The Horizon 2020-funded project, ASSEMBLE Plus, has a goal stimulate excellence in European research in marine biology and ecology, thereby improving our knowledge- and technology-base for the blue economy, policy and education. Sitting within ASSEMBLE Plus are five research activities covering both applied and fundamental research. One such research activity is entitled “functional genomics”.

Technology has advanced in recent years to make it is quite easy to obtain whole genome or transcriptome data. Whilst much research is focused on this area, it is also vital to study specific functions of single genes to gain a full understanding of how genomes function. However, it is challenging to perform these kinds of functional studies in non-classical biological model organisms. ASSEMBLE Plus through its “functional genomics” research activity is responding to this call.

ASSEMBLE Plus partners have been performing single-gene function studies using up-to-date approaches such as CRISPR-Cas9. This activity has developed new and built upon existing knowledge relating to both, the genetic transformation and genome editing of selected model marine organisms, ranging from bacteria to metazoans (animals). 

Multiple publications and protocols are beginning to be generated by the project ensuring that these results are shared. To provide a broad overview, the findings are summarised below:

• Descriptions of the outcomes of the Assemble Plus project that have occurred over the course of the project, including:
  • Ectocarpus as a model organism to study diverse aspects of brown algal biology¹
  • Light regulation in marine Synechococcus cyanobacteria³
  • Tail regeneration in the Bahamas lancelet, Asymmetron lucayanum^4,5
  • Development of the nerve cord in the Neptune’s Heart Sea Squirt⁸
  • Identification of a new “cryptic species” - an animal that appears identical but differs genetically - Asymmetron rubrum¹¹
• Established links between genomic information and phenotypes of marine model species, including:
  • Amphioxus, a marine animal representing the earliest diverging evolutionary lineage of all chordates - animals that possess a dorsal notochord in at least some developmental stage, including vertebrates²
• Reference sets of carefully phenotyped or genotyped genetic resources of different marine organisms ranging from bacteria to metazoans, including:
  • Urochordates, cephalochordates, cnidarians, brown algae, cyanobacterias, etc
• The development of specific protocols for generation of genetic resources for a panel of emerging/prospective marine model organisms, including:
  • Generation of strains of the jellyfish species Clytia and maintain their whole life cycle in the laboratory⁶
  • Manipulation and transformation of amphioxus embryos⁷
  • Transformation of marine Synechococcus cyanobacteria strains^9,10
  • Transformation protocols for different ascidian species

“Developing these techniques for a broad range of organisms might not have an obvious application now; however, they can be expected to have a long or midterm impact on society. We are looking at species that are representative of all different organisms from microorganisms to metazoans and so our findings can be adapted and applied by other labs for any organisms, and for different applications” said Hector Escrivá, the Work Package leader for Functional Genomics who is based at the Observatoire Océanologique de Banyuls-sur-Mer (OOB) in France.

The project anticipates that many more publications, datasets and protocols will be released as the project progresses. The protocols developed are for metazoans, macroalgae and microorganisms that represent strategically important resources for academia and also for industry (e.g. bio-actives for food, feed, pharmaceuticals and cosmetics). 

To stay up-to-date on the project’s progress, please join the ASSEMBLE Plus mailing list or contact the Work Package leader, Hector Escrivá (CNRS) for more information. A full list of ASSEMBLE Plus publications can be found at: /projects/assembleplus/results/publications

 

Funding

This project has received funding from the European Commission’s Horizon 2020 research and innovation programme under grant agreement No 730984 (ASSEMBLE Plus). This output reflects the views only of the author(s), and the European Commission cannot be held responsible for any use which may be made of the information contained therein. The project began in October 2017 and will run until September 2022. The project is coordinated by Sorbonne Université.

About ASSEMBLE Plus

Website: assembleplus.eu

Twitter: @ASSEMBLE_Plus

For press queries, please contact Mercedes Arjona (mercedes.arjona@sorbonne-universite.fr) 

References

1. Badis, Y., Scornet, D., Harada, M., Caillard, C., Godfroy, O., Raphalen, M., Gachon, C.M.M., Coelho, S.M., Motomura, T., Nagasato, C., and J.M. Cock (2021) Targeted CRISPR-Cas9-based gene knockouts in the model brown alga Ectocarpus. New Phytologist. doi: 10.1111/nph.17525.
2. Bertrand, S., Carvalho, J.E., Daug, A D., Matentzoglu, N., Daric, V., Yu, J.-K., Schubert, M., and H. Escrivá (2021) The Ontology of the Amphioxus Anatomy and Life Cycle (AMPHX). Frontiers in Cell and Developmental Biology, 9(992). doi: 10.3389/fcell.2021.668025.
3. Grébert, T., Nguyen, A.A., Pokhrel, S., Joseph, K.L, Ratin, M., Dufour, L., Chen, B., Haney, A.M., Karty, J.A., Trinidad, J.C., Garczarek, L., Schluchter, W.M., Kehoe, D.M, and F. Partensky (2021) Molecular bases of an alternative dual-enzyme system for light color acclimation of marine Synechococcus cyanobacteria. Proceedings of the National Academy of Sciences, 118 (9) e2019715118. doi: 10.1073/pnas.2019715118.
4. Holland, N.D., and I.M.L. Somorjai (2020^a) Tail regeneration in a cephalochordate, the Bahamas lancelet, Asymmetron lucayanum. Journal of Morphology. doi: 10.1002/jmor.21297.
5. Holland, N.D., and I.M.L. Somorjai (2020^b) Serial blockface SEM suggests that stem cells may participate in adult notochord growth in an invertebrate chordate, the Bahamas lancelet. EvoDevo, 11(1):22. doi: 10.1186/s13227-020-00167-6.
6. Lechable, M., Jan, A., Duchene, A., Uveira, J., Weissbourd, B., Gissat, L., Collet, S., Gilletta, L., Chevalier, S., Leclère, L., Peron, S., Barreau, C., Lasbleiz, R., Houliston, E., and T. Momose (2020) An improved whole life cycle culture protocol for the hydrozoan genetic model Clytia hemisphaerica. Biology Open, 9(11). doi: 10.1242/bio.051268.
7. Le Petillon, Y., Bertrand, S., and H. Escrivá (2020) Spawning Induction and Embryo Micromanipulation Protocols in the Amphioxus Branchiostoma lanceolatum. In: Sprecher S. (eds) Brain Development. Methods in Molecular Biology, vol 2047. Humana, New York, NY. doi: 10.1007/978-1-4939-9732-9_19
8. McDougall, A., Hebras, C., Gomes, I., and R. Dumollard (2021) Gene Editing in the Ascidian Phallusia mammillata and Tail Nerve Cord Formation Methods and Protocols. Methods in Molecular Biology, 2219. doi: 10.1007/978-1-0716-0974-3_13.
9. Ratin, M., Garczarek, L., Grébert, T., and C. Halouze (2019^a) Transformation of marine Synechococcus strains by conjugation [protocol]. ID: 27861.
10. Ratin, M., Garczarek, L., Grébert, T., and C. Halouze (2019^b) Transformation of marine Synechococcus strains by electroporation [protocol]. ID: 27854.
11. Subirana, L., Farstey, V., Bertrand, S., and H. Escrivá (2020). Asymmetron lucayanum: How many species are valid? PLOS ONE, 15(3): e0229119. doi: 10.1371/journal.pone.0229119.