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

Type Article
Date 2023-04
Language English
Author(s) Berthelier JérémyORCID1, 2, 3, Saint-Jean BrunoORCID4, Casse Nathalie2, Bougaran GaelORCID5, Carrier GregoryORCID4
Affiliation(s) 1 : Laboratory PBA, Ifremer, Nantes, France
2 : Laboratory of Biology of Organisms Stress Health Environment (BiOSSE), Le Mans University, Le Mans, France
3 : Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
4 : Laboratory PHYTOX GENALG, Ifremer, Nantes, France
5 : Laboratory PHYTOX PHYSALG, Ifremer, Nantes, France
Source Plos One (1932-6203) (Public Library of Science (PLoS)), 2023-04 , Vol. 18 , N. 4 , P. e0284656 (20p.)
DOI 10.1371/journal.pone.0284656
Abstract

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. 441 KB Open access
S2 Fig. Alignment of ONT long reads supporting a TE deletion event in TisoS2M2 with heterozygosity. 534 KB Open access
S3 Fig. Violin plot of the length distribution of specific TE insertions in TisoArg and TisoS2M2 supported by short reads and long reads. 148 KB Open access
S4 Fig. Sequence structures of the TE families Tc1-Mariner/Luffy, hAT/Ace, and hAT/Shanks. 600 KB Open access
S5 Fig. Alignment of ONT long reads supporting TE indels in TisoS2M2 that may impact two candidate genes associated to lipid GO term. 443 KB Open access
S1 Data. Comparison of the lipid contents and growth rates between TisoArg and TisoS2M2 in 2019. 25 KB Open access
S2 Data. List of shared and specific SNPs between TisoArg and TisoS2M2, and predictions of their impacts on genes. 10 MB Open access
S3 Data. Pipeline used to predict specific TE indels in TisoArg and TisoS2M2 using Illumina sequencing data. 2 146 KB Open access
S4 Data. List of predictions of shared and specific indels detected by Pindel, Breakdancer, Mobster, and Sniffles in TisoArg and TisoS2M2. 848 KB Open access
S5 Data. Predicted sequences by Pindel of the deletion events located at the contigs 93 and 142 of T. lutea. 2 113 KB Open access
S6 Data. List of annotated TEs of Shanks and non-autonomous TEs of Ace. 225 KB Open access
S7 Data. Detailed alignment of the ONT long reads supporting the prediction of a TE deletion with heterozygosity in TisoS2M2. 2 1 MB Open access
S8 Data. List of genes predicted to be impacted by TE indels. 42 KB Open access
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