This course will introduce attendees to how the genomic and transcriptomic data can be used to detect homomorphic/heteromorphic sex chromosomes and inform the cause and consequences of sex chromosome differentiation. The instructors will guide students through study design, genomic/transcriptomic data collection methods, handling of raw genomic/transcriptomic data, and methods to identify sex chromosomes. Then, we will work through a suite of analyses looking at the molecular evolution of sex chromosomes, particularly the timing and patterns of recombination suppression, gene gain/loss, gene expression differentiation, and genome divergence. We will provide background on the theory and hands-on exercises, running analysis, and interpreting results. After completing the course, the participants should be able to manipulate, visualize and interpret genomic data and patterns of sex chromosome evolution.

The course is aimed at graduate students and researchers who are interested in using genomic/transcriptomic data to explore the mode of sex chromosome evolution. Participants should have some basic background in evolutionary biology, genetics, bioinformatics, or other relevant disciplines. Basic experience in UNIX-based command line and R is an advantage. Hands-on exercises will be run in a Linux environment on remote servers and data analysis and visualization will be run in R using RStudio.

The course will be delivered fully online over 5 half-day (6 hours) sessions, with a combination of lectures and practical exercises that will be live (synchronous). Discussions among participants and with the instructors on concepts and data analysis will be possible through video conferencing and a dedicated Slack workspace.

1. Conduct computational analysis to detect homo/heteromorphic sex chromosomes.
2. Searching for signals of early stages of sex chromosome differentiation.
4. Detect the timing and patterns of recombination suppression.
5. Conduct computational analysis to detect sex chromosome gene expression differentiation and genome divergence.
6. Study of dosage compensation.
7. Interpret these in the light of evolution.

Monday– Classes 2-8 pm Berlin time
We will introduce different sex determination systems and explore types of sex chromosomes (X0, XY, ZW, UV). We will then discuss the typical workflows from study design, sample collection, through NGS data to sex chromosome identification.
We will start the practical sessions with an introduction to Unix, manipulation of the NGS data and mapping sequencing reads to reference genomes.

Tuesday– Classes 2-8 pm Berlin time
We will continue with sex chromosome identification analysis using coverage-based methods, k-mer based methods and family RNA-seq data with SEX-DETector.

Wednesday– Classes 2-8 pm Berlin time
We will explore the structural characteristics of sex chromosomes (genes, synteny, dS between the X and the Y, strata annotation...). We will use unrelated RNA-seq samples to identify sex chromosomes using Sdpop.

Thursday– Classes 2-8 pm Berlin time
We will use transcriptomic reads from males and females (reproductive and somatic tissues) to investigate sex-biased gene expression patterns in each tissue. Next, we will look at the expression profiles of protein-coding genes on the sex chromosomes and study dosage compensation.
We will investigate the mechanisms of suppression of recombination and expansion of sex-determining regions. We will continue the study of sex chromosome evolution using cross-species comparisons. We will perform genome synteny analysis and infer the rates of gene gain/loss in the sex-specific regions.
We will talk about sex chromosomes turnovers and their evolution.

Friday– Classes 2-8 pm Berlin time
We will talk about sex chromosomes epigenetics and transposable elements accumulation.
There will be time for finishing up the analyses and time for a general discussion.
Each student will be given the opportunity to receive feedback on their datasets and analyses.

Cancellation Policy:

> 30  days before the start date = 30% cancellation fee

< 30 days before the start date= No Refund.

Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.