Teaching code

4S008291

Teacher

Marzia Rossato

Coordinator

Marzia Rossato

Credits

6

Language

Italian

Scientific Disciplinary Sector (SSD)

BIO/18 - GENETICS

Period

Semester 1 dal Oct 2, 2023 al Jan 26, 2024.

Courses Single

Authorized with reserve

Lessons timetable Moodle Seminars 0

Learning objectives

The opportunity to analyze and reconstruct genomes with high processivity and accuracy, even within bioprocesses, allows to exploit genomic data as an irreplaceable source of information for the identification of functional characteristics of biotechnological interest. The course aims to provide knowledge on the structure and function of eukaryotic, prokaryotic and viral genomes, with particular emphasis on organisms of interest for bio-transformations. The course will focus on methods for genome analysis, which include sequencing, mapping, assembly and gene annotation. Metagenomic approaches that exploit second and third generation sequencing will be explored, with a particular focus on those aimed at characterizing the composition of microorganisms in natural environments and bioprocesses (natural or induced). Finally, representative examples of microbiome characterization in different environments will be analyzed.

Prerequisites and basic notions

Basic knowledge of molecular biology and genetics.

Program

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
- Bacterial and plant pan-genome
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 that constitute bioresources.
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 bioresources.
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

Bibliography

Didactic methods

THE LESSONS WILL TAKE PLACE IN DUAL MODE ONLY WHEN NECESSARY (E.G. COVID-19, VISA delay, etc.).
ALL TEACHING MATERIALS AND (when necessary) LESSON RECORDINGS WILL BE AVAILABLE IN THE COURSE'S MOODLE PLATFORM.

Learning assessment procedures

The final exam includes the presentation of a scientific paper and a written exam (5 open questions) covering the course program. The written exam will last 1 hours.
It will be also possible to carry out the exam remotely in case of COVID-19. 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@univr.it

Evaluation criteria

Paper presentation: understanding of the research conducted and the methods applied. Clarity of presentation.
Open questions: Correctness, completeness, clarity and punctuality of the answer with respect to the question.

Criteria for the composition of the final grade

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). The total will be converted to 33 points and the final voting will be expressed in thirtieths.

Exam language

Italiano

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