Plant Genomics
Code: 44782 ECTS Credits: 6| Degree | Type | Year | Semester |
|---|---|---|---|
| 4318297 Plant Biology, Genomics and Biotechnology | OB | 0 | 1 |
Contact
- Name:
- Narciso Campos Martinez
- Email:
- narciso.campos@uab.cat
Teaching groups languages
You can check it through this link. To consult the language you will need to enter the CODE of the subject. Please note that this information is provisional until 30 November 2023.
Teachers
- Luisa Maria Lois Rojas
- Ana Montserrat Martin Hernandez
- Maria Jose Aranzana Civit
- Werner Howad
- Raul Castanera Andres
- Pere Arús Canals
- Cristina Roquet Ruiz
External teachers
- Albert Ferrer Prats
- Igor Flórez Sarasa
- Julia Qüesta
- Santiago Radío
Prerequisites
Good command of English
Good background in genetics, molecular biology and genetic engineering
Objectives and Contextualisation
Provide a global and updated view of the theoretical and technological bases related to the study of the organization, function and evolution of plant genomes and their potential applications to the genetic improvement of crop plants
Learning Outcomes
- CA05 (Competence) Recognise the ethical, social responsibility and legal considerations related to the use of genomic data, valuing respect for human and fundamental rights and the economic and environmental impact to apply them to the scientific and professional environment, in accordance with the Sustainable Development Goals.
- CA06 (Competence) Apply the knowledge acquired in new or unfamiliar environments within broader (or multidisciplinary) contexts related to Plant Biology, Genomics and Biotechnology.
- KA05 (Knowledge) Recognise the role of female scientists in the field of genetics and genomics.
- KA06 (Knowledge) Define concepts related to plant genomics and select the most appropriate methodologies for sequencing and annotating plant genomes.
- SA09 (Skill) Communicate the results of research into the organisation and function of plant genomes in English orally and in writing using appropriate scientific terminology.
- SA10 (Skill) Apply knowledge of plant genomics to the study of evolutionary mechanisms and plant and fungi systematics.
- SA11 (Skill) Apply an omics approach to the identification of new genes and processes of interest in basic and applied research.
- SA12 (Skill) Apply bioinformatic tools to genomic studies of plant systematics and phylogeny.
Content
- Plant genome organization, function and regulation.
- Transcript analysis and function.
- Molecular evolution of plants.
- Genetic markers and molecular breeding.
- Genome sequencing strategies and annotation.
- Omic aproaches
- Bioinformatics tools applied to omic studies.
Methodology
- Lectures covering the different topics of the program. Powerpoint presentations will be available at the Campus Virtual UAB.
- Reading and analysis of selected research papers by the students, for their presentation and discussion in the seminar sessions.
- Practical sessions on bioinformatics tools applied to omic studies
- Visit to the National Center for Genomic Analysis (CNAG-CRG) at the Barcelona Science Park.
Annotation: Fifteen minutes of one class, within the master program, will let students fill out evaluation questionnaires about the subject and the lecturers' performance.
Annotation: Within the schedule set by the centre or degree programme, 15 minutes of one class will be reserved for students to evaluate their lecturers and their courses or modules through questionnaires.
Activities
| Title | Hours | ECTS | Learning Outcomes |
|---|---|---|---|
| Type: Directed | |||
| Bioinformatic sessions | 10 | 0.4 | KA06, SA10, SA11, KA06 |
| Classroom practices | 4 | 0.16 | KA06, SA12, KA06 |
| External visit | 4 | 0.16 | CA06, KA06, CA06 |
| Lectures | 24 | 0.96 | KA05, KA06, SA10, SA11, SA12, KA05 |
| Seminars | 4 | 0.16 | CA05, CA06, KA05, SA09, CA05 |
| Type: Supervised | |||
| Preparation of oral presentations and written report for the seminars | 52 | 2.08 | CA05, CA06, SA09, CA05 |
| Type: Autonomous | |||
| Personal work and learning | 50 | 2 | KA06, SA10, SA11, KA06 |
Assessment
- Written exam
- Written report on the phylogenomics practice
- Written report on the work presented in the seminar
- Oral presentation and defense in a seminar session
- Attendance and participation in the classroom and seminar sessions
- The student will pass the subject when the sum of his/her marks reaches a minimum score of 5 out of 10
This subject does not include the single assessment system
Assessment Activities
| Title | Weighting | Hours | ECTS | Learning Outcomes |
|---|---|---|---|---|
| Oral presentation (seminar) | 25 | 0 | 0 | CA05, CA06, KA05, KA06, SA09, SA10, SA11 |
| Written exam | 30 | 2 | 0.08 | KA06, SA10, SA11, SA12 |
| Written report (phylogenomics) | 20 | 0 | 0 | CA06, KA06, SA09, SA10, SA12 |
| Written report (seminar) | 25 | 0 | 0 | CA06, KA06, SA09, SA10, SA11 |
Bibliography
Specific bibliography (books, book chapters and journal articles) and useful links related to Plant Genomics will be provided at the different sessions of the subject.
Software
Plant Genomics, subject presentation. Sessions program. Seminars. Evaluation. Visit to the CNAG-CRG.
Organization of plant genomes. Nuclear genome. Ploidy. Coding and non-coding regions in the genome. Repetitive DNA. Gene evolution. Pseudogenes. Genomic annotation. Plastid and mitochondrial genomes. RNA editing. Interaction between cell genomes.
Plant genome plasticity and transposable elements. Impact of transposable elements in the structure and evolution of plant genomes.
Coding and non-coding RNAs: types and biological functions. RNA polymerases. Roles of RNAs in protein synthesis and processing. RNAi silencing mechanisms: transcriptional and posttranscriptional. Small RNAs: siRNAs and hpRNAs. miRNAs: action, roles, and applications. lncRNAs.
Epigenomics. Chromatin structure and activity state. Epigenetic marks in plants. DNA methylation. Histone code.
Proteomics.
Metabolomics.
Phenotyping and phenomics.
Molecular markers. Definition. Types of molecular markers. Methods to obtain molecular markers. Genotyping methods.
Genetic linkage: mapping genes and quantitative traits (QTLs).
Linkage disequilibrium and Genome-Wide Association (GWAS).
Hands-on seminar/computer practical: Playing with genotyping data and map construction.
Plant phylogenetics and evolution. Plant molecular evolution. Introductory concepts on phylogenetics. Gene trees versus species trees: Homology, orthology, paralogy. Concerted evolution. Hybridization and introgression. Polyploidy. Lineage sorting or deep coalescence. Molecular markers used in plant phylogenetics and phylogenomics.
Bioinformatics tools in phylogenomic studies. Orthology assessment and multiple sequence alignment. Genetic distances and nucleotide substitution models. Phylogenetic inference. Parsimony analysis. Probabilistic Methods (Maximum Likelihood). Measurements of statistical support. Coalescent-based species trees.
High throughput sequencing. Introduction to Next-Generation Sequencing Platforms. Examples of applications: de novo genome sequencing, genome re-sequencing, exome sequencing, methylome sequencing.
Next-Generation Sequencing Technologies for transcriptomics. Design of RNA-seq experiments. RNA-seq (Illumina) data analysis: identification of differentially expressed genes. Practical use of the AIR platform.
Visit the "Nacional Center of Genomic Analysis" (CNAG-CRG). Overview of the CNAG. Next Generation Sequencing Technologies. Bioinformatics Essentials for Next Generation Sequencing. De novo assembly and annotation in plant genomes
Seminars. Oral presentation of published research by students.