Abstract
<jats:title>Abstract</jats:title> <jats:p> <jats:italic>Mesodinium rubrum</jats:italic> , a marine microbial eukaryote associated with some of the largest red tides on Earth, has the remarkable ability to commandeer the plastids, mitochondria and nuclei from the alga <jats:italic>Teleaulax amphioxeia</jats:italic> for photosynthesis. Here we report analyses of assemblies of <jats:italic>M. rubrum</jats:italic> ’s two nuclear genomes. Unexpectedly, <jats:italic>M. rubrum</jats:italic> appears to have completely lost its spliceosomal introns, most spliceosomal molecules, and the key genes for an intron splicing-associated process, Nonsense-mediated mRNA Decay (NMD). In contrast, non-spliceosomal tRNA introns have been retained, as have thousands of intron analogs spliced out of DNA during ciliate somatic genome development (internal eliminated sequences - IESs). Intron-containing genes, especially from intron-rich species like <jats:italic>T. amphioxeia</jats:italic> , would likely be defunct if horizontally transferred to a host without a spliceosome like <jats:italic>M. rubrum</jats:italic> , and thus we propose that introns can be a roadblock to progressive endosymbiotic genomic integration. </jats:p>