Phenotype stability and dynamics of transposable elements in a strain of the microalga Tisochrysis lutea with improved lipid traits

Microalgal domestication is an expanding research field that aims to multiply and accelerate the potential of microalgae for various biotechnological purposes. We investigated the stability of improved lipid traits and genetic changes of a domesticated strain of the haptophyte Tisochrysis lutea, TisoS2M2, previously obtained by a mutation-selection improvement program. After 7 years of maintenance, TisoS2M2 still displayed improved lipid traits compared with the native strain, demonstrating that a mutation-selection improvement program is suitable for obtaining a domesticated strain with stable, improved phenotype over time. We identified specific genetic variations between the native and domesticated strains and focused on the dynamics of transposable elements (TEs). DNA transposons mainly caused specific TE indels of the domesticated strain TisoS2M2, and some specific TE indels may have impacted genes associated to the neutral lipid pathway. We revealed transposition events for TEs in T. lutea and discussed on the potential role of the improvement program on their activity

Additional file 4: of A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea

Sequences alignment of the peptides matching on the predicted TE proteins. This file contains the alignment of the peptides matching on the predicted proteins of the TIR/Mariner Luffy and the TIR/hAT Ace. (PDF 996 kb

Additional file 5: of A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea

List of non-inventoried sequences added to the databanks used by the pipeline PiRATE. This file lists the non-inventoried sequences added to the databanks used by the pipeline PiRATE, they belong to algae and cyanobacteria. (XLSX 23 kb

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

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. Highlights 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

Additional file 2: of A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea

Percentage of identity between copies of the expressed TE families. This file lists the percentage of identity between the TE copies of the 17 expressed TE families identified in the genome of Tisochrysis lutea. (XLSX 19 kb

Additional file 1: of A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea

Additional supporting information. This file contains the additional supporting figures, tables, results and materials and methods. (PDF 594 kb

Additional file 3: of A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea

Sequences alignment of TE copies of the TIR/Mariner Luffy family. This file contains the sequence alignment of the copies belonging to the TIR/Mariner Luffy described in the genome of Tisochrysis lutea. (PDF 17427 kb