Plant genomics and bioinformatics

Coordinator(s)

Karine Alix, Bénédicte Sturbois

Goals

Understand the basic elements and specificities of genomics as applied to cultivated plants. Use the different bioinformatics databases and their characteristics to perform an appropriate search by selecting specific parameters. Understand the specificities of genome evolution in cultivated plants, as well as the natural and artificial processes involved in creating genetic diversity. 
 Explain the principles of long-read sequencing and evaluate its advantages for de novo assembly up to T2T genomes. Describe the concepts of pangenomes and pangenomics.

Skills

- Explain the importance of high-throughput sequencing and bioinformatics in plant genome analysis, outlining the advantages and limitations of next-generation sequencing techniques.
 - Describe the main mechanisms of plant genome evolution, such as polyploidy, interspecific hybridization, transposition and structural rearrangements.
 - Explain the molecular mechanisms involved in creating useful diversity for improving crops.
 - Know how to use public databases and bioinformatics tool platforms.
 - Present a scientific study and summarise the main results and conclusions; know how to communicate a scientific message.

Content

The application of genomics and bioinformatics tools to the study of the genome of cultivated plants will be presented. The specific features of genome structure, such as duplications, transposable elements and multi-genomes, as well as the genome diversity of cultivated plants, including heterozygosity, will be discussed in relation to the evolution of crops and specific agronomic traits. The specificities of organelle genomes will also be presented and discussed. The available genetic and genomic resources will be presented in light of their potential applications. The section on teaching bioinformatics through practical exercises will expand on the concepts of comparative genomics, protein motif research, and structure-function relationships. It will also introduce gene regulatory networks and protein-protein interaction networks, demonstrating how to construct and analyse them for functional annotation.
 This course provides an overview of the principles of long-read sequencing and its advantages for generating high-quality de novo assemblies, including those of entire genomes from telomere to telomere (T2T). Students will explore methods for evaluating the quality of genome assemblies and discuss their key applications in genomics research. The course will introduce pangenomes and pangenomics, emphasising their role in representing genetic diversity beyond single reference genomes.

Format

- Lectures to introduce and define new concepts. 
 - The course involves mainly practical work using bioanalysis tools to introduce bioinformatics, as well as supervised work for the assessed bioinformatics project.
 - Supervised bibliographic work to analyse articles for an assessed oral presentation.

Language : English

Elective TU

ECTS : 4

Lectures : 17 ;  Directed Study : 2; Practical Study : 12,5; Tutored Project : 4