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The cryptomonads (sometimes called cryptophytes)Barnes, Richard Stephen Kent (2001). The Invertebrates: A Synthesis. Wiley-Blackwell. p. 41. . are a superclass of algae, most of which have chloroplast. They are traditionally considered a division of algae among , under the name of Cryptophyta. They are common in freshwater, and also occur in marine and brackish habitats. Each cell is around 10–50 μm in size and flattened in shape, with an anterior groove or pocket. At the edge of the pocket there are typically two slightly unequal flagellum. Some may exhibit mixotrophy. They are classified as superclass Cryptomonada, which is divided into two classes: heterotrophic Goniomonadea and phototrophic Cryptophyceae. The two groups are united under three shared morphological characteristics: presence of a periplast, ejectisomes with secondary scroll, and mitochondrial cristae with flat tubules. Genetic studies as early as 1994 also supported the hypothesis that Goniomonas was sister to Cryptophyceae. A study in 2018 found strong evidence that the common ancestor of Cryptomonada was an autotrophic protist.
Except for the class Goniomonadea, which lacks plastids entirely, Nuclear genome sequence of the plastid-lacking cryptomonad Goniomonas avonlea provides insights into the evolution of secondary plastids and Cryptomonas paramecium (previously called Chilomonas paramecium), which has , cryptomonads have one or two chloroplasts. These contain a and c, together with and other pigments, and vary in color (brown, red to blueish-green). Each is surrounded by four membranes, and there is a reduced cell nucleus called a nucleomorph between the middle two. This indicates that the plastid was derived from a eukaryote symbiont, shown by genetic studies to have been a red alga. However, the plastids are very different from red algal plastids: phycobiliproteins are present but only in the thylakoid lumen and are present only as phycoerythrin or phycocyanin. In the case of Rhodomonas, the crystal structure has been determined to 1.63Å; and it has been shown that the alpha subunit bears no relation to any other known phycobiliprotein.
A few cryptomonads, such as Cryptomonas, can form stages, but readily escape the surrounding mucus to become free-living flagellates again. Some Cryptomonas species may also form immotile —resting stages with rigid cell walls to survive unfavorable conditions. Cryptomonad flagella are inserted parallel to one another, and are covered by bipartite hairs called mastigonemes, formed within the endoplasmic reticulum and transported to the cell surface. Small scales may also be present on the flagella and cell body. The mitochondrion have flat , and mitosis is open; sexual reproduction has also been reported.
One suggested grouping is as follows: (1) Cryptomonas, (2) Chroomonas/Komma caudata and Hemiselmis, (3) Rhodomonas/Rhinomonas/Storeatula, (4) Guillardia/Hanusia, (5) Geminigera/Plagioselmis/Teleaulax, (6) Proteomonas sulcata, (7) Falcomonas daucoides.
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