Transposable elements
Berlin, 23-27 April 2018
Insructor:
Dr. Alexander Suh (Uppsala University, Sweden)
Topic
Evolution of transposable elements and their de-novo annotation in non-model genomes
Overview
Transposable elements (TEs) are selfish genetic elements which exist in virtually all eukaryotic genomes. Because TEs contain regulatory or coding sequence for their own 'survival' and often occur in large numbers within a genome, they can have strong effects on the transcription or methylation of nearby genes and significantly promote structural variation or genome size expansion. Accurate annotation of TEs is thus important for many studies in genomics and evolutionary biology. However, TEs are rapidly evolving due to arms races with their host genomes and thus often remain undetected in newly sequenced genomes. One may argue that in-depth annotation of TEs is currently one of the biggest bottlenecks in genomics research of non-model organisms. This is because computational TE analyses require knowledge of TE biology as well as some degree of manual curation to overcome incomplete or erroneous annotations. The present course aims to adress this bottleneck by teaching TE biology, computational analyses of TEs in genome assemblies (RepeatModeler, RepeatMasker) and raw read data (dnaPipeTE), and manual analyses of TEs (consensus curation, classification).
Format
At the end of this course, attendants should be able to conduct computational analyses of TEs, interpret the results in the light of TE biology, and improve TE annotations through manual curation. To achieve this, the first three days of the course will provide lectures and practicals on all these topics. The last two days of the course consist entirely of supervised individual practicals to further refine the attendants' skills in computational and manual analyses of TEs, either in their own data or in a course-specific collaborative project. Participation in the collaborative project will be acknowledged through co-authorship on a planned TE manuscript.
Audience
The course is aimed at biologists on the PhD student and postdoc level who are new to TE analyses and/or de-novo annotation of the repetitive fraction of non-model genomes.
Requirements
Attendants will need to use the command line and a sequence alignment program (e.g., BioEdit) on their laptops. Basic knowledge of these will be helpful but is not required. Attendants are encouraged to bring their own genome assembly and/or raw read data but are welcome to join the collaborative project.
Program
Monday 23rd. 09:30-17:30
Day 1: Introduction to TE biology
Lecture on TE diversity
Lecture on TE mechanisms
Lecture on TE classification and nomenclature
Practical on running RepeatModeler/RepeatMasker/dnaPipeTE (I)
Tuesday 24th. 09:30-17:30
Day 2: Introduction to computational analyses of TEs
Lecture on genome size evolution
Practical on running RepeatModeler/RepeatMasker/dnaPipeTE (II)
Practical on running RepeatModeler/RepeatMasker/dnaPipeTE (III)
Practical on classification and nomenclature of TEs
Practical on manual curation of TEs (I)
Wednesday 25th. 09:30-17:30
Day 3: Introduction to manual analyses of TEs
Lecture on genetic conflicts
Practical on manual curation of TEs (II)
Practical on manual curation of TEs (III)
Thursday 26th. 09:30-17:30
Day 4: Individual data analyses
Supervised analysis of own data or participation in a collaborative project (I)
Supervised analysis of own data or participation in a collaborative project (II)
Friday 27th. 09:30-17:30
Day 5: Individual data analyses
Supervised analysis of own data or participation in a collaborative project (III)
Supervised analysis of own data or participation in a collaborative project (IV)
Register now from here
