Genetic and phenotypic intra-species diversity of alga Tisochrysis lutea reveals original genetic structure and domestication potential

Type Article
Date 2024-02
Language English
Author(s) Carrier GregoryORCID1, Berthelier Jérémy2, Maupetit Agathe1, Nicolau ElodieORCID1, Marbouty Martial3, Schreiber Nathalie1, Charrier Aurelie1, Carcopino Clemence4, Leroi LauraORCID4, Saint-Jean BrunoORCID1
Affiliation(s) 1 : IFREMER, Unité Physiologie et Toxines des Microalgues Toxine, PHYTOX, Nantes, F-44311, France
2 : Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa, 904-0495, Japan
3 : Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris, F-75015, France
4 : IFREMER, Service de Bioinformatique de l’Ifremer, SeBiMER, Plouzané, F-29280, France
Source European Journal of Phycology (0967-0262) (Informa UK Limited), 2024-02 , Vol. 59 , N. 1 , P. 94-111
DOI 10.1080/09670262.2023.2249073
Keyword(s) Algae, antioxidant molecules, genetic structure, Haptophyta, intra-species diversity, Tisochrysis lutea

Oceanic phytoplankton species are generally composed of many strains, with intra-species diversity consisting of genetic and phenotypic variability. Despite its importance in ecological and biotechnological contexts, this intra-species diversity and variation among strains has been little studied. We investigated the intra-species diversity of the microalga Tisochrysis lutea, a haptophyte of the Isochrysidales order. Inter-strain diversity of T. lutea was studied because of the economic importance of the species as a feed in aquaculture and for antioxidant metabolite production, particularly fucoxanthin and other carotenoids, which have health benefits. We analysed Tara Ocean datasets which revealed that T. lutea was present in the Pacific, Atlantic and Indian Oceans but not in the Arctic or Austral Oceans. We next made phenotypic and genotypic comparisons of 11 strains of T. lutea from worldwide algal collections. All strains were cultivated in the same controlled conditions for one week, and several phenotypic traits were measured, notably antioxidant content. In parallel, the genomes of each strain were sequenced, and genetic variants identified. At the genetic and phenotypic levels, the strains were distinct from each other and our analysis revealed natural trait variations of interest in relation to further exploitation in domestication programmes. A large number of genetic variations were identified among the strains, but no major differences in genome size were observed. Moreover, limited genetic structure was observed among these strains, which could be a consequence of the complex life history of species within the Isochrysidales. Our study provides new knowledge on the intra-species diversity that should be considered in future environmental studies and breeding programmes.


Tisochrysis lutea is found in many parts of the world’s oceans.

T. lutea has high inter-strain phenotypic and genomic variation.

Genetic structure of strains from culture collections is limited.

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Publisher's official version 19 6 MB Open access
Softwares and tools used in this study 5 376 KB Open access
Supplemental material 179 KB Open access
Results analyze of genetic structuring with sNMF (Frichot et al., 2014) 4 210 KB Open access
Figures 1 MB Open access
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Carrier Gregory, Berthelier Jérémy, Maupetit Agathe, Nicolau Elodie, Marbouty Martial, Schreiber Nathalie, Charrier Aurelie, Carcopino Clemence, Leroi Laura, Saint-Jean Bruno (2024). Genetic and phenotypic intra-species diversity of alga Tisochrysis lutea reveals original genetic structure and domestication potential. European Journal of Phycology, 59(1), 94-111. Publisher's official version : , Open Access version :