**4. Taxonomy**

Although distinguishing cryptophyte cells from other flagellated cells is relatively easy by their movement, gross morphology, and epifluorescence; classifying by genus and species is difficult [9, 82]. Initial investigations proposed the morphology and color as a basis for this definition [20, 23, 25], but color changes depending on the cell stage and culture conditions, mainly light and nitrogen [83, 84]. Characteristics such as the groove/gullet complex, or ultrastructural features such as flagella, the position of NM, pyrenoid, and IPC, can only observed with an electron microscope, but could be characters of taxonomic value. However, this is view has changed after discovery that some species with haploid and diploid phases can have very different morphologies, suggesting that there is an intermediary stage sexual reproduction that could be confounding taxonomic certainty of species [9, 31, 81].

Among the characteristics used in Cryptophyte systematics are the presence or absence and the kind of accessory pigment (PER or PCY) (**Table 1**) [23, 28, 33]. The ultrastructural traits such as the arrangement of flagellar hairs [28], the number and location of the NM in the PC [1, 23], the presence and location of the eyespot in Chroomonas species, the type of scales comprising the outer periplast component, number location, and type of pyrenoids [8, 23], number of chloroplast per cell [85] are some of the taxonomic keys still used. Advances in molecular tools improved the phylogeny of the groups. There is a correspondence between molecular data with biliprotein, but it has not found with other morphological traits like IPC.

Life histories may be another character. Although initially it was thought that all cryptophytes divided only vegetatively, now species such as *Proteomonas sulcata* have been identified to have a dimorphic life cycle [86], *Cryptomonas/Campylomonas* [83], *Teleaulax/Plagioselmis* [13], are known to have complex life cycles. In some cases, those species have shown alternation of generations, with very different forms [10] and haploid/diploid phases. They had even been classified as different species. The aforementioned shows how complicated the taxonomic classification of cryptophytes can be.


*Clay, Kugrens and Lee [23, 90]. The color of the genus indicates the kind of pigment it contains. Red = Cr-phycoerythrin, Blue = Cr-phycocyanin, Black = No color = no photosynthetic, no chloroplasts present.*

#### **Table 2.**

*Cryptomonad classification of the phylum Cryptophyta Cavalier-Smith emend.*

Few of the genes more employed in the cryptophytes phylogeny are nuclear, 18S, ITS1, 5.8S, ITS2, 28S, SSU, LSU rDNA [13, 70, 87]; the nucleomorph SSU rDNA and 18S rDNA [83], and the chloroplast psbA [32].

The Cryptomonad classification of the Phylum Cryptophyta is shown in **Table 2**; however, this table will change in the future to reflect advances in knowledge, culturing, and electron microscopy.
