Teaching code

4S008244

Teacher

Marzia Rossato

Coordinator

Marzia Rossato

Credits

6

Language

Italian

Scientific Disciplinary Sector (SSD)

BIO/18 - GENETICS

Period

Primo semestre dal Oct 4, 2021 al Jan 28, 2022.

Lessons timetable Moodle Seminars 0

Learning outcomes

The advent of next-generation sequencing and its more recent evolutions made genome analysis accessible for all organisms, from the simplest prokaryotes to the more complex ones of agrifood-relevant plants. Genome sequencing is no longer the target but the starting point, a fundamental tool for breeding programs, the study of characters and the biotechnological manipulation. The course will provide the knowledge necessary to interpret and plan the analysis of genomes and their regulation. The course will describe the structure and function of eukaryotic, prokaryotic and viral genomes, with particular emphasis on organisms and microorganisms of interest for agri-food biotechnology. Genome structure, gene composition, features of non-coding portions and repeated regions will be analyzed. Moreover, the course will describe how genomes evolve, the analysis and the comparison of genomes in a population and the concept of pan-genome in plants. Part of the course will focus on the analysis of epigenome and its importance in the regulation of genome expression, with theoretical and methodological notions for the study of chromatin, DNA methylation and histone modifications. Finally, published case studies of plant genomes that represent reference examples will be analyzed.

Program

THE LESSONS WILL TAKE PLACE IN DUAL MODE.
ALL TEACHING MATERIALS AND LESSON RECORDINGS WILL BE AVAILABLE IN THE COURSE'S MOODLE PLATFORM.


Part 1. STRUCTURAL CHARACTERIZATION OF GENOMES
A) The anatomy of genomes
- Structural and genetic organization of prokaryotic genomes and eukaryotic organelles
- Structural and genetic organization of eukaryotic genomes
- Coding and non-coding genes
- Repeated elements
- Pseudogenes

B) Methods for the structural analysis of genomes
- First generation sequencing
- Second generation sequencing methods
- Third generation sequencing methods
- Methods for generating physical and genetic maps
- Introduction to molecular markers and to methods for their analysis
- Sequencing based on linked-reads
C) Approaches for the study and assembly of genomes
- de-novo Assembly:
- hierarchical approach
- shot-gun approach
- hybrid approach
- Comparative analysis:
- reference-based assembly
- re-sequencing
D) Genome Projects
Students will actively carry out the analysis, presentation and discussion of original articles related to genome sequencing projects of organisms relevant for the agrifood field.

Part 2. FUNCTIONAL CHARACTERIZATION OF GENOMES
A) The transcriptome
- Components of the transcriptome
- Classes and functions of long and small non-coding RNA
B) Methods for the analysis of transcriptome
- Transcriptome analysis by second-generation sequencing
- Transcriptome analysis by third generation sequencing
- Analysis of microRNAs (PCR-based methods and sequencing)
C) Annotation of genomes
- Ab initio gene prediction
- Annotation guided by experimental evidence
- Annotation based on synteny analysis
- Genomic browsers
- In-silico functional annotation

D) The epigenome
- DNA organization in the nucleus and chromatin structure
- Introduction to epigenetic markers (histone modifications and DNA methylation)
E) Methods for the analysis of the epigenome
- Chromatin conformation analysis
- Analysis of DNA-protein interaction
- Analysis of histone markers
- Methylation analysis

Part 3. METAGENOMICS
A) Methods for metagenomic analysis
- Sequence-based metagenomics vs functional metagenomics
- DNA barcodes and metabarcoding
- Metagenomics by Whole Genome Shot-gun sequencing
- Shot-gun metagenomics by HiC, linked-reads and long reads
- Meta-transcriptomics
B) Metagenomic projects
Students will actively analyze, present and discuss original articles related to metagenomic projects relevant for relevant for the agrifood field.

Part 4. EVOLUTION OF GENOMES
- The first genomes and evolution of complex genomes
- Mutations and DNA repair
- Gene duplication, gene families and gene conversion
- Chromosomal alterations and polyploidy
- Horizontal transfer to prokaryotes
- Bacterial and plant pan-genome
B) PanGenome projects
Students will actively analyze, present and discuss original articles on pangenome reconstruction and analysis

Examination Methods

The final exam includes the presentation of a scientific paper and a written exam (10 open questions) covering the course program. The written exam will last 2 hours.
The final vote will result from the sum of votes assigned to the paper presentation (max 3 points) and the vote of written exam (maximum 3 points for each question). Voting will be expressed in thirtieths.
It will be also possible to carry out the exam remotely. In this case, the article will be presented in a teleconference and the exame will be oral (via zoom). at this aim, please get in touch via email: marzia.rossato@univ.it