Cryptophyta

Cryptophyta (commonly known as cryptomonads or cryptophytes, class Cryptophyceae, from the Ancient Greek kryptos, "hidden," and phyton, "plant") is a phylum of unicellular, asymmetric biflagellate algae (~200 described species across marine, estuarine, and freshwater habitats, alongside the aplastidic phagotrophic sister clade Goniomonadea and deep-branching Kathablepharida) affiliated with the Cryptista supergroup. Cryptomonads are ecologically vital components of cold-water, deep-chlorophyll-maximum, and ice-covered lacustrine and coastal phytoplankton communities because their high content of polyunsaturated fatty acids (EPA and DHA) and absence of mineralized cell walls make them the highest-quality nutritional food source for herbivorous microzooplankton and copepods.

In evolutionary biology, Cryptophyta is famous as living proof of eukaryotic secondary endosymbiosis ("a cell inside a cell inside a cell"):

1. Retention of the Vestigial Red Algal Nucleus (The Nucleomorph): Whereas stramenopiles (Phaeophyceae, Bacillariophyta) and haptophytes (Haptophyta) fully eliminated the nucleus of their engulfed red algal endosymbiont, photosynthetic cryptomonads (Guillardia theta, Rhodomonas salina, Cryptomonas, Chroomonas) retain the miniature, membrane-bounded, three-chromosome nucleus of the engulfed red alga—the nucleomorph—trapped inside the periplastidial space between the inner and outer pairs of plastid membranes!
2. Soluble Biliproteins Packed Inside the Thylakoid Lumen: Cryptomonads dismantled the ancestral bulky red-algal phycobilisome antenna on the stromal surface of the thylakoid and instead relocated one single dimeric phycobiliprotein (phycoerythrin or phycocyanin) directly into the intralumenal space of paired thylakoids.
3. Ballistic Ribbon Ejectisomes: Lining the ventral furrow/gullet and cell periphery are coiled, bipartite protein ribbons (ejectisomes) that fire outward in milliseconds to propel the cell backward away from predators.

Because a photosynthetic cryptomonad (Guillardia theta) preserves both its own eukaryotic host compartments and the reduced cytoplasmic/nuclear compartments of its engulfed red algal endosymbiont, every single cell of Guillardia theta maintains four distinct, replicationally independent DNA genomes and four separate ribosome populations:

*(Remarkably, only one other group of organisms in nature—the chlorarachniophyte amoebae [such as Bigelowiella natans in Rhizaria], which independently engulfed a green alga—retains a convergent three-chromosome nucleomorph!)*

Sequencing of the 551-kb nucleomorph genome of Guillardia theta (Douglas et al., 2001) alongside Hemiselmis andersenii (572 kb, with zero introns across the entire genome!), Chroomonas mesostigmatica (703 kb), and the colorless osmotroph Cryptomonas paramecium (487 kb) revealed the most gene-dense eukaryotic chromosomes ever discovered:

1. Three Mini-Chromosomes Capped by Inverted rDNA Subtelomeres: All known cryptomonad (and chlorarachniophyte) nucleomorph genomes are organized into three linear chromosomes (each small enough to be resolved as a discrete band by pulsed-field gel electrophoresis!). Each chromosome end is capped by novel telomeric repeats ([AG]7AAG6A in G. theta) promptly adjacent to an inverted subtelomeric ribosomal RNA operon (18S–5.8S–28S rDNA).
2. 1 Gene per ~1,000 Base Pairs and Overlapping Transcription: Non-coding intergenic spacers have been whittled down to an average of just 10 to 50 base pairs (with many adjacent genes mechanically overlapping so that the 3′ UTR or stop codon of one gene lies inside the coding sequence of its neighbor!), while spliceosomal introns are either fully eradicated (0 introns in Hemiselmis) or shrunk to tiny 42–52 bp miniature introns (17 introns in G. theta).
3. Why Has the Nucleomorph Survived Without Being Lost?: Of the ~460–500 genes retained on the nucleomorph chromosomes, nearly 95% encode "housekeeping" proteins required specifically to replicate, transcribe, splice, and translate the nucleomorph's own genes inside the periplastidial space! However, every cryptomonad nucleomorph retains ~30 essential plastid-targeted protein genes—most notably the chloroplast cell-division protein FtsZ, the plastid chaperonin Cpn60 (GroEL), and rubredoxin. Until all ~30 of these plastid-maintenance genes are successfully copied to the host nucleus and acquire bipartite SELMA (Symbiont-Specific ERAD-Like Machinery) transit peptides to cross all four plastid membranes, the cryptomonad cell cannot survive without its nucleomorph.

In red algae (Rhodophyta) and cyanobacteria, light is harvested by giant (3–6 MDa) dome-shaped phycobilisomes sitting on the outer stromal surface of single unstacked thylakoids. Cryptomonads fully reorganized this light-harvesting architecture to exploit dim blue-green light (480–570 nm) deep in the water column:

1. Paired Thylakoids Stuffed with Soluble Phycobiliprotein Dimers: Cryptomonad thylakoids are arranged in loose pairs (two-thylakoid stacks) containing membrane-embedded chlorophyll a / c₂ proteins (and the unique acetylenic carotenoid alloxanthin). The entire aqueous lumen inside each thylakoid sac is densely packed with a single species-specific soluble phycobiliprotein heterotetramer (α₁α₂ββ, ~55 kDa)—either red Cryptomonad Phycoerythrin (Cr-PE 545, Cr-PE 555, or Cr-PE 566) or blue-green Cryptomonad Phycocyanin (Cr-PC 645, Cr-PC 630, or Cr-PC 569).
2. Chimeric α-Subunits and Quantum Coherence at Physiological Temperatures: While the β-subunit of cryptomonad phycobiliprotein is inherited from the red algal plastid genome, the smaller α-subunit is encoded in the host nucleus as a multigene family that evolved de novo! In 2010, Gregory Scholes, Elisabetta Collini, and colleagues used two-dimensional electronic photon-echo spectroscopy on purified Cr-PE 545 (from Rhodomonas CS24) and Cr-PC 645 (from Chroomonas CCMP270) at room temperature (294 K) to demonstrate long-lived (>400 femtosecond) electronic quantum coherence among the open-chain tetrapyrrole bilin chromophores (dihydrobiliverdin and phycoerythrobilin), enabling near-100% excitation-energy transfer efficiency to Photosystem II and Photosystem I.
3. Kleptoplastidy by Mesodinium rubrum and Dinophysis: Because cryptomonad plastids and nucleomorphs are so transcriptionally self-sufficient, the marine planktonic ciliate Mesodinium rubrum (and in turn the diarrhetic-shellfish-poisoning dinoflagellate Dinophysis, which eats Mesodinium) steals living plastids and nucleomorphs (kleptoplastidy) from Teleaulax and Geminigera cryptomonads—keeping the stolen cryptomonad nucleus and nucleomorph transcriptionally active inside the ciliate for weeks to power "red water" photosynthetic ciliate blooms!

• The Proteinaceous Periplast: Rather than a cellulosic wall, cryptomonads are bounded by a flexible periplast consisting of rectangular or hexagonal proteinaceous plates (composed of the glycine-rich protein jectin / periplastin) sandwiched promptly beneath (inner periplast component) and above (surface periplast component) the plasma membrane, anchored at the intramembrane particle seams.
• Bipartite Coiled-Ribbon Ejectisomes: Two rows of large ejectisomes (~0.5–1.0 μm diameter) line the anterior ventral furrow-gullet complex, while dozens of smaller ejectisomes sit at the corners of every periplast plate. Each ejectisome consists of two tightly wound, spring-loaded helical protein ribbons (a large basal ribbon and a smaller apical ribbon sitting at 90°) enclosed in a vesicle. Upon mechanical touch by a grazing copepod or sudden osmotic/chemical shock, influx of Ca²⁺ triggers instantaneous hydration and uncoiling of both ribbons into a 15- to 40-μm-long hollow tube with a hooked tip inside <10 milliseconds—firing like a harpoon that propels the cryptomonad backward in a rapid zigzag escape jump of 10 to 20 body lengths!

1. Douglas, S., Zauner, S., Fraunholz, M., Beaton, M., Penny, S., Deng, L. T., ... & Maier, U. G. (2001). The highly reduced genome of an enslaved algal nucleus. Nature, 410(6832), 1091–1096. Google Scholar
2. Curtis, B. A., Tanifuji, G., Burki, F., Gruber, A., Irimia, M., Maruyama, S., ... & Archibald, J. M. (2012). Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature, 492(7427), 59–65. Google Scholar
3. Collini, E., Wong, C. Y., Wilk, K. E., Curmi, P. M., Brumer, P., & Scholes, G. D. (2010). Coherently wired light-harvesting in photosynthetic marine algae at ambient temperature. Nature, 463(7281), 644–647. Google Scholar
4. Hoef-Emden, K., & Archibald, J. M. (2017). Cryptophyta (Cryptomonads). In Handbook of the Protists (pp. 851–891). Springer. Google Scholar

• Endosymbiotic Theory
• Photosynthesis
• Haptophyta
• Phaeophyceae
• Dinoflagellates