Mots-Clés

phylogenomics phylogenetics evolution genomic conflict repeated genes

Description

Year 2021/2022 (flexible starting date according to the M2 schedule).

M2 internship: “Exploring the evolutionary trajectories of multicopy genes involved in male gametogenesis"

contacts: antoine.molaro@uca.fr ; julie.cocquet@inserm.fr

Muroid Rodents account for ~30% of all mammalian species and yet, they diversified recently from their last common ancestor (less than 50My ago). This tendency for rapid speciation makes it a fascinating model to study evolutionary processes especially in the context of 'genomic conflicts'. We have previously identified and characterized a genomic conflict between multicopy genes of the mouse X and Y chromosomes [1]. Those genes, called Slx and Sly, are transmission distorters (or “selfish” genes), as each favours its own transmission to the detriment of the other. We recently shown that SLX and SLY proteins compete with each other in male gametes and have opposite effect on gene expression [2]. Surprisingly, many of the target genes regulated by this conflict are also present in multicopies in rodent genomes. Yet, we still don’t know if the origins and evolutionary trajectories of these multicopy gene families have been shaped by Sly/Slx genomic conflict.

During this internship, the trainee will use phylogenomic analyses to study the selective pressures that shaped SLX/SLY target genes. In particular, they will focus on the Speer/Takusan gene cluster that amplified >150 times on Mus musculus chromosome 14. They will use (1) phylogenetic inference to date the birth of Muroidae Speer/Takusan orthologs and (2) codon-based selection analyses to identify functional innovations that accompanied their amplification. The host lab has a long and renowned expertise in phylogenomics [3-5].  

The present project will contribute to better understand the impact of genomic conflicts on genome organization and gene evolution.

The internship will take place at the iGreD (Clermont-Ferrand). The trainee will be supervised by Antoine Molaro, group leader at the iGreD and Julie Cocquet, group leader at the Cochin Institute (Paris). Both have an extensive experience in studying multicopy genes and genomic conflicts and will provide scientific guidance.

References related to the project:

1. Cocquet J, Ellis PJ, Mahadevaiah SK, Affara NA, Vaiman D, Burgoyne PS. A genetic basis for a postmeiotic X versus Y chromosome intragenomic conflict in the mouse. PLoS Genet. 2012;8(9):e1002900. Epub 2012/10/03. doi: 10.1371/journal.pgen.1002900.

2. Moretti C, Blanco M, Ialy-Radio C, Serrentino ME, Gobe C, Friedman R, et al. Battle of the Sex Chromosomes: Competition between X and Y Chromosome-Encoded Proteins for Partner Interaction and Chromatin Occupancy Drives Multicopy Gene Expression and Evolution in Muroid Rodents. Molecular biology and evolution. 2020;37(12):3453-68. doi: 10.1093/molbev/msaa175

3. Molaro A, Drinnenberg IA. Studying the Evolution of Histone Variants Using Phylogeny. Methods Mol Biol. 2018;1832:273-91. doi: 10.1007/978-1-4939-8663-7_15.

4. Molaro A, Young JM, Malik HS. Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals. Genome research. 2018;28(4):460-73. doi: 10.1101/gr.229799.117

5. Molaro A, Malik HS, Bourc'his D. Dynamic Evolution of De Novo DNA Methyltransferases in Rodent and Primate Genomes. Molecular biology and evolution. 2020;37(7):1882-92. doi: 10.1093/molbev/msaa044.