Genomics and metagenomics for bioresources (2019/2020)

Course code
4S008291
Name of lecturer
Marzia Rossato
Coordinator
Marzia Rossato
Number of ECTS credits allocated
6
Other available courses
Academic sector
BIO/18 - GENETICS
Language of instruction
Italian
Period
I semestre dal Oct 1, 2019 al Jan 31, 2020.

Lesson timetable

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Learning outcomes

The course will provide knowledge on the structure and functions of genomes for both prokaryotes and eukaryotes, including relevant organisms for biotransformations and the production of bio-compounds. The course will illustrate experimental methods for genome-sequencing analysis and annotation, including different metagenomic approaches necessary to characterize the composition of microorganisms involved in bioprocesses (natural or induced) and the genes underlying relevant functions.

Syllabus

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

Reference books
Author Title Publisher Year ISBN Note
Brown Genomes 4 (Edizione 4) Taylor & Francis 2017 978-0-8153-4508-4

Assessment methods and criteria

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.

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