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Abstract:
Mesodinium rubrum is a free-living mixotrophic ciliate that causes red tides in coastal regions. The ciliate steals plastids (kleptoplasty) after engulfing the cryptophyte alga Teleaulax amphioxeia, exploiting its photosynthesis. M. rubrum also steals the cryptophyte nucleus (karyoklepty), which remains transcriptionally active for an extended time. The stolen nucleus (kleptokaryon) is essential in regulating plastid activity. We sequenced and assembled the somatic and germline genomes from M. rubrum nuclei purified by fluorescence-activated flow sorting. We also generated poly(A) RNA-seq to guide protein-coding gene prediction. We observed no M. rubrum genes with spliceosomal introns. In contrast to other ciliates, we found M. rubrum lacks all spliceosomal snRNAs and most core spliceosomal proteins. We believe the M. rubrum somatic genome assembly is relatively complete since most RNA-seq maps to it (91.44%) and most ribosomal proteins are present. M. rubrum thus appears to be the first known “free-living” ciliate that has lost the spliceosome complex and introns. It also appears M. rubrum lacks the key protein involved in nonsense-mediated decay of mRNAs, Upf1, which surveys unspliced introns. In contrast, organisms known to have lost most introns are typically obligate parasites, and the losses are related to genome minimization. We consider multiple possible evolutionary forces that may have contributed to intron loss in M. rubrum.
