Biodiversity bioinformatics: from large-scale phylogenomics to gene families and functions

Overview

The aims of this biodiversity bioinformatics course are to (i) explore key evolutionary concepts, (ii) examine different methodological approaches, and (iii) gain hands-on experience in comparative genomic analyses, with an emphasis on characterising protein-coding gene evolution and function across multiple animal genomes, both from model and non model species.

This course will focus on concepts and methods for orthology and paralogy of protein-coding genes, complemented with practical examples of applications of comparative genomics approaches to investigate biological and/or evolutionary questions. It will be structured with mostly lectures in the mornings followed by mostly hands-on sessions in the afternoons.

This course may touch on, but will not cover in any detail, topics relating to genome sequencing and assembly, genome annotation, population genomics, or genomics of prokaryotes.

Audience

This course is aimed at PhD students, postdoctoral and other researchers in the life sciences who are planning how to proceed with comparative genomics analyses to investigate biological or evolutionary questions of importance to their study system, particularly to leverage comparative genomics tools and resources to characterise the gene repertoires of their non-model species.

Learning objectives

At the end of the course participants should be able to:

Interpret phylogenetic trees and sequence alignments
Infer orthologs and paralogs using graph- and tree-based methods
Design and implement comparative analyses to interrogate genomics data, e.g. phylogenomics or gene family dynamics

Prerequisites

Knowledge / competencies:

Participants should have a good understanding of command line tools. If you do not feel comfortable with these UNIX commands, please take our UNIX fundamentals e-learning module.

Technical:

Your computer should have an internet connection, and at least 8 GB RAM, 50 GB free disk space.

Application

Registration fees are 300 CHF for academics and 1500 CHF for for-profit companies. You will be informed by email of your registration confirmation. Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 days.

You will be informed by email of your registration confirmation. Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 days.

Deadline for applications is on 16 August 2023. In the case a minimum of 15 participants is not met by this date, SIB may decide to cancel this course. In this case, SIB will informe those who have registered and reimburse the fees already paid.

Deadline for of free-of-charge cancellation is 16 August 2023. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to this and other general conditions, available here.

Venue and time

This course will take place only in person, at the University of Lausanne, in the Campus Sorge.

The course will start at 9:00 and end around 17:00.

Precise information will be provided to the participants in due time.

Schedule

Day 1 - Natasha Glover and Christophe Dessimoz (UniL and SIB) - Introduction to molecular evolution & phylogenetics

Interpret phylogenetic trees and alignments; general understanding of how trees are inferred; knowing the definition of orthology, paralogy and their subtypes; understanding the difference between pairwise and groupwise comparisons; ability to perform orthology inference through tree overlap method; ability to retrieve orthology information from the OMA database; ability to infer orthologs using the OMA standalone pipeline. Teaching assistants for practical exercises: Yannis Nevers and Sina Majidian.

9:00-12:00: Lectures - Introduction to molecular evolution & phylogenetics; Inferring Orthology and Paralogy
12:00 - 13:00: Lunch break
13:00-17:00: Hands-on - exercises on orthology inference through tree overlap methods, tree reconciliation, OMA database, OMA standalone

Day 2 - Robert Waterhouse (UniL and SIB) - Orthology-focused arthropod comparative genomics

Understand the principles of graph-based orthology delineation using OrthoDB as an example; learn how to browse and programmatically query OrthoDB; learn how to use BUSCO to assess genomics data quality; learn how to formulate comparative genomics questions, develop and apply approaches to address them (with a focus on using orthology data), and then critically interpret them, through case studies from arthropods. Teaching assistant for practical exercises: Giulia Campli and Antonin Thiébaut.

9:00-12:00: Lectures - Introduction to OrthoDB & BUSCO; case studies from Arthropod Comparative Genomics
12:00 - 13:00: Lunch break
13:00-17:00: Hands-on - exercises with BUSCO for phylogenomics and OrthoDB for gene family evolution

Day 3 - Marc Robinson-Rechavi (UniL and SIB) - Duplication of genes and genomes, expression

Understand the importance of gene and genome duplication in comparative genomics; understand the difficulty of comparing “function” between homologous genes, and know some tools to do so. Teaching assistant for practical exercises: Marina Braso Vives and Alessandro Brandulas Cammarata

9:00-12:00: Lectures - Introduction to Bgee (curated data, ontologies, present calls, homology, TopAnat); patterns of gene and genome duplication; evolution after duplication
12:00 - 13:00: Lunch break
13:00-17:00: Hands-on - exercises with gene set enrichment of biased duplicate retention, expression comparison, positive selection, functional shifts, Bgee SPARQL endpoint

Additional information

Coordination: Patricia Palagi

We will recommend 0.75 ECTS credits for this course (given a passed exam at the end of the course).

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

Please note that participation in SIB courses is subject to our general conditions.

SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.

For more information, please contact training@sib.swiss.