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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 is relatively complete since most RNA-seq maps to it (91.44%) and most ribosomal proteins are present. M. rubrum thus appears to be a “free-living” ciliate that lost the spliceosome complex and introns. In contrast, organisms known to have lost most introns are typically obligate parasites, and the losses are related to genome minimization. The shortest known spliceosomal introns are characteristic of a different ciliate class from Mesodinium, Heterotrichea, in which most introns are 15 bp. Heterotrich ciliates also have substantially lower intron densities than ciliates with longer introns (e.g. Tetrahymena). If M. rubrum’s ancestor also possessed tiny introns, they could have progressively been lost, potentially occurring through exonization of those of length 3n. After the loss of the last introns, spliceosomal genes would no longer be needed and eventually be lost.
