Chromista Explained

Chromista is a proposed but polyphyletic[1] biological kingdom, refined from the Chromalveolata, consisting of single-celled and multicellular eukaryotic species that share similar features in their photosynthetic organelles (plastids). 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.

Chromista as a taxon was created by the British biologist Thomas Cavalier-Smith in 1981 to distinguish the stramenopiles, haptophytes, and cryptophytes.[2] 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.[3]

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.[4]

Biology

Members of Chromista are single-celled and multicellular eukaryotes having basically either or both features:[2]

  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). Molecular evidence indicates that the plastids in chromists were derived from red algae through secondary symbiogenesis in a single event.[5] In contrast, plants acquired their plastids from cyanobacteria through primary symbiogenesis.[6] 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.[7] Additional symbiogenesis of green algae has provided genes retained in some members (such as heterokonts),[8] and bacterial chlorophyll (indicated by the presence of ribosomal protein L36 gene, rpl36) in haptophytes and cryptophytes.[9]

History and groups

Some examples of classification of the groups involved, which have overlapping but non-identical memberships, are shown below.[10] [11]

Chromophycées (Chadefaud, 1950)

The Chromophycées (Chadefaud, 1950),[12] renamed Chromophycota (Chadefaud, 1960),[13] 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;[2] the earlier names Chromophyta, Chromobiota and Chromobionta correspond to roughly the same group. It has been described as consisting of three different groups:[14] 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]

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

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).

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.[15] 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.[16] Harper & Keeling (2003) described haptophyte homologs and considered them further evidence of a single endosymbiotic event involving the ancestor of all chromists.[17]

Chromalveolata (Adl et al., 2005)

The Chromalveolata included Stramenopiles, Haptophyta, Cryptophyta and Alveolata.[18] However, in 2008 the group was found not to be monophyletic,[19] [20] and later studies confirmed this.[21]

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:[22]

Cavalier-Smith 2018

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):[3]

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.[23] [24] Cryptista specifically may be sister or part of Archaeplastida,[25] though this could be an artefact due to acquisition of genes from red algae by cryptomonads.

A 2020 phylogeny of the eukaryotes states that "the chromalveolate hypothesis is not widely accepted" (noting Cavalier-Smith et al 2018[26] as an exception), explaining that the host lineages do not appear to be closely related in "most phylogenetic analyses".[27] 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.[28]

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.[4] 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:[4]

Rhodophytina → Cryptophytina → Ochrophyta

 ↘ Haptophyta → Myzozoa

See also

External links

Notes and References

  1. 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 . 1994PNAS...9111368C . 10.1073/pnas.91.24.11368 . 45232 . 7972066 . free.
  2. Cavalier-Smith . Thomas . Thomas Cavalier-Smith . Eukaryote kingdoms: seven or nine? . Bio Systems . 14 . 3–4 . 461–81 . 1981 . 7337818 . 10.1016/0303-2647(81)90050-2 .
  3. Cavalier-Smith . Thomas . Thomas Cavalier-Smith . Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences . Protoplasma . 2018 . 255 . 1 . 297–357 . 10.1007/s00709-017-1147-3 . 28875267 . 5756292.
  4. Strassert . Jürgen F. H. . Irisarri . Iker . Williams . Tom A. . Burki . Fabien . 2021-03-25 . A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids . Nature Communications . 12 . 1 . 1879 . 10.1038/s41467-021-22044-z . 33767194 . 7994803 . 2021NatCo..12.1879S . 2041-1723.
  5. Keeling . Patrick J. . Chromalveolates and the Evolution of Plastids by Secondary Endosymbiosis . Journal of Eukaryotic Microbiology . 2009 . 56 . 1 . 1–8 . 10.1111/j.1550-7408.2008.00371.x . 19335769 . 34259721 .
  6. Ponce-Toledo . Rafael I. . Deschamps . Philippe . López-García . Purificación . Zivanovic . Yvan . Benzerara . Karim . Moreira . David . An Early-Branching Freshwater Cyanobacterium at the Origin of Plastids . Current Biology . 2017 . 27 . 3 . 386–391 . 10.1016/j.cub.2016.11.056 . 28132810 . 5650054.
  7. Keeling . Patrick J. . The endosymbiotic origin, diversification and fate of plastids . Philosophical Transactions of the Royal Society B: Biological Sciences . 2010 . 365 . 1541 . 729–748 . 10.1098/rstb.2009.0103 . 20124341 . 2817223.
  8. Morozov . A. A. . Galachyants . Yuri P. . Diatom genes originating from red and green algae: Implications for the secondary endosymbiosis models . Marine Genomics . 2019 . 45 . 72–78 . 10.1016/j.margen.2019.02.003 . 30792089. 2019MarGn..45...72M . 73458340 .
  9. Rice . Danny W . Palmer . Jeffrey D . 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 . 2006 . 4 . 1 . 31 . 10.1186/1741-7007-4-31 . 16956407 . 1570145 . free .
  10. Book: de Reviers, Bruno . 2006 . Biologia e Filogenia das Algas . Editora Artmed . Porto Alegre . 156–157 . 9788536315102 .
  11. Blackwell . Will H. . Chromista revisited: a dilemma of overlapping putative kingdoms, and the attempted application of the botanical code of nomenclature. . Phytologia . 2009 . 91 . 2 . 191–225 .
  12. Chadefaud . Marius . 1950 . Les cellules nageuses des Algues dans l'embranchement des Chromophycées . Seaweed swimming cells in the branch of Chromophyceae . French . Comptes rendus hebdomadaires des séances de l'Académie des Sciences . 231 . 788–790 .
  13. Book: Chadefaud, Marius . 1960 . Les végétaux non vasculaires (Cryptogamie) . Chadefaud . Marius . Emberger . L. . Traité de Botanique Systématique . Tome I . Paris .
  14. Csurös . M. . Rogozin . I. B. . Koonin . Eugene V. . Eugene Koonin . Extremely intron-rich genes in the alveolate ancestors inferred with a flexible maximum-likelihood approach . Molecular Biology and Evolution . 25 . 5 . 903–911 . May 2008 . 18296415 . 10.1093/molbev/msn039 . free .
  15. 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 . en . 3 . 5 . 1169–1175 . 10.1128/EC.3.5.1169-1175.2004 . 1535-9778 . 522617 . 15470245.
  16. 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 . 10.1093/oxfordjournals.molbev.a003818 . 11230543 . 1537-1719. free .
  17. 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 . 10.1093/molbev/msg195 . 12885964 . 0737-4038. free .
  18. Adl . Sina M. . The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists . Journal of Eukaryotic Microbiology . 2005 . 52 . 5 . 399–451 . 10.1111/j.1550-7408.2005.00053.x . 16248873 . 8060916 . etal . free .
  19. Burki . Fabien . Shalchian-Tabrizi . Kamran . Pawlowski . Jan . 2008 . Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes . Biology Letters . 4 . 366–369 . 10.1098/rsbl.2008.0224 . amp . 18522922 . 4 . 2610160 .
  20. 10.1371/journal.pone.0002621 . July 2008 . Kim . E. . Graham . L. E. . Redfield . Rosemary Jeanne . EEF2 analysis challenges the monophyly of Archaeplastida and Chromalveolata. . 3 . 7 . e2621 . 18612431 . 2440802 . PLOS ONE . 2008PLoSO...3.2621K . free .
  21. 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 . 10.1098/rspb.2011.2301 . 279 . 1736 . 2246–2254 . 22298847 . 3321700.
  22. Ruggiero . Michael A. . Gordon . Dennis P. . Orrell . Thomas M. . Bailly . Nicolas . Bourgoin . Thierry . Brusca . Richard C. . Cavalier-Smith . Thomas . Guiry . Michael D. . Kirk . Paul M. . Thuesen . Erik V. . 3 . A higher level classification of all living organisms . PLOS ONE . 2015 . 10 . 4 . e0119248 . 10.1371/journal.pone.0119248 . 25923521 . 4418965 . 2015PLoSO..1019248R . free.
  23. Parfrey . Laura Wegener . Barbero . Erika . Lasser . Elyse . Dunthorn . Micah . Bhattacharya . Debashish . Patterson . David J. . Katz . Laura A. . 3 . Evaluating support for the current classification of eukaryotic diversity . PLOS Genetics . 2 . 12 . e220 . December 2006 . 17194223 . 1713255 . 10.1371/journal.pgen.0020220 . free .
  24. Burki . Fabien . Shalchian-Tabrizi . Kamran . Minge . Marianne . Skjæveland . Åsmund . Nikolaev . Sergey I. . Jakobsen . Kjetill S. . Pawlowski . Jan . 3 . Phylogenomics reshuffles the eukaryotic supergroups . PLOS ONE . 2 . 8 . e790 . August 2007 . 17726520 . 1949142 . 10.1371/journal.pone.0000790 . 2007PLoSO...2..790B . free .
  25. Burki . Fabien . Kaplan . Maia . Tikhonenkov . Denis V. . Zlatogursky . Vasily . Minh . Bui Quang . Radaykina . Liudmila V. . Smirnov . Alexey . Mylnikov . Alexander P. . Keeling . Patrick J. . 3 . Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista . Proceedings. Biological Sciences . 283 . 1823 . 20152802 . January 2016 . 26817772 . 4795036 . 10.1098/rspb.2015.2802 .
  26. Cavalier-Smith . Thomas . Thomas Cavalier-Smith . Chao . Ema E. . Lewis . Rhodri . Multigene phylogeny and cell evolution of chromist infrakingdom Rhizaria: contrasting cell organisation of sister phyla Cercozoa and Retaria . Protoplasma . 255 . 5 . 17 April 2018 . 0033-183X . 10.1007/s00709-018-1241-1 . 1517–1574 . 29666938 . 6133090 .
  27. Book: Burki, F. . The convoluted evolution of eukaryotes with complex plastids . Hirakawa . Y. . Advances in Botanical Research . 84 . Academic Press . 2017 . 1–30.
  28. Burki . Fabien . Roger . Andrew J. . Brown . Matthew W. . Simpson . Alastair G.B. . The New Tree of Eukaryotes . Trends in Ecology & Evolution . Elsevier . 35 . 1 . 2020 . 0169-5347 . 10.1016/j.tree.2019.08.008 . 43–55. 31606140 . 204545629 . free .

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