Chromista

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Chromista
Chromista collage 2.jpg
Chromista collage
Scientific classification OOjs UI icon edit-ltr.svg
(obsolete)
Domain: Eukaryota
Clade: Diaphoretickes
Kingdom: Chromista
Cavalier-Smith 1981
Groups included
Cladistically included but traditionally excluded taxa

Chromista is a proposed but polyphyletic [1] [2] [3] biological kingdom, refined from the Chromalveolata, consisting of single-celled and multicellular eukaryotic species that share similar features in their photosynthetic organelles (plastids). [4] It includes all eukaryotes whose plastids contain chlorophyll c and are surrounded by four membranes. If the ancestor already possessed chloroplasts derived by endosymbiosis from red algae, all non-photosynthetic Chromista have secondarily lost the ability to photosynthesise. Its members might have arisen independently as separate evolutionary groups from the last eukaryotic common ancestor. [1]

Contents

Chromista as a taxon was created by the British biologist Thomas Cavalier-Smith in 1981 to distinguish the stramenopiles, haptophytes, and cryptophytes. [5] According to Cavalier-Smith, the kingdom originally consisted mostly of photosynthetic eukaryotes (algae), but he later brought many heterotrophs (protozoa) into the proposed group. As of 2018, the kingdom was nearly as diverse as the kingdoms Plantae and Animalia, consisting of eight phyla. Notable members include marine algae, potato blight, dinoflagellates, Paramecium , the brain parasite Toxoplasma, and the malarial parasite Plasmodium . [6]

However, Cavalier-Smith's hypothesis of chromist monophyly has been rejected by other researchers, who consider it more likely that some chromists acquired their plastids by incorporating another chromist instead of inheriting them from a common ancestor. This is thought to have occurred repeatedly, so that the red plastids spread from one group to another. The plastids, far from characterising their hosts as belonging to a single clade, thus have a different history from their disparate hosts. They appear to have originated in the Rhodophytina, and to have been transmitted to the Cryptophytina and from them to both the Ochrophyta and the Haptophyta, and then from these last to the Myzozoa. [3]

Biology

Structure of some types of Chromista compared with plant cell (left). The idea was that the Chromista had arisen, supposedly just once (making them monophyletic, and in Tom Cavalier-Smith's view a separate Kingdom) by enslaving a red alga, ending up with multiple membranes around what became their red plastids. Groups lacking red plastids were supposed to have secondarily lost them. The Cryptophyta are within the Cryptista; the Myzozoa are within the Alveolata. Chromista structure.jpg
Structure of some types of Chromista compared with plant cell (left). The idea was that the Chromista had arisen, supposedly just once (making them monophyletic, and in Tom Cavalier-Smith's view a separate Kingdom) by enslaving a red alga, ending up with multiple membranes around what became their red plastids. Groups lacking red plastids were supposed to have secondarily lost them. The Cryptophyta are within the Cryptista; the Myzozoa are within the Alveolata.

Members of Chromista are single-celled and multicellular eukaryotes having basically either or both features: [5]

  1. plastid(s) that contain chlorophyll c and lie within an extra (periplastid) membrane in the lumen of the rough endoplasmic reticulum (typically within the perinuclear cisterna);
  2. cilia with tripartite or bipartite rigid tubular hairs.

The kingdom includes diverse organisms from algae to malarial parasites (Plasmodium). [7] Molecular evidence indicates that the plastids in chromists were derived from red algae through secondary symbiogenesis in a single event. [8] In contrast, plants acquired their plastids from cyanobacteria through primary symbiogenesis. [9] These plastids are now enclosed in two extra cell membranes, making a four-membrane envelope, as a result of which they acquired many other membrane proteins for transporting molecules in and out of the organelles. The diversity of chromists is hypothesised to have arisen from degeneration, loss or replacement of the plastids in some lineages. [10] Additional symbiogenesis of green algae has provided genes retained in some members (such as heterokonts), [11] and bacterial chlorophyll (indicated by the presence of ribosomal protein L36 gene, rpl36) in haptophytes and cryptophytes. [12]

History and groups

Some examples of classification of the groups involved, which have overlapping but non-identical memberships, are shown below. [13] [14]

Chromophycées (Chadefaud, 1950)

The Chromophycées (Chadefaud, 1950), [15] renamed Chromophycota (Chadefaud, 1960), [16] included the current Ochrophyta (autotrophic Stramenopiles), Haptophyta (included in Chrysophyceae until Christensen, 1962), Cryptophyta, Dinophyta, Euglenophyceae and Choanoflagellida (included in Chrysophyceae until Hibberd, 1975).

Chromophyta (Christensen 1962, 1989)

The Chromophyta (Christensen 1962, 2008), defined as algae with chlorophyll c, included the current Ochrophyta (autotrophic Stramenopiles), Haptophyta, Cryptophyta, Dinophyta and Choanoflagellida. The Euglenophyceae were transferred to the Chlorophyta.

Chromophyta (Bourrelly, 1968)

The Chromophyta (Bourrelly, 1968) included the current Ochrophyta (autotrophic Stramenopiles), Haptophyta and Choanoflagellida. The Cryptophyceae and the Dinophyceae were part of Pyrrhophyta (= Dinophyta).

Chromista (Cavalier-Smith, 1981)

The name Chromista was first introduced by Cavalier-Smith in 1981; [5] the earlier names Chromophyta, Chromobiota and Chromobionta correspond to roughly the same group. It has been described as consisting of three different groups: [17] It includes all protists whose plastids contain chlorophyll c. [1]

In 1994, Cavalier-Smith and colleagues indicated that the Chromista is probably a polyphyletic group whose members arose independently, sharing no more than descent from the common ancestor of all eukaryotes: [1]

The four phyla that contain chromophyte algae (those with chlorophyll c--i.e., Cryptista, Heterokonta, Haptophyta, Dinozoa) are distantly related to each other and to Chlorarachniophyta on our trees. However, all of the photosynthetic taxa within each of these four phyla radiate from each other very substantially after the radiation of the four phyla themselves. This favors the view that the common ancestor of these four phyla was not photosynthetic and that chloroplasts were implanted separately into each much more recently. This probable polyphyly of the chromophyte algae, if confirmed, would make it desirable to treat Cryptista, Heterokonta, and Haptophyta as separate kingdoms, rather than to group them together in the single kingdom Chromista. [1]

In 2009, Cavalier-Smith gave his reason for making a new kingdom, saying: [7]

I established Chromista as a kingdom distinct from Plantae and Protozoa because of the evidence that chromist chloroplasts were acquired secondarily by enslavement of a red alga, itself a member of kingdom Plantae, and their unique membrane topology. [7]

Since then Chromista has been defined in different ways at different times. In 2010, Cavalier-Smith reorganised Chromista to include the SAR supergroup (named for the included groups Stramenopiles, Alveolata and Rhizaria) and Hacrobia (Haptista and Cryptista). [7]

Patron et al. (2004) considered the presence of a unique class of FBA (fructose-1,6-biophosphate-aldolase) enzyme not similar to that found in plants as evidence of chromist monophyly. [18] Fast et al. (2001) supported a single origin for the myzozoan (dinoflagellate + apicomplexan), heterokont and cryptophyte plastids based on their comparison of GAPDH (glyceraldehyde-3-phosphate dehydrogenase) genes. [19] Harper & Keeling (2003) described haptophyte homologs and considered them further evidence of a single endosymbiotic event involving the ancestor of all chromists. [20]

Chromalveolata (Adl et al., 2005)

The Chromalveolata included Stramenopiles, Haptophyta, Cryptophyta and Alveolata. [21] However, in 2008 the group was found not to be monophyletic, [22] [23] and later studies confirmed this. [24] [25]

Classification

Cavalier-Smith et al. 2015

In 2015, Cavalier-Smith and his colleagues made a new higher-level grouping of all organisms as a revision of the seven kingdoms model. In it, they classified the kingdom Chromista into 2 subkingdoms and 11 phyla, namely: [26]

Chromista
2015

Cavalier-Smith 2018

Chromista classification according to Cavalier-Smith, 2018, with supposed events marking group divergences Chromista classification.jpg
Chromista classification according to Cavalier-Smith, 2018, with supposed events marking group divergences

Cavalier-Smith made a new analysis of Chromista in 2018 in which he classified all chromists into 8 phyla (Gyrista corresponds to the above phyla Ochrophyta and Pseudofungi, Cryptista corresponds to the above phyla Cryptista and "N.N.", Haptista corresponds to the above phyla Haptophyta and Heliozoa): [6]

Polyphyly and serial endosymbiosis

Molecular trees have had difficulty resolving relationships between the different groups. All three may share a common ancestor with the alveolates (see chromalveolates), but there is evidence that suggests the haptophytes and cryptomonads do not belong together with the heterokonts or the SAR clade, but may be associated with the Archaeplastida. [4] [27] Cryptista specifically may be sister or part of Archaeplastida, [24] though this could be an artefact due to acquisition of genes from red algae by cryptomonads. [3]

A 2020 phylogeny of the eukaryotes states that "the chromalveolate hypothesis is not widely accepted" (noting Cavalier-Smith et al 2018 [28] as an exception), explaining that the host lineages do not appear to be closely related in "most phylogenetic analyses". [2] [29] Further, none of TSAR, Cryptista, and Haptista, groups formerly within Chromalveolata, appear "likely to be ancestrally defined by red secondary plastids". This is because of the many non-photosynthetic organisms related to the groups with chlorophyll c, and the possibility that cryptophytes are more closely related to plants. [2]

The alternative to monophyly is serial endosymbiosis, meaning that the "chromists" acquired their plastids from each other instead of inheriting them from a single common ancestor. Thus the phylogeny of the distinctive plastids, which are agreed to have a common origin in the rhodophytes, is different from the phylogeny of the host cells. [3] In 2021, Jürgen Strassert and colleagues modelled the timelines for the presumed spread of the red plastids, concluding that "the hypotheses of serial endosymbiosis are chronologically possible, as the stem lineages of all red plastid-containing groups overlap in time" during the Mesoproterozoic and Neoproterozoic eras. They propose that the plastids were transmitted between groups as follows: [3]

Rhodophytina → Cryptophytina → Ochrophyta
 ↘ Haptophyta → Myzozoa

See also

Related Research Articles

<span class="mw-page-title-main">Stramenopile</span> Clade of eukaryotes

The Stramenopiles, also called Heterokonts, are a clade of organisms distinguished by the presence of stiff tripartite external hairs. In most species, the hairs are attached to flagella, in some they are attached to other areas of the cellular surface, and in some they have been secondarily lost. Stramenopiles represent one of the three major clades in the SAR supergroup, along with Alveolata and Rhizaria.

<span class="mw-page-title-main">Kingdom (biology)</span> Taxonomic rank

In biology, a kingdom is the second highest taxonomic rank, just below domain. Kingdoms are divided into smaller groups called phyla.

<span class="mw-page-title-main">Alveolate</span> Superphylum of protists

The alveolates are a group of protists, considered a major clade and superphylum within Eukarya. They are currently grouped with the stramenopiles and Rhizaria among the protists with tubulocristate mitochondria into the SAR supergroup.

<span class="mw-page-title-main">Cryptomonad</span> Subphylum of algae

The cryptomonads are a group of algae, most of which have plastids. 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 flagella.

<span class="mw-page-title-main">Thomas Cavalier-Smith</span> British evolutionary biologist (1942–2021)

Thomas (Tom) Cavalier-Smith, FRS, FRSC, NERC Professorial Fellow, was a professor of evolutionary biology in the Department of Zoology, at the University of Oxford.

<span class="mw-page-title-main">Bikont</span> Group of eukaryotes

A bikont is any of the eukaryotic organisms classified in the group Bikonta. Many single-celled and multi-celled organisms are members of the group, and these, as well as the presumed ancestor, have two flagella.

<span class="mw-page-title-main">Chromalveolata</span> Group of eukaryotic organisms

Chromalveolata was a eukaryote supergroup present in a major classification of 2005, then regarded as one of the six major groups within the eukaryotes. It was a refinement of the kingdom Chromista, first proposed by Thomas Cavalier-Smith in 1981. Chromalveolata was proposed to represent the organisms descended from a single secondary endosymbiosis involving a red alga and a bikont. The plastids in these organisms are those that contain chlorophyll c.

<span class="mw-page-title-main">Archaeplastida</span> Clade of eukaryotes containing land plants and some algae

The Archaeplastida are a major group of eukaryotes, comprising the photoautotrophic red algae (Rhodophyta), green algae, land plants, and the minor group glaucophytes. It also includes the non-photosynthetic lineage Rhodelphidia, a predatorial (eukaryotrophic) flagellate that is sister to the Rhodophyta, and probably the microscopic picozoans. The Archaeplastida have chloroplasts that are surrounded by two membranes, suggesting that they were acquired directly through a single endosymbiosis event by phagocytosis of a cyanobacterium. All other groups which have chloroplasts, besides the amoeboid genus Paulinella, have chloroplasts surrounded by three or four membranes, suggesting they were acquired secondarily from red or green algae. Unlike red and green algae, glaucophytes have never been involved in secondary endosymbiosis events.

<span class="mw-page-title-main">Telonemia</span> Phylum of single-celled organisms

Telonemia is a phylum of microscopic eukaryotes commonly known as telonemids. They are unicellular free-living flagellates with a unique combination of cell structures, including a highly complex cytoskeleton unseen in other eukaryotes.

<span class="mw-page-title-main">Corticata</span> Type of plant

Corticata, in the classification of eukaryotes, is a clade suggested by Thomas Cavalier-Smith to encompass the eukaryote supergroups of the following two groups:

<span class="mw-page-title-main">Ochrophyte</span> Phylum of algae

Ochrophytes, also known as heterokontophytes or stramenochromes, are a group of algae. They are the photosynthetic stramenopiles, a group of eukaryotes, organisms with a cell nucleus, characterized by the presence of two unequal flagella, one of which has tripartite hairs called mastigonemes. In particular, they are characterized by photosynthetic organelles or plastids enclosed by four membranes, with membrane-bound compartments called thylakoids organized in piles of three, chlorophyll a and c as their photosynthetic pigments, and additional pigments such as β-carotene and xanthophylls. Ochrophytes are one of the most diverse lineages of eukaryotes, containing ecologically important algae such as brown algae and diatoms. They are classified either as phylum Ochrophyta or Heterokontophyta, or as subphylum Ochrophytina within phylum Gyrista. Their plastids are of red algal origin.

<span class="mw-page-title-main">SAR supergroup</span> Eukaryotes superphylum

SAR or Harosa is a highly diverse clade of eukaryotes, often considered a supergroup, that includes stramenopiles (heterokonts), alveolates, and rhizarians. It is a node-based taxon, including all descendants of the three groups' last common ancestor, and comprises most of the now-rejected Chromalveolata. Their sister group has been found to be telonemids, with which they make up the TSAR clade.

<span class="mw-page-title-main">Bigyra</span> Phylum of single-celled organisms

Bigyra is a phylum of microscopic eukaryotes that are found at the base of the Stramenopiles clade. It includes three well-known heterotrophic groups Bicosoecida, Opalinata and Labyrinthulomycetes, as well as several small clades initially discovered through environmental DNA samples: Nanomonadea, Placididea, Opalomonadea and Eogyrea. The classification of Bigyra has changed several times since its origin, and its monophyly remains unresolved.

<span class="mw-page-title-main">Hacrobia</span> Group of algae

The cryptomonads-haptophytes assemblage is a proposed but disputed monophyletic grouping of unicellular eukaryotes that are not included in the SAR supergroup. Several alternative names have been used for the group, including Hacrobia ; CCTH ; and "Eukaryomonadae".

<span class="mw-page-title-main">Diaphoretickes</span> Taxon of eukaryotes

Diaphoretickes is a major group of eukaryotic organisms, with over 400,000 species. The majority of the earth's biomass that carries out photosynthesis belongs to Diaphoretickes.

<span class="mw-page-title-main">Halvaria</span> Infrakingdom of protists

Halvaria is a taxonomic grouping of protists that includes Alveolata and Stramenopiles (Heterokonta).

<span class="mw-page-title-main">Cryptista</span> Phylum of algae

Cryptista is a clade of alga-like eukaryotes. It is most likely related to Archaeplastida which includes plants and many algae, within the larger group Diaphoretickes.

<span class="mw-page-title-main">Haptista</span> Group of protists

Haptista is a proposed group of protists made up of centrohelids and haptophytes. Phylogenomic studies indicate that Haptista, together with Ancoracysta twista, forms a sister clade to the SAR+Telonemia supergroup, but it may also be sister to the Cryptista (+Archaeplastida). It is thus one of the earliest diverging Diaphoretickes.

Endohelea is a proposed clade of eukaryotes that are related to Archaeplastida and the SAR supergroup. They used to be considered heliozoans, but phylogenetically they belong to a group of microorganisms known as Cryptista.

<span class="mw-page-title-main">Cortical alveolum</span> Cellular organelle found in protists

The cortical alveolum is a cellular organelle consisting of a vesicle located under the cytoplasmic membrane, to which they give support. The term "corticate" comes from an evolutionary hypothesis about the common origin of kingdoms Plantae and Chromista, because both kingdoms have cortical alveoli in at least one phylum. At least three protist lineages exhibit these structures: Telonemia, Alveolata and Glaucophyta.

References

  1. 1 2 3 4 5 Cavalier-Smith, Thomas; Allsopp, M. T.; Chao, E. E. (November 1994). "Chimeric conundra: are nucleomorphs and chromists monophyletic or polyphyletic?". Proceedings of the National Academy of Sciences of the United States of America. 91 (24): 11368–11372. Bibcode:1994PNAS...9111368C. doi: 10.1073/pnas.91.24.11368 . PMC   45232 . PMID   7972066.
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  8. ↑ Keeling, Patrick J. (2009). "Chromalveolates and the Evolution of Plastids by Secondary Endosymbiosis". Journal of Eukaryotic Microbiology. 56 (1): 1–8. doi:10.1111/j.1550-7408.2008.00371.x. PMID   19335769. S2CID   34259721.
  9. ↑ Ponce-Toledo, Rafael I.; Deschamps, Philippe; López-García, Purificación; Zivanovic, Yvan; Benzerara, Karim; Moreira, David (2017). "An Early-Branching Freshwater Cyanobacterium at the Origin of Plastids". Current Biology. 27 (3): 386–391. doi:10.1016/j.cub.2016.11.056. PMC   5650054 . PMID   28132810.
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  11. ↑ Morozov, A. A.; Galachyants, Yuri P. (2019). "Diatom genes originating from red and green algae: Implications for the secondary endosymbiosis models". Marine Genomics. 45: 72–78. Bibcode:2019MarGn..45...72M. doi:10.1016/j.margen.2019.02.003. PMID   30792089. S2CID   73458340.
  12. ↑ Rice, Danny W; Palmer, Jeffrey D (2006). "An exceptional horizontal gene transfer in plastids: gene replacement by a distant bacterial paralog and evidence that haptophyte and cryptophyte plastids are sisters". BMC Biology. 4 (1): 31. doi: 10.1186/1741-7007-4-31 . PMC   1570145 . PMID   16956407.
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  14. ↑ Blackwell, Will H. (2009). "Chromista revisited: a dilemma of overlapping putative kingdoms, and the attempted application of the botanical code of nomenclature" (PDF). Phytologia. 91 (2): 191–225.
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  16. ↑ Chadefaud, Marius (1960). "Les végétaux non vasculaires (Cryptogamie)". In Chadefaud, Marius; Emberger, L. (eds.). Traité de Botanique Systématique. Paris: Tome I.
  17. ↑ Csurös, M.; Rogozin, I. B.; Koonin, Eugene V. (May 2008). "Extremely intron-rich genes in the alveolate ancestors inferred with a flexible maximum-likelihood approach". Molecular Biology and Evolution. 25 (5): 903–911. doi: 10.1093/molbev/msn039 . PMID   18296415.
  18. ↑ Patron, Nicola J.; Rogers, Matthew B.; Keeling, Patrick J. (2004). "Gene Replacement of Fructose-1,6-Bisphosphate Aldolase Supports the Hypothesis of a Single Photosynthetic Ancestor of Chromalveolates". Eukaryotic Cell. 3 (5): 1169–1175. doi:10.1128/EC.3.5.1169-1175.2004. ISSN   1535-9778. PMC   522617 . PMID   15470245.
  19. ↑ Fast, Naomi M.; Kissinger, Jessica C.; Roos, David S.; Keeling, Patrick J. (2001-03-01). "Nuclear-Encoded, Plastid-Targeted Genes Suggest a Single Common Origin for Apicomplexan and Dinoflagellate Plastids". Molecular Biology and Evolution. 18 (3): 418–426. doi: 10.1093/oxfordjournals.molbev.a003818 . ISSN   1537-1719. PMID   11230543.
  20. ↑ Harper, J. T. (2003-06-27). "Nucleus-Encoded, Plastid-Targeted Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) Indicates a Single Origin for Chromalveolate Plastids". Molecular Biology and Evolution. 20 (10): 1730–1735. doi: 10.1093/molbev/msg195 . ISSN   0737-4038. PMID   12885964.
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  24. 1 2 Burki, Fabien; Kaplan, Maia; Tikhonenkov, Denis V.; et al. (January 2016). "Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista". Proceedings. Biological Sciences. 283 (1823): 20152802. doi:10.1098/rspb.2015.2802. PMC   4795036 . PMID   26817772.
  25. ↑ Burki, F.; Okamoto, N.; Pombert, J. F.; Keeling, P. J. (2012). "The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins". Proceedings of the Royal Society. 279 (1736): 2246–2254. doi:10.1098/rspb.2011.2301. PMC   3321700 . PMID   22298847.
  26. ↑ Ruggiero, Michael A.; Gordon, Dennis P.; Orrell, Thomas M.; et al. (2015). "A higher level classification of all living organisms". PLOS ONE. 10 (4): e0119248. Bibcode:2015PLoSO..1019248R. doi: 10.1371/journal.pone.0119248 . PMC   4418965 . PMID   25923521.
  27. ↑ Burki, Fabien; Shalchian-Tabrizi, Kamran; Minge, Marianne; et al. (August 2007). "Phylogenomics reshuffles the eukaryotic supergroups". PLOS ONE. 2 (8): e790. Bibcode:2007PLoSO...2..790B. doi: 10.1371/journal.pone.0000790 . PMC   1949142 . PMID   17726520.
  28. ↑ Cavalier-Smith, Thomas; Chao, Ema E.; Lewis, Rhodri (17 April 2018). "Multigene phylogeny and cell evolution of chromist infrakingdom Rhizaria: contrasting cell organisation of sister phyla Cercozoa and Retaria". Protoplasma. 255 (5): 1517–1574. doi:10.1007/s00709-018-1241-1. ISSN   0033-183X. PMC   6133090 . PMID   29666938.
  29. ↑ Burki, F. (2017). "The convoluted evolution of eukaryotes with complex plastids". In Hirakawa, Y. (ed.). Advances in Botanical Research. Vol. 84. Academic Press. pp. 1–30.
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