Real time mobilization of a novel diatom Mutator-Like Element (MULE) transposon to inactivate the uridine monophosphate synthase (UMPS) locus in Phaeodactylum tricornutum

Abstract

Diatoms are photosynthetic unicellular microalgae that drive global ecological phenomena in the biosphere and are emerging sustainable feedstock for an increasing number of industrial applications. Diatoms exhibit enormous taxonomic and genetic diversity, which often result in peculiar biochemical and biological traits. Transposable elements (TE) represent a substantial portion of diatom genomes and have been hypothesized to exert a relevant role in enriching genetic diversity and centrally contribute to genome evolution. Here, through long-read whole genome sequencing, we identified a novel Mutator-Like Element (MULE) in the model diatom Phaeodactylum tricornutum, and we report the direct observation of its mobilization within the course of one single laboratory experiment. Under selective conditions, this novel TE inactivated the uridine monophosphate synthase (UMPS) gene of P. tricornutum, one of the two only endogenous genetic loci currently targeted for selectable auxotrophy in functional genetics and genome editing applications. We report the first, real-time observation of the mobilization of a transposon in diatoms that possesses novel peculiar features. These include the combined presence of a MULE transposase domain with Zinc finger, SWIM-type domains, and of a diatom-specific E3 ubiquitin ligase of the zinc finger UBR type, which indicate a novel mobilization mechanism. Our findings provide new elements for the understanding of the role of TEs in diatom genome evolution and in the enrichment of intraspecific genetic variability. Ultimately, this raises relevant concerns on the targeting of loci such as UMPS as selectable markers for functional genetics and biotechnological applications in diatoms. Significance StatementWe identified a novel DNA transposon in the diatom Phaeodactylum tricornutum. This new Mutator-Like Element encodes a transposase and a diatom-specific E3 ubiquitin ligase, which suggest a novel mobilization mechanism. We documented independent insertions in real-time, which spontaneously inactivated the uridine monophosphate synthase (UMPS) locus, a common selectable marker. We provide new insights on the role of transposons in diatom genome dynamics and evolution and on the unsuitability of UMPS as selection locus in diatoms.