Cell biology

Their cells contain chloroplasts (unless secondarily lost) that contain chlorophylls a and c as photosynthetic pigments, in addition to fucoxanthin.^[6] These plastids are located within the membranes of the periplastidial endoplasmic reticulum (PER), which is often connected to the nuclear envelope. As a result, plastids are generally enclosed by four membranes. The tripartite flagellar hairs, characteristic of stramenopiles, are produced within either the PER or the nuclear envelope. In many ochropytes, one thylakoid differentiates into the girdle lamella, which runs around the periphery of the plastid, beneath the innermost membrane. The remaining thylakoids are arranged in stacks of three. Chlorophyll a binds to thylakoids, while the c pigment is present in the stroma.^[7] Some groups contain species with leucoplasts, choroplasts that have lost photosynthetic capacity and pigments but presumably continue to play a role in the synthesis of aminoacids, lipids and heme groups.^[7]

Chemical structure of fucoxanthin

The most frequent accessory pigment in ochrophytes is the yellow β-carotene. The golden-brown or brown pigmentation in diatoms, brown algae, golden algae and others is conferred by the xanthophyll fucoxanthin. In the yellow-green or yellow-brown raphidophyceans, eustigmatophyceans and xanthophyceans, vaucheriaxanthin is dominant instead. These pigment combinations extend their photosynthetic ability beyond chlorophyll a alone. Additionally, xanthophylls protect the photosystems from high intensity light.^[7]

Ochrophytes accumulate chrysolaminarin as storage product,^[7] within cytoplasmic vesicles.^[6] Cytoplasmic lipid droplets are also common.^[7] They uniformly have tubular mitochondrial cristae.^[7]

External

The ochrophytes constitute a highly diverse clade within Stramenopila, a eukaryotic supergroup that also includes several heterotrophic lineages of protists such as oomycetes, hyphochytrids, labyrinthuleans, opalines and bicosoecids.^[8][1][9] Stramenopiles, also known as heterokonts, are characterized by the presence of two flagella, one of which has hollow tripartite tubular hairs called mastigonemes, but these are secondarily lost in some groups.^[1]

The total group of ochrophytes is estimated to have evolved between 874 and 543 million years ago.^[10] They originated from an event of secondary endosymbiosis where a red alga was transformed into the chloroplast of the common ancestor of ochrophytes.^[1][11][12]

Internal

Relationships among many classes of ochrophytes remain unresolved, but three main clades (called SI, SII and SIII) are supported in most phylogenetic analyses. The SI lineage, containing the diverse and multicellular class Phaeophyceae, or brown algae, experienced an evolutionary radiation during the late Paleozoic (around 310 million years ago). The class Schizocladiophyceae is the sister lineage to brown algae, followed by a clade of closely related classes Xanthophyceae, Phaeosacciophyceae^[13] and Chrysoparadoxophyceae.^[14] This is in turn the sister lineage to a clade containing Aurearenophyceae and Phaeothamniophyceae,^[1] which are sometimes treated as one class Aurophyceae.^[12] The Raphidophyceae are the most basal within the SI. The SII lineage contains the golden algae or Chrysophyceae, as well as smaller classes Synurophyceae, Eustigmatophyceae, Pinguiophyceae and Picophagea (also known as Synchromophyceae). Both clades, SI and SII, compose the Chrysista lineage. The remaining classes are grouped within the sister lineage Diatomista, equivalent to the SIII lineage; these are the diatoms or Bacillariophyceae, Bolidophyceae, Dictyochophyceae (including the silicoflagellates) and Pelagophyceae.^[1] A new class of algae, Olisthodiscophyceae, was described in 2021 and recovered as part of the SII lineage.^[2]

The cladogram below shows the evolutionary relationships between all ochrophyte classes, based on the latest phylogenetic analyses,^{[15][12][13][2]} and the approximate number of species in each class.^[1]

One group of heterotrophic heliozoan protists, Actinophryida,^[16] is included in some classifications as the sister lineage to the raphidophytes, and both groups are treated as one class Raphidomonadea on the basis of 18S rDNA phylogenetic analyses.^[17] However, a recent phylogenomic study places one actinophryid, Actinophrys sol, as the probable sister group to ochrophytes.^[18]

Hierarchical

In hierarchical classifications, where taxonomic ranks (kingdom, phylum, class, order...) are utilized, the ochrophytes are commonly regarded as an entire phylum (or division in botanical nomenclature) by the name of Ochrophyta, within the Stramenopila or Heterokonta.^[8] The phylum was first described by protozoologist Thomas Cavalier-Smith in 1986.^[19] It remained as a phylum-level taxon until 2018, when the same author lowered it to subphylum level and modified the name to Ochrophytina to match the -phytina suffix in botanical nomenclature, which corresponds to subdivisions. The phylum to which ochrophytes belong in his classification system is Gyrista, a clade that also contains some heterotrophic stramenopiles, namely the Pseudofungi and the Bigyromonada.^[12] Gyrista and Bigyra compose the two main branches of stramenopiles, which are regarded as the superphylum Heterokonta within the kingdom Chromista. However, this classification system is in disuse, due to the non-monophyletic nature of the kingdom.^[9]

Cladistic

As opposed to the hierarchical classification, the cladistic classification only recognizes clades as valid groups, rejecting the use of paraphyletic or polyphyletic groups. This method of classification is preferred among protistologists. The latest revision of the International Society of Protistologists, in 2019, recognizes Ochrophyta as a valid taxon within the higher Stramenopiles group, within the SAR supergroup.^[9]

Below is the present classification of ochrophytes according to the most recent revision of 2019,^[9] with the inclusion of three new classes of algae described in posterior years.^[14][13][2] The subdivision of ochrophytes between Chrysista and Diatomista is fully accepted by the scientific community and backed up by phylogenetic analyses.^[9] According to this revision, the diatoms (Diatomeae) do not form a single class Bacillariophyceae. Instead, they are divided into numerous classes of new description, to reflect the phylogenetic advances over the previous decade.^[9]

• Chrysista Cavalier-Smith 1986
  • Aurearenophyceae Kai et al. 2008^[20]
  • Chrysoparadoxophyceae Wetherbee et al. 2019^[14]
  • Chrysophyceae Pascher 1914
  • Eustigmatophyceae Hibberd 1981
  • Olisthodiscophyceae Barcytė, Eikrem & M. Eliáš, 2021^[2]
  • Phaeophyceae Hansgirg 1886
  • Phaeosacciophyceae R.A.Andersen, L.Graf & H.S.Yoon 2020^[13]
  • Phaeothamniophyceae Andersen & Bailey in Bailey et al. 1998^[21]
  • Raphidophyceae Cahdefaud 1950, emend. Silva 1980
  • Schizocladiophyceae Kawai et al. 2003^[22]
  • Xanthophyceae Allorge 1930 emend. Fritsch 1935 (=Heterokontae Luther 1899; Heteromonadea Leedale 1983; Xanthophyta Hibberd 1990; Tribophyceae^[23])
• Diatomista Derelle et al. 2016, emend. Cavalier-Smith 2017
  • Dictyochophyceae Silva 1980
  • Pelagophyceae Andersen & Saunders 1993
  • Pinguiophyceae Kawachi et al. 2003
  • Bolidophyceae Guillou et al. 1999
  • Diatomeae Dumortier 1821 (=Bacillariophyta Haeckel 1878)
    • Leptocylindrophytina D.G. Mann in Adl et al. 2019
      • Leptocylindrophyceae D.G. Mann in Adl et al. 2019
      • Corethrophyceae D.G. Mann in Adl et al. 2019
    • Ellerbeckiophytina D.G. Mann in Adl et al. 2019
    • Probosciophytina D.G. Mann in Adl et al. 2019
    • Melosirophytina Medlin & Kaczmarska 2004, emend. Adl et al. 2019
    • Coscinodiscophytina D.G. Mann in Adl et al. 2019
    • Rhizosoleniophytina D.G. Mann in Adl et al. 2019
    • Arachnoidiscophytina D.G. Mann in Adl et al. 2019
    • Bacillariophytina Medlin & Kaczmarska 2004, emend. Adl et al. 2019
      • Mediophyceae Jouse & Proshkina-Lavrenko in Medlin & Kaczmarska 2004
      • Biddulphiophyceae D.G. Mann in Adl et al. 2019
      • Bacillariophyceae Haeckel 1878, emend. Adl et al. 2019