Archaeplastida

{{Short description|Clade of eukaryotes containing land plants and some algae}} {{Automatic taxobox | fossil_range = {{long fossil range|1600|0|earliest=1600|Calymmian – Present}} | image = Sprague River (Klamath County, Oregon scenic images) (klaDA0073).jpg | image_upright = 1.2 | image_caption = Conifer trees, grasses, algae, and shrubs in and around Sprague River, Oregon | display_parents = 3 | taxon = Archaeplastida | authority = Adl ''et al.'', 2005<ref name=Adl2005/> | subdivision_ranks = Subgroups | subdivision = * Rhodaria<ref>{{Cite journal |last=Cavalier-Smith |first=Thomas |date=2022-05-01 |title=Ciliary transition zone evolution and the root of the eukaryote tree: implications for opisthokont origin and classification of kingdoms Protozoa, Plantae, and Fungi |journal=Protoplasma |language=en |volume=259 |issue=3 |pages=487–593 |doi=10.1007/s00709-021-01665-7 |issn=1615-6102 |pmc=9010356 |pmid=34940909 |doi-access=free |bibcode=2022Prpls.259..487C }}</ref><ref>{{Cite journal |last1=Yazaki |first1=Euki |last2=Yabuki |first2=Akinori |last3=Imaizumi |first3=Ayaka |last4=Kume |first4=Keitaro |last5=Hashimoto |first5=Tetsuo |last6=Inagaki |first6=Yuji |date=2022-04-13 |title=The closest lineage of Archaeplastida is revealed by phylogenomics analyses that include Microheliella maris |journal=Open Biology |volume=12 |issue=4 |article-number=210376 |doi=10.1098/rsob.210376 |doi-access=free|pmc=9006020 |pmid=35414259}}</ref><ref>{{Cite journal |last=Seenivasan |first=Ramkumar |last2=Sausen |first2=Nicole |last3=Medlin |first3=Linda K. |last4=Melkonian |first4=Michael |date=2013-03-26 |title=Picomonas judraskeda Gen. Et Sp. Nov.: The First Identified Member of the Picozoa Phylum Nov., a Widespread Group of Picoeukaryotes, Formerly Known as 'Picobiliphytes' |url=https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0059565 |journal=PLOS ONE |language=en |volume=8 |issue=3 |article-number=e59565 |doi=10.1371/journal.pone.0059565 |issn=1932-6203 |pmc=3608682 |pmid=23555709 |doi-access=free}}</ref> ** Picozoa ** Rhodelphidia ** Rhodophyta * Glaucophyta * Viridiplantae (green plants) | synonyms = * Plantae Cavalier-Smith, 1981<ref>{{cite journal | last1=Cavalier-Smith | first1=T. | year=1981 | title=Eukaryote Kingdoms: Seven or Nine?". | journal=BioSystems | volume=14 | issue=3–4| pages=461–481 | doi=10.1016/0303-2647(81)90050-2 | pmid=7337818| bibcode=1981BiSys..14..461C }}</ref> * Primoplastobiota Reviers, 2002{{citation needed|date=July 2015}} * Primoplantae Palmer et al. 2004<ref name="palmer"/> }}

'''Archaeplastida''' (pronounced {{IPAc-en|ɑːr|k|ɪ|'|p|l|ae|s|t|ɪ|d|ə}}) or '''archaeplastids''', sometimes also regarded as the kingdom Plantae ''sensu lato'' ("in a broad sense"), are a large group of eukaryotes comprising the major clades Viridiplantae (green algae and land plants) and Rhodophyta (red algae), as well as the minor division Glaucophyta ("grey algae").<ref name="pmid21220783">{{cite journal |last1=Ball |first1=S. |last2=Colleoni |first2=C. |others=a, U.; Raj, J.N.; Tirtiaux, C. |title=The evolution of glycogen and starch metabolism in eukaryotes gives molecular clues to understand the establishment of plastid endosymbiosis |journal=Journal of Experimental Botany |volume=62 |issue=6 |pages=1775–1801 |date=January 2011 |pmid=21220783 |doi=10.1093/jxb/erq411 |doi-access=free }}</ref> While the vast majority of archaeplastids are autotrophs, the group also includes heterotrophic lineages such as the predatorial (eukaryotrophic) flagellates Rhodelphidia, and probably also the microscopic picoplankton Picozoa,<ref>{{Cite web |url=https://www.the-scientist.com/news-opinion/picozoans-are-algae-after-all-study-68741 |title=Picozoans Are Algae After All: Study {{!}} The Scientist Magazine® |work=The Scientist Magazine® |access-date=2021-05-10 |archive-date=2022-01-07 |archive-url=https://web.archive.org/web/20220107095249/https://www.the-scientist.com/news-opinion/picozoans-are-algae-after-all-study-68741 }}</ref> both may be sister to Rhodophyta and altogether forming the larger solid clade Rhodaria.

With the exception of the picozoans, archaeplastids are all primary algae whose cells have pigment-bearing membrane-bound organelles called plastids, and most of their plastids contain the red/blue light-sensitive photopigment chlorophyll, which acts as the core component of oxygenic photosynthesis reaction centers. These chlorophyllic plastids, known as chloroplasts, are surrounded by two biological membranes, suggesting that they were endosymbionts evolved directly from phagocytosis of cyanobacteria, which did not result in intracellular digestion but instead achieved mutualistic symbiosis within the endomembrane system.<ref>{{Cite journal |last1=Papanin Institute for Biology of Inland Waters, Russian Academy of Science's |last2=Tikhonenkov |first2=Denis V. |date=2020 |title=Predatory flagellates – the new recently discovered deep branches of the eukaryotic tree and their evolutionary and ecological significance|url=http://www.zin.ru/journals/protistology/num14_1/tikhonenkov_protistology_14-1.pdf |journal=Protistology |volume=14 |issue=1 |doi=10.21685/1680-0826-2020-14-1-2|doi-access=free }}</ref> In contrast, other photosynthetic algae, besides the amoeboid rhizarian genus ''Paulinella'' (which also obtained cyanobionts directly, but independently and much later), are secondary algae with chloroplasts surrounded by three or four membranes, suggesting they were indirectly acquired via phagocytosis and subsequent endosymbiosis of archaeplastids (red or green algae) or other secondary algae,{{#tag:ref|The exceptional two plastid membranes of the stramenopile alga ''Chrysoparadoxa'' are probably the result of secondary reduction.<ref name="Wetherbee_2018">{{cite journal |last1=Wetherbee |first1=Richard |last2=Jackson |first2=Christopher J. |last3=Repetti |first3=Sonja I. |last4=Clementson |first4=Lesley A. |last5=Costa |first5=Joana F. |last6=van de Meene |first6=Allison |last7=Crawford |first7=Simon |last8=Verbruggen |first8=Heroen |title=The golden paradox – a new heterokont lineage with chloroplasts surrounded by two membranes |journal=Journal of Phycology |date=9 December 2018 |volume=22 |issue=2 |pages=257–278 |doi=10.1111/jpy.12822 |pmid=30536815 |hdl=11343/233613 |s2cid=54477112 |hdl-access=free }}</ref>|group="note"|name="Chrysoparadoxa"}} in what can be considered a form of permanent kleptoplasty. Unlike red and green algae, glaucophytes are not known to be ever involved in such secondary endosymbiosis events.<ref>[https://books.google.com/books?id=0-PIBAAAQBAJ&dq=%22no+endosymbiotic+events+from+Glaucophyta+are+reported%22&pg=PA29 Handbook of Marine Microalgae: Biotechnology Advances]</ref>

Archaeplastid cells typically lack centrioles and have mitochondria with flat cristae. They usually have a cell wall that contains cellulose, and photosynthesized carbohydrates are stored intracellularly in the form of starch, but these characteristics are also shared with other eukaryotes. Different archaeplastid clades differ slightly in cellular biochemistry. Red algae are pigmented with chlorophyll ''a'' and phycobiliproteins like most cyanobacteria, and accumulate starch ''outside'' the chloroplasts. Green algae, land plants (embryophytes) and the minor basal group Prasinodermophyta – together known as Viridiplantae (Latin for "green plants") or Chloroplastida – are pigmented with both chlorophyll ''a'' and chlorophyll ''b'', but lack phycobiliproteins, and starch is accumulated ''inside'' the chloroplasts.<ref name=Viola>{{cite journal|title=The unique features of starch metabolism in red algae |first1=R. |last1=Viola |first2=P. |last2=Nyvall |first3=M. |last3=Pedersén |journal=Proceedings of the Royal Society B: Biological Sciences|volume=268 |issue=1474|date=2001|pages=1417–1422 |doi=10.1098/rspb.2001.1644|pmid=11429143|pmc=1088757}}</ref> The glaucophytes have typical cyanobacterial pigments like those of red algae, but their plastids (called cyanelles) differ in having a peptidoglycan outer layer.<ref name=Adl2005>{{cite journal |first= S.M. |last=Adl |s2cid=8060916 |title=The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists |journal=Journal of Eukaryotic Microbiology |year=2005 |volume=52 |issue=5 |pages=399–451 |doi= 10.1111/j.1550-7408.2005.00053.x |pmid=16248873 |display-authors=etal|doi-access=free }}</ref>

The main evidence that archaeplastids form a monophyletic group comes from genetic studies, which indicate their plastids likely had a single origin. This evidence is however disputed,<ref>{{cite journal |author=Parfrey. L. W. |author2=Barbero, E. |author3=Lasser, E |title=Evaluating support for the current classification of eukaryotic diversity |journal=PLOS Genetics |volume=2 |issue=12 |article-number=e220 |date=December 2006 |pmid=17194223 |pmc=1713255 |doi=10.1371/journal.pgen.0020220 |display-authors=etal |doi-access=free }}</ref><ref name="kim">{{cite journal |pmc= 2440802 |doi= 10.1371/journal.pone.0002621 |date=July 2008 |author= Kim, E |author2=Graham, L. E. |title= EEF2 analysis challenges the monophyly of Archaeplastida and Chromalveolata |volume= 3 |issue= 7 |article-number= e2621 |pmid= 18612431 |journal= PLOS ONE |editor1-last= Redfield |editor1-first= Rosemary Jeanne|bibcode= 2008PLoSO...3.2621K |doi-access= free }}</ref> and based on the evidence to date, it is not possible to definitively confirm or refute alternative evolutionary scenarios to a single primary endosymbiosis event.<ref>{{cite journal | last1=Mackiewicz | first1=P. | last2=Gagat | first2=P. | year=2014 | title=Monophyly of Archaeplastida supergroup and relationships among its lineages in the light of phylogenetic and phylogenomic studies. Are we close to a consensus?. | journal=Acta Societatis Botanicorum Poloniae | volume=83 | issue=4| pages=263–280 | doi=10.5586/asbp.2014.044| bibcode=2014AcSBP..83..263M | doi-access=free }}</ref> Photosynthetic organisms with plastids of indirect origin (such as brown algae, euglenids, diatoms and dinoflagellates) do not belong to Archaeplastida and are instead grouped into numerous other protist classifications, making the term "algae" a rather vague polyphyletic group.

Archaeplastida should not be confused with the older and obsolete name Archiplastideae, which refers to cyanobacteria and other groups of bacteria.<ref>Copeland, H. F. (1956). ''The Classification of Lower Organisms''. Palo Alto: Pacific Books, p. 29, [https://archive.org/stream/ost-biology-classificationof00cope/classificationof00cope#page/n47/mode/2up].</ref><ref>{{cite journal | last1=Bessey | first1=C. E. | year=1907 | title=A Synopsis of Plant Phyla | url=https://www.biodiversitylibrary.org/item/94530#page/329/mode/1up | journal=Univ. Nebraska Studies | volume=7 | pages=275–358 }}</ref>

==Taxonomy== {{See also|Eukaryote#Phylogeny}} The consensus in 2005, when the group consisting of the glaucophytes and red and green algae and land plants was named 'Archaeplastida',<ref name=Adl2005/> was that it was a clade, i.e. was monophyletic. Many studies published since then have provided evidence in agreement.<ref name="Burki2007">{{cite journal|title=Phylogenomics Reshuffles the Eukaryotic Supergroups|author=Burki, Fabien |author2=Kamran Shalchian-Tabrizi|author3=Marianne Minge|author4=Åsmund Skjæveland|author5=Sergey I. Nikolaev|author6=Kjetill S. Jakobsen|author7= Jan Pawlowski|journal=PLOS ONE|volume=2|issue=8|doi=10.1371/journal.pone.0000790|pmc=1949142|pmid=17726520|year=2007|article-number=e790|editor1-last=Butler|editor1-first=Geraldine|bibcode=2007PLoSO...2..790B|doi-access=free }}</ref><ref name="Burki2009">{{Cite journal |last1=Burki |first1=F. |last2=Inagaki |year=2009 |first2=Y. |last3=Brate |first3=J. |last4=Archibald |first4=J. M. |last5=Keeling |first5=P. J. |last6=Cavalier-Smith |first6=T. |title=Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic Chromalveolates |journal=Genome Biology and Evolution |volume=1 |pages=231–238 |doi=10.1093/gbe/evp022 |pmid=20333193 |pmc=2817417|display-authors=etal}}</ref><ref name="CavalierSmith2009">{{Cite journal|last=Cavalier-Smith |first=Thomas |author-link=Thomas Cavalier-Smith |year=2009 |title=Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree |journal=Biology Letters|volume=6 |pages=342–345 |doi=10.1098/rsbl.2009.0948 |pmid=20031978 |pmc=2880060|issue=3}}</ref><ref>{{Cite journal|last1=Rogozin |first1=I. B. |last2=Basu |first2=M. K.|last3=Csürös |first3=M.|last4=Koonin|first4=E. V. |year=2009 |title=Analysis of Rare Genomic Changes Does Not Support the Unikont–Bikont Phylogeny and Suggests Cyanobacterial Symbiosis as the Point of Primary Radiation of Eukaryotes |journal=Genome Biology and Evolution|pmid=20333181 |volume=1|pmc=2817406|pages=99–113 |doi=10.1093/gbe/evp011 |name-list-style=amp }}</ref> Other studies, though, have suggested that the group is paraphyletic.<ref>{{cite journal | doi=10.1126/science.290.5493.972 | title=A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data | date=2000 | last1=Baldauf | first1=Sandra L. | last2=Roger | first2=A. J. | last3=Wenk-Siefert | first3=I. | last4=Doolittle | first4=W. F. | journal=Science | volume=290 | issue=5493 | pages=972–977 | pmid=11062127 | bibcode=2000Sci...290..972B }}</ref><ref>Lipscomb, Diana. 1991. Broad classification: the kingdoms and the protozoa. In: Parasitic Protozoa, Vol. 1, 2nd ed., J.P. Kreier, J.R. Baker (eds.), pp. 81-136. Academic Press, San Diego.</ref><ref name="Nozaki"/><ref name="kim"/><ref name="pmid31268560">{{cite journal |author=Palmgren M, Sørensen DM, Hallström BM, Säll T, Broberg K |title=Evolution of P2A and P5A ATPases: ancient gene duplications and the red algal connection to green plants revisited |journal=Physiol. Plant. |volume=168 |issue=3 |pages=630–647 |date=August 2019 |pmid=31268560 |doi=10.1111/ppl.13008 |pmc=7065118 }}</ref> To date, the situation appears unresolved, but a strong signal for Plantae (Archaeplastida) monophyly has been demonstrated in a recent study (with an enrichment of red algal genes).<ref name="Chan CX 2011"/> The assumption made here is that Archaeplastida is a valid clade.

Various names have been given to the group. Some authors have simply referred to the group as plants or Plantae.<ref name="7-or-9">{{cite journal |author=T. Cavalier-Smith |title=Eukaryote Kingdoms: Seven or Nine? |journal=BioSystems |year=1981 |volume=14 |pages=461–481 |doi=10.1016/0303-2647(81)90050-2 |pmid=7337818 |issue=3–4|bibcode=1981BiSys..14..461C }}</ref><ref>{{cite journal |first= Debashish |last= Bhattacharya |author2= Yoon, Hwan Su|author3= Hackett, Jeremiah |title= Photosynthetic eukaryotes unite: endosymbiosis connects the dots |journal= BioEssays |year= 2003 |volume= 26 |pages= 50–60 |doi= 10.1002/bies.10376 |pmid= 14696040 |issue= 1}}</ref> However, the name Plantae is ambiguous, since it has also been applied to less inclusive clades, such as Viridiplantae and embryophytes. To distinguish, the larger group is sometimes known as Plantae ''sensu lato'' ("plants in the broad sense").

To avoid ambiguity, other names have been proposed. Primoplantae, which appeared in 2004, seems to be the first new name suggested for this group.<ref name="palmer">{{cite journal |author1=Palmer, Jeffrey D. |author2=Soltis, Douglas E. |author3=Chase, Mark W. |title=The plant tree of life: an overview and some points of view |journal=American Journal of Botany |year=2004 |volume=91 |pages=1437–1445 |doi=10.3732/ajb.91.10.1437 |issue=10 |pmid=21652302|doi-access=free |bibcode=2004AmJB...91.1437P }}</ref> Another name applied to this node is Plastida, defined as the clade sharing "plastids of primary (direct prokaryote) origin [as] in ''Magnolia virginiana'' Linnaeus 1753".<ref>{{cite journal |first= A. G. B. |last= Simpson |title= Highest-level taxa within Eukaryotes |journal= First International Phylogenetic Nomenclature Meeting. Paris, July 6–9 |year= 2004}}</ref>

Although many studies have suggested the Archaeplastida form a monophyletic group,<ref name="pmid20952597">{{cite journal |author=Vinogradov S. N. |author2=Fernández, I. |author3=Hoogewijs, D. |author4=Arredondo-Peter, R. |title=Phylogenetic Relationships of 3/3 and 2/2 Hemoglobins in Archaeplastida Genomes to Bacterial and Other Eukaryote Hemoglobins |journal=Molecular Plant |volume=4 |issue=1 |pages=42–58 |date=October 2010 |pmid=20952597 |doi=10.1093/mp/ssq040 |doi-access=free }}</ref> a 2009 paper argues that they are in fact paraphyletic.<ref name="Nozaki">{{cite journal |author=Nozaki, H. |author2=Maruyama, S.|author3= Matsuzaki, M.|author4= Nakada, T.|author5= Kato, S.|author6= Misawa, K. |title=Phylogenetic positions of Glaucophyta, green plants (Archaeplastida) and Haptophyta (Chromalveolata) as deduced from slowly evolving nuclear genes |journal=Molecular Phylogenetics and Evolution |volume=53 |issue=3 |pages=872–80 |date=December 2009 |pmid=19698794 |doi=10.1016/j.ympev.2009.08.015 |bibcode=2009MolPE..53..872N }}</ref> The enrichment of novel red algal genes in a recent study, however, demonstrates a strong signal for Plantae (Archaeplastida) monophyly and an equally strong signal of gene sharing history between the red/green algae and other lineages.<ref name="Chan CX 2011">{{Cite journal |year=2011 |issue=4 |title=Red and green algal monophyly and extensive gene sharing found in a rich repertoire of red algal genes |journal=Current Biology |volume=21 |pages=328–333 |doi=10.1016/j.cub.2011.01.037 |pmid=21315598 |author1=Chan, C. X. |author2=Yang, E. C. |author3=Banerjee, T. |author4=Yoon, H. S. |author5=Martone, P. T. |author6=Estevez, J. M. |author7=Bhattacharya, D. |s2cid=7162977 |doi-access=free |bibcode=2011CBio...21..328C }}</ref> This study provides insight on how rich mesophilic red algal gene data are crucial for testing controversial issues in eukaryote evolution and for understanding the complex patterns of gene inheritance in protists.

The name Archaeplastida was proposed in 2005 by a large international group of authors (Adl ''et al.''), who aimed to produce a classification for the eukaryotes which took into account morphology, biochemistry, and phylogenetics, and which had "some stability in the near term." They rejected the use of formal taxonomic ranks in favour of a hierarchical arrangement where the clade names do not signify rank. Thus, the phylum name 'Glaucophyta' and the class name 'Rhodophyceae' appear at the same level in their classification. The divisions proposed for the Archaeplastida are shown below in both tabular and diagrammatic form.<ref name=Adl2005/>

'''Archaeplastida''': [[File:Glaucocystis sp.jpg|thumb|upright|The glaucophyte ''Glaucocystis'' ]] * Glaucophyta Skuja, 1954 (Glaucocystophyta Kies & Kremer, 1986) – glaucophytes :*Glaucophytes are a small group of freshwater single-celled algae. Their plastids, called cyanelles, have a peptidoglycan layer, making them more similar to cyanobacteria than those of the remaining Archaeplastida.

[[File:Laurencia.jpg|thumb|upright|The rhodophyte ''Laurencia'']] * Rhodophyceae Thuret, 1855, emend. Rabenhorst, 1863, emend. Adl ''et al.'', 2005 (Rhodophyta Wettstein 1901) – red algae ::Red algae form one of the largest groups of algae. Most are seaweeds, being multicellular and marine. Their red colour comes from phycobiliproteins, used as accessory pigments in light capture for photosynthesis. * Chloroplastida Adl ''et al.'', 2005 (Viridiplantae Cavalier-Smith 1981; Chlorobionta Jeffrey 1982, emend. Bremer 1985, emend. Lewis and McCourt 2004; Chlorobiota Kendrick and Crane 1997) ::Chloroplastida is the term chosen by Adl ''et al.'' for the group made up of the green algae and land plants (embryophytes). Except where lost secondarily, all have chloroplasts without a peptidoglycan layer and lack phycobiliproteins.

[[File:Stigeoclonium sp zugespitzte seitenzweige.jpeg|thumb|upright|The chlorophyte ''Stigeoclonium'']] :* Chlorophyta Pascher, 1914, emend. Lewis & McCourt, 2004 – green algae (part) :::Adl et al. employ a narrow definition of the Chlorophyta; other sources include the Chlorodendrales and Prasinophytae, which may themselves be combined. ::* Ulvophyceae Mattox & Stewart, 1984 ::* Trebouxiophyceae Friedl, 1995 (Pleurastrophyceae Mattox et al. 1984; Microthamniales Melkonian 1990) ::* Chlorophyceae Christensen, 1994 :* Chlorodendrales Fritsch, 1917 – green algae (part) :* Prasinophytae Cavalier-Smith, 1998, emend. Lewis & McCourt, 2004 – green algae (part) :* ''Mesostigma'' Lauterborn, 1894, emend. McCourt ''in'' Adl ''et al.'', 2005 (Mesostigmata Turmel, Otis, and Lemieux 2002) :* Charophyta Karol ''et al.'', 2001, emend. Lewis & McCourt, 2004 (Charophyceae Smith 1938, emend. Mattox and Stewart 1984) – green algae (part) and land plants :::Charophyta ''sensu lato'', as used by Adl ''et al.'', is a monophyletic group which is made up of some green algae, including the stoneworts (Charophyta ''sensu stricto''), as well as the land plants (embryophytes). ::* Sub-divisions other than Streptophytina (below) were not given by Adl et al. ::::Other sources would include the green algal groups Chlorokybales, Klebsormidiales, Zygnematales and Coleochaetales.<ref name="pmid16236178">{{cite journal |author=Turmel, M. |author2=Otis, C.|author3= Lemieux, C. |title=The complete chloroplast DNA sequences of the charophycean green algae ''Staurastrum'' and ''Zygnema'' reveal that the chloroplast genome underwent extensive changes during the evolution of the Zygnematales |journal=BMC Biology |volume=3|article-number=22 |year=2005 |issue=1 |pmid=16236178 |pmc=1277820 |doi=10.1186/1741-7007-3-22 |doi-access=free |bibcode=2005BMCB....3...22T }}</ref> ::* Streptophytina Lewis & McCourt, 2004 – stoneworts and land plants :::* Charales Lindley 1836 (Charophytae Engler, 1887) – stoneworts :::* Plantae Haeckel 1866 (Cormophyta Endlicher, 1836; Embryophyta Endlicher, 1836, emend. Lewis & McCourt, 2004) – land plants (embryophytes)

=== External phylogeny ===

Below is a consensus reconstruction of the relationships of Archaeplastida with its nearest neighbours, mainly based on molecular data.<ref name="Leliaert20122">{{cite journal |last1=Leliaert |first1=Frederik |last2=Smith |first2=David R. |last3=Moreau |first3=Hervé |last4=Herron |first4=Matthew D. |last5=Verbruggen |first5=Heroen |last6=Delwiche |first6=Charles F. |last7=De Clerck |first7=Olivier |year=2012 |title=Phylogeny and Molecular Evolution of the Green Algae |url=http://images.algaebase.org/pdf/5628E58F0ecc431F0CsJm2B04CAD/49951.pdf |journal=Critical Reviews in Plant Sciences |volume=31 |issue=1 |pages=1–46 |doi=10.1080/07352689.2011.615705 |bibcode=2012CRvPS..31....1L |s2cid=17603352 |access-date=2017-10-15 |archive-date=2015-09-24 |archive-url=https://web.archive.org/web/20150924201133/http://images.algaebase.org/pdf/5628E58F0ecc431F0CsJm2B04CAD/49951.pdf }}</ref><ref name="Cook etal-2017">{{Cite book |title=Handbook of the Protists |last1=Cook |first1=Martha E. |last2=Graham |first2=Linda E. |chapter=Chlorokybophyceae, Klebsormidiophyceae, Coleochaetophyceae |date=2017 |publisher=Springer International Publishing |isbn=978-3-319-28147-6 |editor-last=Archibald |editor-first=John M. |pages=185–204 |doi=10.1007/978-3-319-28149-0_36 |editor-last2=Simpson |editor-first2=Alastair G. B. |editor-last3=Slamovits |editor-first3=Claudio H.}}</ref><ref name="Lewis&McCourt-2004">{{cite journal |last=Lewis |first=Louise A. |author2=McCourt, Richard M. |year=2004 |title=Green algae and the origin of land plants |journal=American Journal of Botany |volume=91 |issue=10 |pages=1535–1556 |doi=10.3732/ajb.91.10.1535 |pmid=21652308 |bibcode=2004AmJB...91.1535L }}</ref><ref>{{Cite journal |last1=Adl |first1=Sina M. |last2=Simpson |first2=Alastair G. B. |last3=Lane |first3=Christopher E. |last4=Lukeš |first4=Julius |last5=Bass |first5=David |last6=Bowser |first6=Samuel S. |last7=Brown |first7=Matthew W. |last8=Burki |first8=Fabien |last9=Dunthorn |first9=Micah |date=2012-09-01 |title=The Revised Classification of Eukaryotes |journal=Journal of Eukaryotic Microbiology |volume=59 |issue=5 |pages=429–514 |doi=10.1111/j.1550-7408.2012.00644.x |pmid=23020233 |pmc=3483872}}</ref>

{{Clade |style=line-height:80%|label1=Diaphoretickes |{{clade |1={{clade |state=dashed |1={{clade |1=Meteora 60px |2=Hemimastigophora 40px }} |2=? (Provora) |3={{clade |1={{clade |1=Provora |state1=dashed |2=Haptista 60px |label3=TSAR |3={{clade |1=Telonemia |state1=dashed |label2=SAR |2={{clade |1=Rhizaria 60px |label2=Halvaria |2={{clade |1=Stramenopiles 50px |2=Alveolata 90px }} }} }} }} |label2=CAM |2={{clade |1={{clade |1=Cryptista 70px |2=''Microheliella maris''<ref name="Yazaki_2021">{{cite bioRxiv |last1=Yazaki |first1=Euki |last2=Yabuki |first2=Akinori |last3=Imaizumi |first3=Ayaka |last4=Kume |first4=Keitaro |last5=Hashimoto |first5=Tetsuo |last6=Inagaki |first6=Yuji |title=Phylogenomics invokes the clade housing Cryptista, Archaeplastida, and ''Microheliella maris'' |biorxiv=10.1101/2021.08.29.458128 |date=31 August 2021}}</ref> }} |2='''Archaeplastida''' 60px }} }} }} }} }} There has been disagreement near the Archaeplastida root, e.g. whether Cryptista emerged within the Archaeplastida. In 2014 a thorough review was published on these inconsistencies.<ref>{{Cite journal |last1=Mackiewicz |first1=Paweł |last2=Gagat |first2=Przemysław |date=2014-12-31 |title=Monophyly of Archaeplastida supergroup and relationships among its lineages in the light of phylogenetic and phylogenomic studies. Are we close to a consensus? |journal=Acta Societatis Botanicorum Poloniae |volume=83 |issue=4 |pages=263–280 |doi=10.5586/asbp.2014.044 |bibcode=2014AcSBP..83..263M |doi-access=free}}</ref> The position of Telonemia and Picozoa are not clear. Also Hacrobia (Haptista + Cryptista) may be completely associated with the SAR clade. The SAR are often seen as eukaryote-eukaryote hybrids, contributing to the confusion in the genetic analyses.

A sister of Gloeomargarita lithophora has been engulfed by an ancestor of the Archaeplastida, leading to the plastids which are living in permanent endosymbiosis in most of the descendant lineages. Because both Gloeomargarita and related cyanobacteria, in addition to the most primitive archaeplastids, all live in freshwater, it seems the Archaeplastida originated in freshwater, and only colonized the oceans in the late Proterozoic.<ref>{{cite journal |doi=10.1016/j.cub.2016.12.006 |pmid=28171752 |volume=27 |title=Endosymbiosis: Did Plastids Evolve from a Freshwater Cyanobacterium? |year=2017 |journal=Current Biology |pages=R103–R105 |last1=de Vries |first1=Jan |last2=Archibald |first2=John M. |issue=3 |doi-access=free |bibcode=2017CBio...27.R103D }}</ref><ref>{{Cite journal |pmc=5604047|year=2017 |last1=Lewis |first1=L. A. |title=Hold the salt: Freshwater origin of primary plastids |journal=PNAS |volume=114 |issue=37 |pages=9759–9760 |pmid=28860199 |doi=10.1073/pnas.1712956114 |bibcode=2017PNAS..114.9759L |doi-access=free}}</ref>

=== Internal phylogeny ===

In 2019, a phylogeny of the Archaeplastida based on genomes and transcriptomes from 1,153 plant species was proposed.<ref name="1000plants">{{cite journal |last1=Leebens-Mack |first1=M. |last2=Barker |first2=M. |last3=Carpenter |first3=E. |author4-link=Michael Deyholos |last4=Deyholos |first4=M. K. |last5=Gitzendammer |first5=M. A. |last6=Graham |first6=S.W. |last7=Grosse |first7=I. |last8=Li |first8=Zheng |display-authors=3 |title=One thousand plant transcriptomes and the phylogenomics of green plants |journal=Nature |volume=574 |issue=7780 |year=2019 |pages=679–685 |doi=10.1038/s41586-019-1693-2 |pmid=31645766 |pmc=6872490 |doi-access=free }}</ref> The placing of algal groups is supported by phylogenies based on genomes from the Mesostigmatophyceae and Chlorokybophyceae that have since been sequenced. Both the "chlorophyte algae" and the "streptophyte algae" are treated as paraphyletic (vertical bars beside phylogenetic tree diagram) in this analysis.<ref name="MvirideGenome1">{{cite journal |last1=Liang |first1=Zhe |display-authors=etal |title=Mesostigma viride Genome and Transcriptome Provide Insights into the Origin and Evolution of Streptophyta |journal=Advanced Science |volume=7 |issue=1 |year=2019 |article-number=1901850 |doi=10.1002/advs.201901850 |pmid=31921561 |pmc=6947507 |doi-access=free }}</ref><ref name="Mv_and_Ca_Genomes">{{cite journal |last1=Wang |first1=Sibo |display-authors=etal |title=Genomes of early-diverging streptophyte algae shed light on plant terrestrialization |journal=Nature Plants |volume=6 |issue=2 |year=2020 |pages=95–106 |doi=10.1038/s41477-019-0560-3 |pmid=31844283 |pmc=7027972 |bibcode=2020NatPl...6...95W |doi-access=free }}</ref> The classification of Bryophyta is supported both by Puttick ''et al.'' 2018,<ref name="Puttick2018">{{cite journal |last1=Puttick |first1=Mark |display-authors=etal |title=The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte |journal=Current Biology |volume=28 |issue=5 |year=2018 |pages=733–745 |doi=10.1016/j.cub.2018.01.063 |pmid=29456145|doi-access=free |bibcode=2018CBio...28E.733P |hdl=1983/ad32d4da-6cb3-4ed6-add2-2415f81b46da |hdl-access=free }}</ref> and by phylogenies involving the hornwort genomes that have also since been sequenced.<ref name="HornwortGenome1">{{cite journal |last1=Zhang |first1=Jian |display-authors=etal |title=The hornwort genome and early land plant evolution |journal=Nature Plants |volume=6 |issue=2 |year=2020 |pages=107–118 |doi=10.1038/s41477-019-0588-4|pmid=32042158 |pmc=7027989 |bibcode=2020NatPl...6..107Z |doi-access=free }}</ref><ref name="HornwortGenome2">{{cite journal |last1=Li |first1=Fay Wei |display-authors=etal |title=Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts |journal=Nature Plants |volume=6 |issue=3 |year=2020 |pages=259–272 |doi=10.1038/s41477-020-0618-2|pmid=32170292 |pmc=8075897 |bibcode=2020NatPl...6..259L |doi-access=free }}</ref> Recent work on non-photosynthetic algae places Rhodelphidia as sister to Rhodophyta or to Glaucophyta and Viridiplantae;<ref name="Gawryluk Tikhonenkov Hehenberger Husnik 2019 pp. 240–243">{{cite journal |last1=Gawryluk |first1=Ryan M. R. |last2=Tikhonenkov |first2=Denis V. |last3=Hehenberger |first3=Elisabeth |last4=Husnik |first4=Filip |last5=Mylnikov |first5=Alexander P. |last6=Keeling |first6=Patrick J. |title=Non-photosynthetic predators are sister to red algae |journal=Nature |volume=572 |issue=7768 |date=17 July 2019 |doi=10.1038/s41586-019-1398-6 |pages=240–243|pmid=31316212 |bibcode=2019Natur.572..240G |s2cid=197542583 }}</ref><ref>{{cite bioRxiv |last1=Novak |first1=Lukas V. F. |title=Nucleomorph phylogenomics suggests a deep and ancient origin of cryptophyte plastids within Rhodophyta |date=2024-03-11 |biorxiv=10.1101/2024.03.10.584144 |last2=Muñoz-Gómez |first2=Sergio A. |last3=Beveren |first3=Fabian van |last4=Ciobanu |first4=Maria |last5=Eme |first5=Laura |last6=López-García |first6=Purificación |last7=Moreira |first7=David}}</ref> and Picozoa sister to that pair of groups.<ref name="Schön Zlatogursky Singh Poirier 2021 p.">{{cite journal |last1=Schön |first1=Max E. |last2=Zlatogursky |first2=Vasily V. |last3=Singh |first3=Rohan P. |last4=Poirier |first4=Camille |last5=Wilken |first5=Susanne |last6=Mathur |first6=Varsha |last7=Strassert |first7=Jürgen F. H. |last8=Pinhassi |first8=Jarone |last9=Worden |first9=Alexandra Z. |last10=Keeling |first10=Patrick J. |last11=Ettema |first11=Thijs J. G. |last12=Wideman |first12=Jeremy G. |last13=Burki |first13=Fabien |title=Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae |journal=Nature Communications |volume=12 |issue=1 |date=17 November 2021 |page=6651 |doi=10.1038/s41467-021-26918-0|pmid=34789758 |pmc=8599508 |bibcode=2021NatCo..12.6651S }}</ref>

{{clade|style=font-size:90%;line-height:80%; |grouplabel1={{clade labels |label1="chlorophyte algae"|top1=15% |label2="streptophyte algae"|top2=40%}} |label1='''Archaeplastida''' |1={{clade |label1=Rhodaria |1={{clade |1=Picozoa 30px |2={{clade |1=Rhodelphidia |2=Rhodophyta 50px }} }} |2={{clade |1=Glaucophyta 50px |label2='''Viridiplantae''' |sublabel2= (green plants) |2={{clade |1=Chlorophyta 50px |bar1=darkgreen |2={{clade |1=Prasinococcales |bar1=darkgreen |2=  |state2=none |style2=font-size:50%;line-height:50%;  |label3=Streptophyta/ |sublabel3=Charophyta * |3={{clade |1= {{clade |1=Mesostigmatophyceae|bar1=blue |2={{clade |1=Chlorokybophyceae|bar1=blue |2=''Spirotaenia'' 30px |bar2=blue }} }} |2={{clade |1=Klebsormidiales 50px |bar1=blue |2={{clade |1=''Chara'' 40px |bar1=blue |2={{clade |1=Coleochaetales|bar1=blue |2={{clade |1=Zygnematophyceae 50px |bar1=blue |label2=Embryophytes |sublabel2= (land plants) |2={{clade |1={{clade |label1=Bryophytes |1={{clade |1=Hornworts 40px |2={{clade |1=Liverworts 50px |2=Mosses 20px }} }} }} |2={{clade |1=Lycophytes 50px |label2=Euphyllophyta |2={{clade |1=Ferns 50px |label2=Spermatophytes |sublabel2= (seed plants) |2={{clade |1=Gymnosperms 40px |2=Angiosperms 50px }} }} }} }} }} }} }} }} }} }} }} }} }} }}

== Morphology == All archaeplastidans have plastids (chloroplasts) that carry out photosynthesis and are believed to be derived from endosymbiotic cyanobacteria. In glaucophytes, perhaps the most primitive members of the group, the chloroplast is called a ''cyanelle'' and shares several features with cyanobacteria, including a peptidoglycan cell wall, that are not retained in other members of the group. The resemblance of cyanelles to cyanobacteria supports the endosymbiotic theory.

The cells of most archaeplastidans have walls, commonly but not always made of cellulose.{{citation needed|date=June 2024}}

The Archaeplastida vary widely in the degree of their cell organization, from isolated cells to filaments to colonies to multi-celled organisms. The earliest were unicellular, and many groups remain so today. Multicellularity evolved separately in several groups, including red algae, ulvophyte green algae, and in the green algae that gave rise to stoneworts and land plants.

==Endosymbiosis== {{main|Endosymbiotic theory}}

Because the ancestral archaeplastidan is hypothesized to have acquired its chloroplasts directly by engulfing cyanobacteria, the event is known as a ''primary endosymbiosis'' (as reflected in the name chosen for the group 'Archaeplastida' i.e. 'ancient plastid'). In 2013 it was discovered that one species of green algae, ''Cymbomonas tetramitiformis'' in the order Pyramimonadales, is a mixotroph and able to support itself through both phagotrophy and phototrophy. It is not yet known if this is a primitive trait and therefore defines the last common ancestor of Archaeplastida, which could explain how it obtained its chloroplasts, or if it is a trait regained by horizontal gene transfer.<ref>{{cite journal|title=Cells inside Cells: Symbiosis and Continuing Phagotrophy|journal=Current Biology|volume=23|issue=12|pages=R530–R531|doi=10.1016/j.cub.2013.05.006|pmid=23787050|year=2013|last1=Raven|first1=John A.|doi-access=free|bibcode=2013CBio...23.R530R }}</ref> Since then more species of mixotrophic green algae, such as ''Pyramimonas tychotreta'' and ''Mantoniella antarctica'', has been found.<ref>{{cite journal | doi=10.1038/s41396-021-00899-w | title=Experimental identification and in silico prediction of bacterivory in green algae | year=2021 | last1=Bock | first1=Nicholas A. | last2=Charvet | first2=Sophie | last3=Burns | first3=John | last4=Gyaltshen | first4=Yangtsho | last5=Rozenberg | first5=Andrey | last6=Duhamel | first6=Solange | last7=Kim | first7=Eunsoo | journal=The ISME Journal | volume=15 | issue=7 | pages=1987–2000 | pmid=33649548 | pmc=8245530 | bibcode=2021ISMEJ..15.1987B }}</ref>

Evidence for primary endosymbiosis includes the presence of a double membrane around the chloroplasts; one membrane belonged to the bacterium, and the other to the eukaryote that captured it. Over time, many genes from the chloroplast have been transferred to the nucleus of the host cell through endosymbiotic gene transfer (EGT). It is estimated that 6–20% of the archaeplastidan genome consist of genes transferred from the endosymbiont.<ref>{{cite journal | doi=10.3389/fpls.2013.00366 | doi-access=free | title=Algal endosymbionts as vectors of horizontal gene transfer in photosynthetic eukaryotes | year=2013 | last1=Qiu | first1=Huan | last2=Yoon | first2=Hwan Su | last3=Bhattacharya | first3=Debashish | journal=Frontiers in Plant Science | volume=4 | page=366 | pmid=24065973 | pmc=3777023 | bibcode=2013FrPS....4..366Q }}</ref> The presence of such genes in the nuclei of eukaryotes without chloroplasts suggests this transfer happened early in the evolution of the group.<ref>{{cite journal |last= Andersson |first= Jan O. |author2=Roger, Andrew J. |title= A cyanobacterial gene in non-photosynthetic protists – an early chloroplast acquisition in eukaryotes? |journal= Current Biology |year= 2002 |volume= 12 |issue= 2 |pages= 115–119 |doi= 10.1016/S0960-9822(01)00649-2 |pmid= 11818061|s2cid= 18809784 |doi-access= free |bibcode= 2002CBio...12..115A }}</ref>

Other eukaryotes with chloroplasts appear to have gained them by engulfing a single-celled archaeplastidan with its own bacterially-derived chloroplasts. Because these events involve endosymbiosis of cells that have their own endosymbionts, the process is called ''secondary endosymbiosis''. The chloroplasts of such eukaryotes are typically surrounded by more than two membranes, reflecting a history of multiple engulfment. The chloroplasts of euglenids, chlorarachniophytes and a small group of dinoflagellates appear to be captured green algae,<ref>{{Cite journal | doi=10.1098/rstb.2009.0103| pmid=20124341| pmc=2817223| title=The endosymbiotic origin, diversification and fate of plastids| journal=Philosophical Transactions of the Royal Society B: Biological Sciences| volume=365| issue=1541| pages=729–748| year=2010| last1=Keeling| first1=Patrick J.}}</ref> whereas those of the remaining photosynthetic eukaryotes, such as heterokont algae, cryptophytes, haptophytes, and dinoflagellates, appear to be captured red algae.<ref>{{cite journal|last1=Stadnichuk|first1=I.N.|last2=Kusnetsov|first2=V.V.|title=Endosymbiotic Origin of Chloroplasts in Plant Cells' Evolution|journal=Russian Journal of Plant Physiology|volume=68|pages=1–16|year=2021|doi=10.1134/S1021443721010179|s2cid=255012748|issue=1 |bibcode=2021RuJPP..68....1S }}</ref>

==Fossil record== Perhaps the most ancient remains of Archaeplastida are putative red algae (''Rafatazmia'') within stromatolites in 1600 Ma (million years ago) rocks in India,<ref name=Rafatazmia>{{cite journal|doi=10.1371/journal.pbio.2000735|pmid=28291791|pmc=5349422|title=Three-dimensional preservation of cellular and subcellular structures suggests 1.6 billion-year-old crown-group red algae|journal=PLOS Biology|volume=15|issue=3|article-number=e2000735|year=2017|last1=Bengtson|first1=Stefan|last2=Sallstedt|first2=Therese|last3=Belivanova|first3=Veneta|last4=Whitehouse|first4=Martin |doi-access=free }}</ref> as well as possible alga fossils (''Tuanshanzia'') from China's Gaoyuzhuang Biota of a similar age.<ref>{{Cite journal|last1=Chen |first1=K. |last2=Miao |first2=L. |last3=Zhao |first3=F. |last4=Zhu |first4=M. |title=Carbonaceous macrofossils from the early Mesoproterozoic Gaoyuzhuang Formation in the Yanshan Range, North China |year=2023 |journal=Precambrian Research |volume=392 |article-number=107074 |doi=10.1016/j.precamres.2023.107074 |bibcode=2023PreR..39207074C }}</ref> Somewhat more recent are microfossils from the Roper group in northern Australia. The structure of these single-celled fossils resembles that of modern green algae. They date to the Mesoproterozoic Era, about 1500 to 1300 Ma.<ref>{{cite journal |last= Javaux |first= Emmanuelle J. |author2= Knoll, Andrew H.|author3= Walter, Malcolm R. |s2cid= 53600639 |title= TEM evidence for eukaryotic diversity in mid-Proterozoic oceans |journal= Geobiology |year= 2004 |volume= 2 |issue= 3 |pages= 121–132 |doi= 10.1111/j.1472-4677.2004.00027.x|bibcode= 2004Gbio....2..121J }}</ref> These fossils are consistent with a molecular clock study that calculated that this clade diverged about 1500 Ma.<ref>{{cite journal |last= Yoon |first= Hwan Su |author2= Hackett, Jeremiah D.|author3= Ciniglia, Claudia|author4= Pinto, Gabriele|author5= Bhattacharya, Debashish |title= A molecular timeline for the origin of photosynthetic eukaryotes |journal= Molecular Biology and Evolution |year= 2004 |volume= 21 |issue= 5 |pages= 809–818 |doi= 10.1093/molbev/msh075 |pmid= 14963099|doi-access= free }}</ref> The oldest fossil that can be assigned to a specific modern group is the red alga ''Bangiomorpha'', from 1200 Ma.<ref>{{cite journal |last= Butterfield |first= Nicholas J. |title= ''Bangiomorpha pubescens'' n. gen., n. sp.: implications for the evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes |journal= Paleobiology |year= 2000 |volume= 26 |issue= 3 |pages= 386–404 |doi= 10.1666/0094-8373(2000)026<0386:BPNGNS>2.0.CO;2|bibcode= 2000Pbio...26..386B |s2cid= 36648568 }}</ref>

In the late Neoproterozoic Era, algal fossils became more numerous and diverse. Eventually, in the Paleozoic Era, plants emerged onto land, and have continued to flourish up to the present.

==Notes== {{reflist|group=note}}

==References== {{Reflist|32em}}

==External links== {{Wikispecies}} * [http://tolweb.org/Eukaryotes/3 Tree of Life Eukaryotes]

Category:Archaeplastida Category:Diaphoretickes taxa