Generalities
Diatoms are one of the most significant groups of phytoplankton. These photosynthetic eukaryotes are key organisms for monitoring marine resources and predicting climate change. They also allows a better understanding of some evolutionary mechanisms, as their genomes results from a fusion of three genomes derived from their ancestors. In addition, they have multiple applications in biotechnology: in nanotechnology for their silica, as feed in aquaculture and as a biofactory for the production of molecules of interest such as omega-3 fatty acids, as well as biofuels. However, little is known about the biology of diatoms.
The complete sequencing of Phaeodactylum tricornutum (P. tricornutum) genome gives insights to expand our knowledge of the biology of diatoms. In addition, knowledge about P. tricornutum genes will promote the use of this organism as a potential cell for expressing the genes of other brown algae of interest to the industry.
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- Phaeodactylum tricornutum
- Name: Phaeodactylum tricornutom
- Phylogenetic classification: diatom (heterokonte), family Phaeodactylaceae
- Sequenced genome and epigenome
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Genome size: about 27,4 Mbp.
Number of genes predicted: 12,233.
Reproduction
Life cycle: one division per day.
Possible cycle synchronization.
Sexual reproduction never observed in culture.
Diatoms have an essentially diplophasic life cycle. Diploid cells multiply by mitosis for several months or years. However, at each cell division, one of the two daughter diatoms is smaller than the initial diatom, while the other daughter is about the same size. Thus, during successive divisions, smaller diatoms appear and one of the lineages of descendants decreases in size with each generation. This decrease on size does not continue indefinitely: below a definite threshold (30% of the initial size), these cells start meiosis and produce gametes. The gamete fusion zygote (auxospore) grows to the maximum size specific to the species or population.
Tools
- cDNA libraries (130,000), small RNA libraries (240,000)
- Routine genetic transformation by biolistics, conjugation and electroporation
- Gateway™, uLoop vector kits
- Double hybride libraries
- Tools for transcriptomic and epigenetic analyses
- RNAi, CRISPR/Cas9 gene silencing
- Bioinformatics: genome and epigenome browser and digital gene expression database
Databases
Genomic database:
http://genome.jgi-psf.org/Phatr2/Phatr2.home.html
Transcriptomic and epigénomic database:
https://protists.ensembl.org/Phaeodactylum_tricornutum/Info/Index
Infrastructures
- UMR 8197 Institut de Biologie de l’Ecole normale supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL - équipe de Chris Bowler, Génomique des Plantes et Algues
- http://www.ibens.ens.fr/?rubrique36
- Paris
- UMR7141 Biology and Light-sensing in Microalgae, Institut de Biologie Physico-Chimique - équipe d'Angela FALCIATORE
- http://www.ibpc.fr/UMR7141/en/home/
- angela.falciatore@ibpc.fr
- Paris
- Institut National des Sciences Appliquées de Toulouse - équipe Biologie synthétique chez les microalgues(INSA) - équipe de Faiza DABOUSSI
- http://www.toulouse-biotechnology-institute.fr/fr/la_recherche/pole-ingenierie-metabolique/biologie-synthetique-chez-les-microalgues.html
- fayza.daboussi@insa-toulouse.fr
- Versailles
- UFR Sciences Pharmaceutiques et biologiques - Laboratoire Mer, Molécules, Santé (EA 2160 MMS) - Université du Maine à Le Mans - équipe MIMMA (Benoit SCHOEFS)
- https://mms.univ-nantes.fr/
- benoit.schoefs@univ-lemans.fr
- Nantes
Experts
- Chris BOWLER
- cbowler@biologie.ens.fr
- UMR 8197 Institut de Biologie de l’Ecole normale supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris
Bibliography
- Articles
De Martino, A., Meichenin, A., Shi, J., Pan, K. and Bowler, C. Genetic and phenotypic characterisation of Phaeodactylum tricornutum (Bacillariophyceae) accessions. J. Phycol. 43: 992-1009 (2007).
Bowler C. et al. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature, 456: 239-244 (2008).
Bowler, C. and Falciatore, A. Genome of the Month: Phaeodactylum tricornutum. Trends Genet. 35:706-707 (2019).
Karas, B.J. et al. Designer diatom episomes delivered by bacterial conjugation. Nat. Commun. 6, 6925 (2015).
Nymark, M. et al. A CRISPR/Cas9 system adapted for gene editing in marine algae. Sci. Rep. 6, 24951 (2016).
Rastogi, A. et al. Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms. Sci. Rep. 8, 4834 (2018).
Serif, M. et al. One-step generation of multiple gene knock-outs in the diatom Phaeodactylum tricornutum by DNA-free genome editing. Nat. Commun. 9, 3924 (2018).
- Ressources web