Mots-Clés

comparative genomics - evolution - biodiversity

Description

Sujet de stage de M2

Equipe DYOGEN (https://www.biologie.ens.fr/dyogen)

Encadrant: H. Roest Crollius (DR1 CNRS)

Période février-juillet 2024 (flexible).

Large-scale comparative analysis of fish genomes in the era of biodiversity sequencing

The DYOGEN team at the Institute of Biology of the ENS (IBENS) seeks to make sense of the information contained in vertebrate genomes through the comparative study of their evolution, organization, gene content and regulatory sequence content. For several years now, the team has been particularly interested in fish genomes, which underwent a complete duplication before the great radiation of the teleosts, which has given rise to about 30,000 species today. The team is at the heart of the ATLASea project, which aims to sequence the genomes of 4500 marine species from the french coastline (https://www.atlasea.fr). This massive data is ideal material to identify genotype-phenotype relationships using either "Forward” or “Reverse” genomics strategies [1–3], where one seeks to associate signatures of phenotypic changes with genomic changes.   

The internship will build on the team’s expertise in bioinformatics and fish comparative genomics to develop such strategies applied to known cases of convergent evolution in teleost fish. Convergent evolution, where the same phenotype has evolved more than once in independent lineages, is a powerful approach to identify genotype-phenotype relationships because it involves replicate observations. It has been documented numerous times in fish, such as for the emergence of amphibiousness, viviparity, osmoregulation, endothermy, extreme short or long lifespan, or the loss of the swim bladder, of the stomach, of scales, of fins. The approach will consist in building reference datasets for protein coding gene phylogenies and conserved non-coding element (CNE) families. More than 450 high-quality fish genomes are currently available, and will provide the necessary raw data from which relevant data subsets (gene families, multiple genome alignments, etc.) will be established. When no specific genomic elements (genes or CNEs) can be ascribed to a phenotype of interest through discrete retention or loss patterns, two strategies will be employed to broaden the range of the genotype to be considered. First, gene annotations (gene ontology, metabolic pathways, paralogy relationships) will serve to extend the biological context to consider. Second, a continuous signal of molecular evolutionary rate change will be measured across phylogenies, instead of a binary retention/loss of sequences.

The project is an exciting opportunity to leverage the abundance of high-quality genomic data that biodiversity sequencing projects are currently producing[4]. IBENS is equipped with a substantial bioinformatics platform providing access to a local high-performance computing cluster (>4500 CPUs, > 20 Tb RAM).

1.         Chen HI, Turakhia Y, Bejerano G, Kingsley DM. Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse Fish Lineages. Molecular Biology and Evolution. 2023;40: msad188. doi:10.1093/molbev/msad188

2.         Hiller M, Schaar BT, Indjeian VB, Kingsley DM, Hagey LR, Bejerano G. A “Forward Genomics” Approach Links Genotype to Phenotype using Independent Phenotypic Losses among Related Species. Cell Reports. 2012;2: 817–823. doi:10.1016/j.celrep.2012.08.032

3.         Prudent X, Parra G, Schwede P, Roscito JG, Hiller M. Controlling for Phylogenetic Relatedness and Evolutionary Rates Improves the Discovery of Associations Between Species’ Phenotypic and Genomic Differences. Molecular Biology and Evolution. 2016;33: 2135–2150. doi:10.1093/molbev/msw098

4.         Lewin HA, Richards S, Aiden EL, Allende ML, Archibald JM, Bálint M, et al. The Earth BioGenome Project 2020: Starting the clock. PNAS. 2022;119. doi:10.1073/pnas.2115635118