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.

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S1 Fig. Additional phenotypic comparison between the native TisoArg and the domesticated strain TisoS2M2 in 2019.
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S2 Fig. Alignment of ONT long reads supporting a TE deletion event in TisoS2M2 with heterozygosity.
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S3 Fig. Violin plot of the length distribution of specific TE insertions in TisoArg and TisoS2M2 supported by short reads and long reads.
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S4 Fig. Sequence structures of the TE families Tc1-Mariner/Luffy, hAT/Ace, and hAT/Shanks.
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S5 Fig. Alignment of ONT long reads supporting TE indels in TisoS2M2 that may impact two candidate genes associated to lipid GO term.
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S1 Data. Comparison of the lipid contents and growth rates between TisoArg and TisoS2M2 in 2019.
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S2 Data. List of shared and specific SNPs between TisoArg and TisoS2M2, and predictions of their impacts on genes.
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S3 Data. Pipeline used to predict specific TE indels in TisoArg and TisoS2M2 using Illumina sequencing data.
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S4 Data. List of predictions of shared and specific indels detected by Pindel, Breakdancer, Mobster, and Sniffles in TisoArg and TisoS2M2.
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S5 Data. Predicted sequences by Pindel of the deletion events located at the contigs 93 and 142 of T. lutea.
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S6 Data. List of annotated TEs of Shanks and non-autonomous TEs of Ace.
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S7 Data. Detailed alignment of the ONT long reads supporting the prediction of a TE deletion with heterozygosity in TisoS2M2.
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S8 Data. List of genes predicted to be impacted by TE indels.
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How to cite
Berthelier Jérémy, Saint-Jean Bruno, Casse Nathalie, Bougaran Gael, Carrier Gregory (2023). Phenotype stability and dynamics of transposable elements in a strain of the microalga Tisochrysis lutea with improved lipid traits. Plos One. 18 (4). e0284656 (20p.).,

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