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 change of a domesticated strain of the haptophyte Tisochrysis lutea, TisoS2M2, previously obtained by a mutation-selection improvement program.  from the native wild-type stain TisoArg. We explored the genetic changes of the domesticated strain compared to the native strain by focusing on the dynamics of transposable elements by generating an improved TE annotation (v2) and generating Illumina and Oxford Nanopore sequencing technologies. The new TE annotation v2 is based on the genome assembly v2: https://doi.org/10.17882/52231 .