Item

Abstract

Mesodinium rubrum is a distinctive marine microbial eukaryote associated with some of the largest red tides on Earth. M. rubrum captures, redistributes and harnesses the plastids, mitochondria and nucleus of the cryptophyte algae Teleaulax amphioxeia. We obtained draft somatic (~191 Mbp) and germline (~347 Mbp) genome assemblies for M. rubrum using nuclear flow sorting. Remarkably, we could not detect the defining eukaryotic genomic sequence feature — spliceosomal introns — in either genome, nor most of the necessary spliceosomal ncRNAs and proteins. The key proteins for nonsense-mediated decay of aberrantly spliced mRNAs, Upf1, Upf2 and Upf3 also appear absent. In contrast, one kind of non-spliceosomal intron has been retained in M. rubrum’s standard tyrosine tRNA genes, as have ribosomal RNA ITS sequences, consistent with known functional roles for both noncoding sequences in other eukaryotes. Furthermore, M. rubrum’s germline genome contains thousands of internally eliminated sequences (IESs): intron analogs which are spliced out of DNA during germline to somatic genome development. As far as we are aware, the only other eukaryotic genomes reported without spliceosomal introns are extremely reduced (< 10 Mb), belonging to an intracellular parasite and a vestigial endosymbiont nucleus (nucleomorph). Contrary to the popular notion that alternative splicing is selectively advantageous, observations in the M. rubrum lineage fit the idea that no spliceosomal intron provided an appreciable benefit like the non-spliceosomal tyrosine tRNA intron; thus all spliceosomal introns have been lost.