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Functional and evolutionary genomics

Master in Life Science, ENS
Bio-M2_E10 | Functional and evolutionary genomics
Year and Semester: M2 | S1
Where: Biology department, ENS
Duration: 1 week, 30h | 20h course / 10h practicals
First and last day of class: January 9th-13th, 2023
Hours: 9:00-12:00 | 14:00-17:00
Maximum class size: 12-24 students

Coordination

Hugues Roest Crollius, CNRS-ENS

Credits

3 ECTS

Keywords

Genome evolution and organization | Comparative genomics | Gene and genome duplication | Sex chromosomes | Genomic robustness | Ancestral genomes.

Course prerequisites

A basic understanding of genome organisation (chromosomes, genes) and molecular biology, and a basic understanding of evolutionary principles. The most important fundamentals will be re-explained so in principle the course is also accessible to biologists from a broad range of backgrounds. A ½ day of practical session on computers requiring only limited knowledge of Linux/bash commands (and no programmation) is planned.

Course objectives and description

Aims: Students will become familiar with concepts of molecular evolution in the context of functional genomics and genome evolution. The teaching is mainly based around published studies to understand how researchers formulate questions and hypotheses, collect data to test these, and interpret the results.
Themes: Topics will cover the evolution of genes and genomes in vertebrate animals by duplication, the evolution of genes on sex-chromosomes, the evolution of genome organization through rearrangements and how ancestral genomes can help address these issues, and the concept of genomic robustness, by which genomes protect themselves against future deleterious mutations.
Organisation: This course is organised as one full week, generally with formal presentations in the morning, and research seminars or practical sessions in the afternoon.

Assessment

The evaluation will be based on a written report.

Course material

A PDF file of the course will be made available to the students before the course.

Teaching team

Hugues Roest Crollius (ENS-CNRS, Paris)
One or two invited lecturers from the research community.

Suggested readings in relation with the module content

• Blaxter, Mark, John M. Archibald, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Federica Di Palma, Richard Durbin, et al. “Why Sequence All Eukaryotes?” Proceedings of the National Academy of Sciences 119, no. 4 (January 25, 2022): e2115636118.
https://doi.org/10.1073/pnas.2115636118.
• Graves, J. A. “Evolution of Vertebrate Sex Chromosomes and Dosage Compensation.” Nat Rev Genet, November 30, 2015.
https://doi.org/10.1038/nrg.2015.2.
• Innan, H., and F. Kondrashov. “The Evolution of Gene Duplications: Classifying and Distinguishing between Models.” Nat Rev Genet 11, no. 2 (February 2010): 97–108.
https://doi.org/10.1038/nrg2689.
• Wilke, Claus O. “Transcriptional Robustness Complement Nonsense-Mediated Decay in Humans” Plos Genetics 7, no. 10 (2011): 1002296.
https://doi.org/10.1371/journal.pgen.1002296
• Jaillon, Olivier, et al. “Genome Duplication in the Teleost Fish Tetraodon Nigroviridis Reveals the Early Vertebrate Proto-Karyotype” Nature 431, no. 7011 (October 21, 2004): 946–57.
https://doi.org/10.1038/nature03025.
• Ellegren, Hans. “Comparative Genomics and the Study of Evolution by Natural Selection” Molecular Ecology 17, no. 21 (November 2008): 4586–96.
https://doi.org/10.1111/j.1365-294X.2008.03954.x.