Irakasgaiaren azalpena eta testuingurua

Genomic research is a powerful tool to provide new knowledge on the demographic and adaptation of marine resources, to support for conservation management and ecosystem health protection.



Seventy-one percent of the earth’s surface is covered by ocean which contains almost 80% of the world’s phyla. In times of overfishing and climate change, marine resources are extremely vulnerable.



The marine environment is dominated by microorganisms from the three domains of life, namely Archaea, Bacteria and Eukarya, being responsible for up to 98% of marine primary productivity and playing key roles in marine food webs as well as in carbon and energy cycles. The unprecedented microbial diversity found on marine realm represents a challenge for the understanding of and exploitation of the biology and biochemistry of the ocean environment. Furthermore, the vast majority of the world’s fish stocks have already collapsed. In this fragile context, the need to drive fisheries towards sustainability has become a priority.



AIM



The course aims to initiate students into population genomic and metagenomic research in the marine world by exploring current research cases, understanding of cutting-edge lab technologies, building bioinformatics/biostatistic skills.

Irakasgaia ikastean lortuko diren emaitzak

At the end of the Unit, student should be able to apply



-Population genomic approaches to survey patterns of variation within and among marine fish and shellfish populations.



-Metagenomic/metabarcoding approaches to study complete communities directly in their natural environments and estimate its abundance and diversity

Ohiko deialdia: orientazioak eta uko egitea

• ATTENDANCE IS COMPULSORY. If students have to miss a class it is mandatory to get in contact with the teacher previously.

• Proactive participation in the activities, practical and oral sessions, will be evaluated

• MARINE POPULATION GENOMICS topic will be evaluated through a test after the formal lecture and an individual report should be conducted following completion of the computer practices (50% of the total grade)

• METAGENOMICS topic will be evaluated through a report following completion of the computer practices (50% of the total grade).



(The report has to be written in scientific format, and should explain what you did in your computer practices, what you learned, and what the results meant. Thus, argument, research problem statement, methodology and presentation and expression will be evaluated.

Ezohiko deialdia: orientazioak eta uko egitea

The final grade will be established in the same way as in the ordinary call, or in exceptional situations, the evaluation system will be established with the student.

Irakasgai-zerrenda

The course is taught using

1- Formal lectures (16h) to provide a lively and up-to-date overview of each topic. Case studies from ongoing projects will be illustrated.

2- Computer based exercises (18 h) for each topic to train the students into bioinformatics skills. Guided lectures and Individual work.





Programme (Topics)



0. Essentials of Genomics

1. Population genomics in non-model organisms

2. Metabarcoding /Metagenomics



0. ESSENTIALS OF GENOMICS (4h)



- Understanding Genomes

- Next Generation Sequencing methods

- DNA Variation:

• Marker discovery

•. DNA Barcoding

• QTL



1. MARINE POPULATION GENOMICS (18 h)



BASIC PRINCIPLES OF FISH POPULATION GENETICS (4h)



- The stock concept

- Genetics and fisheries management.

- Population genetics: Genes and genotypes, polymorphism and heterozygosity, H-W equilibrium, factors affecting allelic and genotypic frequencies.



MOLECULAR MARKERS APPLICATION IN FISHERIES AND AQUACULTURE (4h)



- Molecular markers and polymorphism

- Genetic and genomic applications in fisheries: Attributes of harvested species, impact of fishing, biosecurity, post harvest regulation

- Genetic and genomic applications in aquaculture: Marker Assisted Selection (MAS), parentage-based tagging, genotype-phenotype association.



UNIX INTRODUCTION: (2 h)



- Basic introduction to the Operative System UNIX (GNU/Linux)

- UNIX command line. Access a computer remotely

- Navigating the file system. Directory and file handing

- Output redirection (pipelines)

- File manipulation

- Loops and conditionals

- Scripting



COMPUTER PRACTICE: TUTORIAL (4h)



- A TUTORIAL with step by step commands will be provided to explore different softwares for statistical analysis mainly through the command line: ADMIXTURE, BCFtools, BWA, FreeBayes, GATK, PLINK, psmc, RStudio, VCFools.



COMPUTER PRACTICE: Exercise dataset (4h)



- A SNPs dataset from a real research work will be provided to the students to be analyzed following the methodology previously taught in the Tutorial classes.



2. METAGENOMICS (12 h)



BASIC CONCEPTS (2h)



- Definitions and overview of methodologies for marine organisms’ identification (bacteria and eucaryotes)

- Limitations and advantages of traditional and DNA based methodologies from complex communities



APPLICATIONS (2h)



Showcasing real studies:

- Bacterial diversity across the globe: The Earth Microbiome Project (EMP)

- Marine and estuarine community assessment studies: Tara Ocean, Malaspina, invasive species identification, harmful algae bloom detections etc.

- Marine food webs: Diet characterization



COMPUTER PRACTICE: TUTORIAL using QIIME2 (4 h)



- Overview of Qiime2: main commands and data visualization

- Statistical analysis: alpha-beta diversity, PCOA, anova, adonis…

- A step by step guide of commands will be provided to the student to follow a metagenomic data analysis pipeline, from sequence processing to statistical analysis



COMPUTER PRACTICE: Exercise dataset (4h)



- A dataset from a real research work will be provided to the students to be analyzed following the methodology previously taught in the Tutorial classes.

Bibliografia

Nahitaez erabili beharreko materiala

- The material to be used in the lectures will be provided through egela and /or forwarded by email to the ikasle accounts







- Online classes will be done by WebEx or a similar platform

Oinarrizko bibliografia

0) ESSENTIALS OF GENOMICS



- Ashton, D., Ritchie, P.A., Wellenreuther, M. (2017). Fifteen years of quantitative trait loci studies in fish:challenges and future directions. Molecular Ecology (26, 1465–1476). doi: 10.1111/mec.13965

- Quince, C., Walker, A., Simpson, J. et al. (2017). Shotgun metagenomics, from sampling to analysis. Nat Biotechnol 35, 833–844. https://doi.org/10.1038/nbt.3935

- Davey JW, Blaxter ML, (2010). RADSeq: next-generation population genetics Briefings in Functional Genomics, Volume 9, Issue 5-6, December 2010, Pages 416–423, https://doi.org/10.1093/bfgp/elq031





1) POPULATION GENOMICS



- Knutsen, et al. (2022). Combining population genomics with demographic analyses highlights habitat patchiness and larval dispersal as determinants of connectivity in coastal fish species. Molecular Ecology, 31(9), 2562-2577. https://doi.org/10.1111/mec.16415

- Benestan, L. (2019). Population Genomics Applied to Fishery Management and Conservation. In: Oleksiak, M., Rajora, O. (eds) Population Genomics: Marine Organisms. Population Genomics. Springer, Cham. https://doi.org/10.1007/13836_2019_66

- De Jode, A., David, R., Haguenauer, A., Cahill, A. E., Erga, Z., Guillemain, D., ... & Chenuil, A. (2019). From seascape ecology to population genomics and back. Spatial and ecological differentiation among cryptic species of the red algae Lithophyllum stictiforme/L. cabiochiae, main bioconstructors of coralligenous habitats. Molecular phylogenetics and evolution, 137, 104-113. https://doi.org/10.1016/j.ympev.2019.04.005

- Oleksiak, M.F. (2018). Adaptation Without Boundaries: Population Genomics in Marine Systems. In: Rajora, O. (eds) Population Genomics. Population Genomics. Springer, Cham. https://doi.org/10.1007/13836_2018_32

- Zhao, Y., Peng, W., Guo, H. et al. (2018). Population Genomics Reveals Genetic Divergence and Adaptive Differentiation of Chinese Sea Bass (Lateolabrax maculatus). Mar Biotechnol 20, 45–59 https://doi.org/10.1007/s10126-017-9786-0

- Pérez-Portela, R., Riesgo, A. (2018). Population Genomics of Early-Splitting Lineages of Metazoans. In: Oleksiak, M., Rajora, O. (eds) Population Genomics: Marine Organisms. Population Genomics. Springer, Cham. https://doi.org/10.1007/13836_2018_13

- Hohenlohe, P.A., Hand, B.K., Andrews, K.R., Luikart, G. (2018). Population Genomics Provides Key Insights in Ecology and Evolution. In: Rajora, O. (eds) Population Genomics. Population Genomics. Springer, Cham. https://doi.org/10.1007/13836_2018_20



2. METAGENOMICS

- Keck, F., Blackman, R.C., Bossart, R., Brantschen, J., Couton, M., Hürlemann, S., Kirschner, D., Locher, N., Zhang, H., Altermatt, F., (2022). Meta-analysis shows both congruence and complementary of DNA and eDNA metabarcoding to traditional methods for biological community assessment. Mol. Ecol.Vol. 31 (6): 1820-1835, doi:10.1111/MEC.16364.

- Bruce, K., Blackman, R., Bourlat, S. J., Hellström, A. M., Bakker, J., Bista, I., & Deiner, K. (2021). A practical guide to DNA-based methods for biodiversity assessment. Advanced Books, 1, e68634. https://doi.org/10.3897/ab.e68634

- Aylagas, E., Borja, Á., Muxika, I., & Rodríguez-Ezpeleta, N. (2018). Adapting metabarcoding-based benthic biomonitoring into routine marine ecological status assessment networks. Ecological Indicators, 95, 194– 202. https://doi.org/10.1016/j.ecolind.2018.07.044

- Aguirre, M., et al. (2017). Unraveling the environmental and anthropogenic drivers of bacterial community changes in the estuary of Bilbao and its tributaries. PlosOne. 12(6):e0178755

- Albaina, A. et al. (2016). 18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species. Ecology and Evolution. 6-6, pp. 1809-1824.

- Cristescu, M.E. (2014) From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity. Trends in Ecology & Evolution. 29, 10, 566-571

- Pompanon et al. (2012) Who is eating what: diet assessment using next generation sequencing. Molecular Ecology 21, 1931–1950

Gehiago sakontzeko bibliografia

idem

Aldizkariak

Taberlet, P., Bonin, A., Zinger, L., & Coissac, E. (2018). Environmental DNA: For biodiversity research and monitoring. Oxford, UK: Oxford University Press. https://doi.org/10.1093/oso/9780198767220.001. 0001

Estekak

-Linux Tutorial



https://ryanstutorials.net/linuxtutorial/







-R Tutorial



https://www.statmethods.net/r-tutorial/index.html/







-454 sequencing



https://youtu.be/KzdWZ5ryBlA







-Next generation sequencers



http://genetika08-09.blogspot.com/