Estructural and functional genomics

Acquire knowledge about basic principles of genomic analysis
Acquire knowledge on the applications of genomic analysis for the sustainable improvement of aquaculture species.

Acquire knowledge on techniques:
Structural and Functional genomic analysis
Bioinformatic analysis of genomic data

Description of the subject: Genomic analysis. Genomic sequencing. Genotype by sequencing. Structural genomics: genetic and physical maps, comparative mapping and gene mining of QTL (quantitative trait loci), genome wide association analysis. Functional genomics: transcriptomics, regulatory regions, epigenomics, technology of single cell, metagenomics. Genomic edition. Genomic analysis of the genetic basis of productive traits. Aplications of genomic tools in aquaculture.

Program:

Unit 1. Structure and organization of genomes. Genomic analysis.
Size and organization of genomes. Fragmentation and separation of genomic sequences. Isolation of chromosomes. In situ hybridization. In vitro and in vivo libraries. Vectors. Strategies of genomic sequencing: Modifications of Sanger method (high throughput sequencing, NGS and NNGS). Genotyping by sequencing (RAD-seq). Revision in aquaculture.

Unit 2. Genetic maps and comparative mapping.
Linkage and recombination. Segregating populations and genetic markers. Genetic cartography, High-resolution linkage mapping. Comparative mapping and evolutionary genomics. Identification of QTL (quantitative trait loci). Integration of genetic and physical maps. Fine mapping. Positional cloning. Genome mining. Targeted sequencing. Genome Mining. Mapping of candidate genes. Genome wide association analysis (GWAS). Revision and applications in aquaculture.

Unit 3. Functional Genomics.
Transcriptomics: microarray and RNAseq. Regulatory regions. Epigenomics: 3D structure of DNA, DNA methylation, histone modification, access to DNA. Metagenomics. Genomic edition. Single-cell genomic technologies. Identification of candidate genes and pathways related to biological processes of productive and evolutionary interest. Applications in aquaculture.

Practical classes:

GENOMIC ANALYSIS: Platform for sequencing and functional genomics: equipment and technologies. Sampling, RNA extraction: amount and quality, library preparation for sequencing. Discussion on practical cases in aquaculture species to study the functional genetic basis of productive traits.

BIOINFORMÁTICS. Management, annotation of genomic sequences. In silico characterization and genotyping of microsatellite and SNPs markers. Genetic and comparative mapping. Genome mining. Analysis of differential expression starting from (single-cell) RNAseq data. Practical cases in aquaculture species

Basic

-Figueras A. y Martínez P. 2009. Genética y Genómica en Acuicultura (Coord.: P. Martínez y A. Figueras). Publicaciones Científicas y Tecnológicas de la Fundación OESA, CSIC. Madrid. http://www.fundacionoesa.es/images/stories/publicaciones/libros/genetic…
-Lesk, AM. 2017. Introduction to genomics. Oxford University Press, Oxford.
-Liu, Z. 2017. Bioinformatics in Aquaculture: Principles and Methods. John Wiley & Sons Ltd. Online Books. https://onlinelibrary.wiley.com/doi/book/10.1002/9781118782392
-Gallego, F. J. 2019. Genómica y proteómica. Editoral Síntesis, Madrid.
-Pierce, B.A. 2020. Genetics: A conceptual approach. 7th Ed. Macmillan International Higher Education, New York.

Complementary

-Clark, E.L. et al. 2020. From FAANG to fork: application of highly annotated genomes to improve farmed animal production. Genome Biol. 2020 Nov 24;21(1):285. doi: 10.1186/s13059-020-02197-8.
-Daniels, R.R. et al. 2023. Single cell genomics as a transformative approach for aquaculture research and innovation. Reviews in Aquaculture, doi:10.1111/raq.12806.
-Figueras, A. et al. 2016. Whole genome sequencing of turbot (S. maximus; Pleuronectiformes): a fish adapted to demersal life. DNA Res 23: 181-192.
-Gavery and Roberts. 2017. Epigenetic considerations in aquaculture. PeerJ 5: e4147.
-Gratacap, R.L. et al. 2019. Genome editing to improve aquaculture breeding and production. Trends Genet 35: 672-684.
-Houston, R.D. et al. 2022. Animal board invited review: Widespread adoption of genetic technologies is key to sustainable expansion of global aquaculture. Animal 16: 100642.
-Houston, R.D. et al. 2020. Harnessing genomics to fast-track genetic improvement in aquaculture. Nat Rev Genet 21: 389–409.
-Johnston, I. A. et al. 2024. Advancing fish breeding in aquaculture through genome functional annotation. Aquaculture. 583: 740589. 10.1016/j.aquaculture.2024.740589.
-Lorgen-Ritchie, M. et al. Microbiomes in the context of developing sustainable intensified aquaculture. Front. Microbiol. 2023, 14, 1200997.
-MacKenzie, S.A. and Jentoft, S. (eds) 2016. Genomics in aquaculture. Academic Press, Elsevier. Londres.
-Maroso, F. et al. 2018 Highly dense linkage maps from 31 full-sibling families of turbot provide insights into recombination patterns throughout a newly refined genome assembly. DNA Res 25: 439–450.
Martínez, P. et al. 2021. A genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiated ZZ/ZW sex determination of turbot. Genomics 113: 1705-1718.
-Nguyen, T.V. and Alfaro, A.C. 2020. Applications of omics to investigate responses of bivalve haemocytes to pathogen infections and environmental stress. Aquaculture 518: 734488.
-Nguyen NH. Genetics and Genomics of Infectious Diseases in Key Aquaculture Species. Biology (Basel). 2024 Jan 4;13(1):29. doi: 10.3390/biology13010029. PMID: 38248460; PMCID: PMC10813283.
-Natnan, M.E. et al. 2021. Omics Strategies in Current Advancements of Infectious Fish Disease Management. Biology 2021, 10, 1086.
-Nicholl, D.S.T. 2023. An introduction to genetic engineering. 4rd ed. Cambridge: Cambridge University Press.
-Peng, X. et al. 2020. Editorial: Genetic Dissection of Important Traits in Aquaculture: Genome-Scale Tools Development, Trait Localization and Regulatory Mechanism Exploration. Front Genet 11: 642.
-Peters, L. et al. 2018. Environmental DNA: a new low-cost monitoring tool for pathogens in salmonid aquaculture. Front Microbiol 9: 3009.
-Potts, R.W.A. et al. 2021. Potential of genomic technologies to improve disease resistance in molluscan aquaculture. Phil. Trans. R. Soc. B 376: 20200168.
-Robinson, N.A. et al. 2022. Applying genetic technologies to combat infectious diseases in aquaculture. Reviews in Aquaculture, doi:10.1111/raq.12733.
-Robledo, D. et al. 2018. Genotyping by sequencing in aquaculture breeding and genetics. Rev Aquacult 10: 670–682.
-Satam, H.; et al. 2023. Next-Generation Sequencing Technology: Current Trends and Advancements. Biology 12: 997. https://doi.org/10.3390/biology12070997
-You, X. et al. 2020.Research advances in the genomics and applications for molecular breeding of aquaculture animals. Aquaculture 526: 735357.
-Yuan, J. et al. 2023. Recent advances in crustacean genomics and their potential application in aquaculture. Rev Aquac. 2023; 1- 21. doi:10.1111/raq.12791


WEB Resources:

Databases of genomic and transcriptomic sequences. Animal and aquaculture species; resources of genetic and comparative mapping; bioinformatic tools:
http://www.ensembl.org/
http://www.ncbi.nlm.nih.gov/
https://gold.jgi.doe.gov/
https://www.genomicus.bio.ens.psl.eu/genomicus-109.01/cgi-bin/search.pl

Compilation of bioinformatics scripts from the aquaculture genetics group of the Roslin Institute:
https://github.com/Roslin-Aquaculture

General competences
• CG03- Importance of multidisciplinary analysis and relation between knowledge to solve problems and analyse critical points.
• CG04- Use of proper scientific terminology.
• CX08- Promote the use of foreign languages.

Specific competences
• CE10- Identifying significant research aims and planning strategies to reach goals.
• CE11- Acquire basic and applied knowledge in genetics, genomics and proteomics in aquaculture.

Basic competences:
• CB02- Warranting students to be able to apply acquired knowledge and problem-solving within pioneering, multidisciplinary contexts, related to the field of study.

Transversal competences:
• CT2 - Capacity for autonomous work and decision making.
• CT4 - Ability for searching, analysing and interpreting different information sources in distinct languages (preferably English).

-Classes and seminars. Multimedia presentations and proposal of exercises/case studies to support the conceptual development of the program.

-Practical activities. Laboratory (equipment and processes for functional and structural genomic analysis), bioinformatics (analysis and management of genomic and transcriptomic sequences, genetic and comparative mapping, genome mining, differential gene expression analysis from RNAseq data).
Practical classes will be held in USC-Campus Terra, Lugo.

-Tutorial support for solving doubts and support to achieve the proposed aims of the course.

ASSESMENT SYSTEM
Exam (60%); Practices (participation and utilization; 15%); realization of seminars (15%); attendance and participation (10%).

Presencial time: Classes (7 hours), seminars (3 h), practical activities (9 h).
Tutorial support (3 h). Exam realization and revision (2h)
Individual work: 51 h (study time, resolution of problems, preparation of seminars/works and exam).
Total time: 75 h.

Attendance to expositive and interactive classes, practical sessions and seminars.
Participate in classes. Study regularly.
Consult questions about the class presentations and guides to support practical activities.
Consult the recommended literature.
Use the tutorial support and.