Marine genomics

Semester 1

Semester 2

Semester 3

Semester 4

ECTS
3

FUNDAMENTALS


Ghent University, Université de Bretagne Occidentale, University of Algarve, University of Oviedo

Synopsis

The course deals with genome-enabled insights into the broader framework of environmental marine science. Topics within the course include evolutionary as well as functional aspects of genes, genomes and metagenomes of marine organisms from the individual to the ecosystem-level.

Content

The course is divided in modules which outline the use of genomic approaches, from the ecosystem-level, gradually narrowing to species-, population and individual -levels. Theoretical aspects and commonly used techniques will be demonstrated using examples and practical exercises from the marine environment.
a) Community-level addresses the use of genome data in assessing community structure of marine ecosystems. Techniques discussed include amplicon sequencing, qPCR, metagenomics (+ metatranscriptomics, metaproteomics, metabolomics).
b) Species-level offers an introduction to sequence alignment techniques, phylogenetics, species-delimitation, and phylogeography.
c) Population-level addresses the factors influencing population structure such as genetic drift, dispersal, mutation and selection. These aspects will be addressed using traditional organelle (mtDNA) and co-dominant markers (e.g. microsatellites) as well as NGS-based genome reduction techniques (Radseq, GBS). Aspects of speciation in the marine realm will be addressed also.
d) Individual-level: Heritability of physiological and morphological traits will be addressed using quantitative genetics, in combination with genome scans, QTL analyses and RNA-seq.

Bourlat S.J. [ed.]. Marine Genomics, Methods and protocols. Methods in Molecular Biology Series. Springer Protocols.

Pre-requisites

Bachelor in sciences. Basic knowledge in ecology, evolution and genetics is highly recommended.

Aims

The course aims to provide students an introduction to the field of molecular ecology, specifically directed toward the marine environment on its organisms. The course is concerned with applying molecular population genetics, phylogenetics, as well as (meta-)genomics and (meta-)transcriptomics to traditional ecological and evolutionary questions (e.g., species diagnosis, conservation and assessment of biodiversity, quantitative genetics, heritability of traits and breeding studies, and questions of behavioral ecology).

Objectives

The graduated student understands the ecological and evolutionary processes acting at the genomic level in populations of marine organisms.
The graduated student has a good knowledge of the terminology used in the field of molecular ecology.
The graduated students understands the underlying principles of the commonly used molecular techniques, including preservation of tissues and specimens.
The graduated student is able to make a considerate choice of molecular techniques to address specific ecologically or evolutionary questions.
The graduated student has acquired the knowledge to correctly analyse and interpret molecular datasets from the individual to the community level.

Key skills acquired

The graduated student has acquired the necessary skills to design a fitting sampling strategy in the field of molecular ecology directed toward hypothesis testing.
The graduated student can autonomously analyse molecular datasets ranging from gene sequences for phylogenetic, phylogeographic or population genetic studies, amplicon sequencing for meta-barcoding studies, genome scans for QTL analyses and analyses of heritability and transcriptomes for functional studies.
The graduate student can autonomously interpret results of molecular analyses and draw justified conclusions.

Bibliography

Bourlat S.J. [ed.]. Marine Genomics, Methods and protocols. Methods in Molecular Biology Series. Springer Protocols.

Assessment

UGent: Exam 80%; Evaluation of presentation 20%

Involved teachers

Yaisel Juan Borrell (UniOvi) Olivier De Clerck (UGent) Nele De Meester (UGent) Sofie Derycke (UGent) Christophe Lejeusne (UPMC) Deborah Power (UAlg) Nathalie Simon (UPMC)

Contact hours

lectures
12

practicals
0

seminars
4

computerclass
12

fieldwork
0

other
0