Supporting data for "Limits to the control of sequestered cryptophytes in the marine ciliate Mesodinium rubrum"

The marine ciliate <i>Mesodinium rubrum</i> is famous for its ability to acquire and use chloroplasts and other cell organelles from some cryptophyte algal species. However, adjustments to the transcriptional activity of the cryptophyte prey as well as the ciliate host upon organelle sequestration remain poorly understood. We sequenced genomes and transcriptomes of free-swimming <i>Teleaulax amphioxeia</i>, as well as well-fed and starved <i>M. rubrum</i> in order to understand transcriptional changes upon sequestration under different food and light conditions. We found strong transcriptional rewiring of the cryptophyte nucleus upon sequestration, where 35% of the <i>T. amphioxeia</i> genes were significantly differentially expressed within well-fed <i>M. rubrum</i>. Qualitatively, 68% of all genes expressed within well-fed <i>M. rubrum</i> originated from <i>T. amphioxeia</i>. Well-fed and prey-starved <i>M. rubrum</i> contributed ~48 and ~11%, respectively, to the global transcriptome. <i>M. rubrum</i> contains no photosynthesis related genes itself, but considerable transcriptional control of the acquired cryptophyte. However, this control is not fine-tuned, as light dependent transcriptional changes that are found in free-swimming <i>T. amphioxeia</i> got lost after sequestration. Even when exposed to different prey concentrations, <i>M. rubrum</i> can only force one expression pattern out of its acquired cryptophyte organelles. This tertiary endosymbiosis system functions for several weeks when deprived of prey. After this time, the ciliate dies if not supplied with fresh prey cells. <i>M. rubrum</i> represents one evolutionary way of the acquiring photosystems from its algal prey.<br>Files provided in this dataset: 1. Tamp.rna.asm.fasta.gz: gene assembly of <i>Teleaulax amphioxeia</i> in fasta format 2. Tamp.rna.asm.fasta.gz.md5sum: MD5 checksum for file "Tamp.rna.asm.fasta.gz" 3. Mrub.rna.asm.fasta.gz: gene assembly of <i>Mesodinium rubrum</i> in fasta format 4. Mrub.rna.asm.fasta.gz.md5sum: MD5 checksum for file "Mrub.rna.asm.fasta.gz"5. Scripts used during data analyses