Master's degree in Agri-Food Biotechnology

Structure and function of genomes

Course code
4S000870
Name of lecturer
Marzia Rossato
Coordinator
Marzia Rossato
Number of ECTS credits allocated
6
Academic sector
BIO/18 - GENETICS
Language of instruction
Italian
Period
I semestre dal Oct 1, 2018 al Jan 31, 2019.

Lesson timetable

Go to lesson schedule

Learning outcomes

The course introduces to the structure and functions of genomes for both prokaryotes and eukary-otes. Main topic will be structural genomics, that rapidly evolved thanks to next-generation sequenc-ing, assembly of huge datasets, comparison of assembled genomes, annotation of the main charac-teristics and sequences contained in the assembled genomes, prediction and classification of genes and non-coding portions, transposable and retrotransposon elements.

In addition, the course will illustrate approaches for genome mapping, both physical and genetic. It will provide knowledge on methods for the development of molecular markers and maps; it will spe-cifically introduce the use of genetic and molecular information for the interpretation of sequencing data and their use in the assembling and understanding of genome structure and information con-tained therein. It will introduce to the annotation of genomes and to the critical interpretation of aforementioned gene functions. An introduction to epigenetic and epigenomic analyses is also planned.

Finally, the course will illustrate the major genome projects, from the human genome to specific ex-amples of bacterial, fungal and plant genomes. Case studies will be presented along with their critical reading; the aim will be to analyse the strategies adopted in the sequencing of genomes of the main crops of agricultural interest, from cereals to industrial plants, from model plants to fruit plants. Finally, the course will provide an introduction to metagenomics, illustrating some significant projects, from the study of the oceans to extreme habitats.

Syllabus

GENOME MAPPING
- Genetic and physical maps
- Markers for genome mapping
- Methods for the generation of physical maps and optical maps

GENOME SEQUECING
- Sanger sequencing
- Second generation sequencing methods
- Third generation sequencing methods
- Hierarchical e shot-gun sequencing approaches for genome de-novo assembly
- Resequencing and targeted resequencing
- Genome sequencing projects

GENOME ANNOTATION
- Genome annotation ab initio
- RNA-sequencing
- Genome annotation data-driven
- Genome browsers

EUKARIOTIC GENOMES
- Genomic and genetic organization of eukaryotic genomes
- Gene families
- Non-coding genes and pseudogenes
- Repetitive elements

GENOMES OF PROKARYOTES AND EUKARIOTIC ORGANELLES
- Physical and genetic features of prokaryotic genomes
- The genome of Escherichia coli K-12
- Bacterial pangenome
- Eukaryotic organellar genomes
- Metagenomics

VIRAL GENOMES AND MOBILE GENETIC ELEMENTS
- Genomes of bacteriophages and eukaryotic viruses
- Mobile genetic elements

EPIGENOMICS
- Organization of DNA inside the nucleus
- Chromatin modifications and chromatin remodelling
- DNA methylation
- Methods for the analysis of epigenetic markers

GENOME EXPRESSION IN THE CELL AND IN THE ORGANISM
- Genome response to extra-cellular signals
- Genome variations in cell differentiation and organism development

EVOLUTION OF GENOMES
- The first genomes
- Evolution of complex genomes
- Today's genomes and their diversity

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 acquisition of subjects covered by the course will be verified through a written exam with open questions. Voting will be expressed in thirtieths.

STUDENT MODULE EVALUATION - 2017/2018






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