The marine ciliate Mesodinium rubrum is famous for its ability to acquire and exploit chloroplasts and other cell organelles from some cryptophyte algal species. We sequenced genomes and transcriptomes of free-swimming Teleaulax amphioxeia, as well as well-fed and starved M. rubrum in order to understand cellular processes upon sequestration under different prey and light conditions. From its prey, the ciliate acquires the ability to photosynthesize as well as the potential to metabolize several essential compounds including lysine, glycan, and vitamins that elucidate its specific prey dependency. M. rubrum does not express photosynthesis-related genes itself, but elicits considerable transcriptional control of the acquired cryptophyte organelles. This control is limited as light-dependent transcriptional changes found in free-swimming T. amphioxeia got lost after sequestration. We found strong transcriptional rewiring of the cryptophyte nucleus upon sequestration, where 35% of the T. amphioxeia genes were significantly differentially expressed within well-fed M. rubrum. Qualitatively, 68% of all genes expressed within well-fed M. rubrum originated from T. amphioxeia. Quantitatively, these genes contributed up to 48% to the global transcriptome in well-fed M. rubrum and down to 11% in starved M. rubrum. This tertiary endosymbiosis system functions for several weeks, when deprived of prey. After this point in time, the ciliate dies if not supplied with fresh prey cells. M. rubrum represents one evolutionary way of acquiring photosystems from its algal prey, and might represent a step on the evolutionary way towards a permanent tertiary endosymbiosis.
Subscribe to Journal
Get full journal access for 1 year
only $41.58 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
The raw sequencing reads produced in this study are deposited in the CNGB Nucleotide Sequence Archive (CNSA) [62, 63] with accession number CNP0000925. The nucleotide sequences and functional annotations of the reference gene sets for Teleaulax amphioxeia and Mesodinium rubrum are deposited in the figshare repository under the link 10.6084/m9.figshare.12360836.
Altenburger A, Blossom HE, Garcia-Cuetos L, Jakobsen HH, Carstensen J, Lundholm N, et al. Dimorphism in cryptophytes—the case of Teleaulax amphioxeia/Plagioselmis prolonga and its ecological implications. Sci Adv. 2020;6:eabb1611.
Burki F, Kaplan M, Tikhonenkov DV, Zlatogursky V, Minh BQ, Radaykina LV, et al. Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista. Proc R Soc B. 2016;283:20152802.
Cavalier-Smith T. Membrane heredity and early chloroplast evolution. Trends Plant Sci. 2000;5:174–82.
Douglas SE, Murphy CA, Spencer DF, Gray MW. Cryptomonad algae are evolutionary chimaeras of two phylogenetically distinct unicellular eukaryotes. Nature. 1991;350:148–51.
Cavalier-Smith T. Principles of protein and lipid targeting in secondary symbiogenesis: euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree. J Eukaryot Microbiol. 1999;46:347–66.
Curtis BA, Tanifuji G, Burki F, Gruber A, Irimia M, Maruyama S, et al. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature. 2012;492:59–65.
Douglas S, Zauner S, Fraunholz M, Beaton M, Penny S, Deng LT, et al. The highly reduced genome of an enslaved algal nucleus. Nature. 2001;410:1091–6.
Hoef-Emden K, Archibald JM. Cryptophyta (Cryptomonads). In: Archibald JM, Simpson AGB, Slamovits CH, editors. Handbook of the protists. Cham: Springer International Publishing; 2017. p. 851–91.
Ward BA, Follows MJ. Marine mixotrophy increases trophic transfer efficiency, mean organism size, and vertical carbon flux. Proc Natl Acad Sci U S A. 2016;113:2958–63.
Herfort L, Peterson TD, Campbell V, Futrell S, Zuber P. Myrionecta rubra (Mesodinium rubrum) bloom initiation in the Columbia River estuary. Estuar Coast Shelf Sci. 2011;95:440–6.
Johnson MD, Beaudoin DJ, Laza-Martinez A, Dyhrman ST, Fensin E, Lin S, et al. The genetic diversity of Mesodinium and associated cryptophytes. Front Microbiol. 2016;7:2017.
Lindholm T. Mesodinium rubrum—a unique photosynthetic ciliate. Adv Aquat Microbiol. 1985;3:1–48.
Nowack EC, Melkonian M. Endosymbiotic associations within protists. Philos Trans R Soc B. 2010;365:699–712.
Johnson MD, Oldach D, Delwiche CF, Stoecker DK. Retention of transcriptionally active cryptophyte nuclei by the ciliate Myrionecta rubra. Nature. 2007;445:426–8.
Hansen PJ, Moldrup M, Tarangkoon W, Garcia-Cuetos L, Moestrup O. Direct evidence for symbiont sequestration in the marine red tide ciliate Mesodinium rubrum. Aquat Micro Ecol. 2012;66:63–75.
Kim M, Drumm K, Daugbjerg N, Hansen PJ. Dynamics of sequestered cryptophyte nuclei in Mesodinium rubrum during starvation and refeeding. Front Microbiol. 2017;8:1–14.
Nam SW, Park JW, Yih W, Park MG, Shin W. The fate of cryptophyte cell organelles in the ciliate Mesodinium cf. rubrum subjected to starvation. Harmful Algae. 2016;59:19–30.
Juel Hansen P, Fenchel T. The bloom-forming ciliate Mesodinium rubrum harbours a single permanent endosymbiont. Mar Biol Res. 2006;2:169–77.
Smith M, Hansen PJ. Interaction between Mesodinium rubrum and its prey: importance of prey concentration, irradiance and pH. Mar Ecol Prog Ser. 2007;338:61–70.
Matthew DJ, Diane KS. Role of feeding in growth and photophysiology of Myrionecta rubra. Aquat Micro Ecol. 2005;39:303–12.
Fenchel T, Hansen PJ. Motile behaviour of the bloom-forming ciliate Mesodinium rubrum. Mar Biol Res. 2006;2:33–40.
Gustafson DE, Stoecker DK, Johnson MD, Van Heukelem WF, Sneider K. Cryptophyte algae are robbed of their organelles by the marine ciliate Mesodinium rubrum. Nature. 2000;405:1049–52.
Peltomaa E, Johnson M. Mesodinium rubrum exhibits genus-level but not species-level cryptophyte prey selection. Aquat Micro Ecol. 2017;78:147–59.
Kim GH, Han JH, Kim B, Han JW, Nam SW, Shin W, et al. Cryptophyte gene regulation in the kleptoplastidic, karyokleptic ciliate Mesodinium rubrum. Harmful Algae. 2016;52:23–33.
Lasek-Nesselquist E, Wisecaver JH, Hackett JD, Johnson MD. Insights into transcriptional changes that accompany organelle sequestration from the stolen nucleus of Mesodinium rubrum. BMC Genom. 2015;16:805.
Chen Y, Chen Y, Shi C, Huang Z, Zhang Y, Li S, et al. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience. 2018;7:1–6.
Parekh S, Ziegenhain C, Vieth B, Enard W, Hellmann I. The impact of amplification on differential expression analyses by RNA-seq. Sci Rep. 2016;6:25533.
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29:644–52.
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013;8:1494–512.
Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28:3150–2.
Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22:1658–9.
Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017;14:417–9.
Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 2016;17:132.
Ondov BD, Starrett GJ, Sappington A, Kostic A, Koren S, Buck CB, et al. Mash screen: high-throughput sequence containment estimation for genome discovery. Genome Biol. 2019;20:232.
Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34:3094–100.
Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002;30:1575–84.
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–60.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–9.
Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011;27:2987–93.
Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31:3210–2.
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841–2.
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinform. 2008;9:559.
Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27–30.
Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, et al. GO::TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics. 2004;20:3710–5.
Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B (Stat Method). 1995;57:289–300.
Merico D, Isserlin R, Stueker O, Emili A, Bader GD. Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS ONE. 2010;5:e13984.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498–504.
Luo W, Brouwer C. Pathview: an R/Bioconductor package for pathway-based data integration and visualization. Bioinformatics. 2013;29:1830–1.
Allen JF, de Paula WBM, Puthiyaveetil S, Nield J. A structural phylogenetic map for chloroplast photosynthesis. Trends Plant Sci. 2011;16:645–55.
Qiu H, Lee Jun M, Yoon Hwan S, Bhattacharya D. Hypothesis: gene-rich plastid genomes in red algae may be an outcome of nuclear genome reduction. J Phycol. 2017;53:715–9.
Grzebyk D, Schofield O, Vetriani C, Falkowski PG. The mesozoic radiation of eukaryotic algae: the portable plastid hypothesis. J Phycol. 2003;39:259–67.
Hehenberger E, Gast RJ, Keeling PJ. A kleptoplastidic dinoflagellate and the tipping point between transient and fully integrated plastid endosymbiosis. Proc Natl Acad Sci USA. 2019;116:17934–42.
Onuma R, Hirooka S, Kanesaki Y, Fujiwara T, Yoshikawa H, Miyagishima S-Y. Changes in the transcriptome, ploidy, and optimal light intensity of a cryptomonad upon integration into a kleptoplastic dinoflagellate. ISME J. 2020;14:2407–23.
McFadden GI. Origin and evolution of plastids and photosynthesis in eukaryotes. Cold Spring Harb Perspect Biol. 2014;6:a016105.
Park MG, Kim M, Kim S. The acquisition of plastids/phototrophy in heterotrophic Dinoflagellates. Acta Protozool. 2014;53:39–50.
Johnson MD, Beaudoin DJ. The genetic diversity of plastids associated with mixotrophic oligotrich ciliates. Limnol Oceanogr. 2019;64:2187–201.
Kim M, Kim S, Yih W, Park MG. The marine dinoflagellate genus Dinophysis can retain plastids of multiple algal origins at the same time. Harmful Algae. 2012;13:105–11.
Tourancheau AB, Tsao N, Klobutcher LA, Pearlman RE, Adoutte A. Genetic code deviations in the ciliates: evidence for multiple and independent events. EMBO J. 1995;14:3262–7.
Heaphy SM, Mariotti M, Gladyshev VN, Atkins JF, Baranov PV. Novel ciliate genetic code variants including the reassignment of all three stop codons to sense codons in Condylostoma magnum. Mol Biol Evol. 2016;33:2885–9.
Johnson MD, Beaudoin DJ, Frada MJ, Brownlee EF, Stoecker DK. High grazing rates on cryptophyte algae in Chesapeake Bay. Front Mar Sci. 2018;5:1–13.
Guo X, Chen F, Gao F, Li L, Liu K, You L, et al. CNSA: a data repository for archiving omics data. Database. 2020;2020:baaa055.
Chen Fengzhen YL, Fan Yang, Lina Wang, Xueqin Guo, Fei Gao, Cong Hua, et al. CNGBdb: China National GeneBank DataBase. Hereditas. 2020;42:799–809.
This project was supported by the Danish Council for Independent Research (Grant number 4181–00484 to PJH), the Major scientific and technological projects of Hainan Province (ZDKJ2019011), the National Key Research and Development Program of China (2018YFC0308401), and the Carlsberg Foundation (2012_01_0515 to LG-C). We acknowledge the China National GeneBank (CNGB) for support with computing resources.
Conflict of interest
The authors declare that they have no conflict of interest.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
About this article
Cite this article
Altenburger, A., Cai, H., Li, Q. et al. Limits to the cellular control of sequestered cryptophyte prey in the marine ciliate Mesodinium rubrum. ISME J (2020). https://doi.org/10.1038/s41396-020-00830-9