate evolution is highly species-specific. (1) Emms, D. M.; Kelly, S. OrthoFinder: Phylogenetic Orthology Inference for Comparative Genomics. Genome Biol 2019 , 20 (1), 238. https://doi.org/10.1186/s13059-019-1832-y. (2) Proost, S.; Fostier, J.; De Witte, D.; Dhoedt, B.; Demeester, P.; Van de Peer, Y.; Vandepoele, K. I-ADHoRe 3.0mFast and Sensitive Detection of Genomic Homology in Extremely Large Data Sets. Nucleic Acids Research 2012 , 40 (2), e11ne11. https://doi.org/10.1093/nar/gkr955.