Editing Chloroplast (section)

== Primary chloroplast lineages ==
All primary chloroplasts belong to one of four chloroplast lineages—the [[glaucophyte]] chloroplast lineage, the [[rhodophyte]] ("red") chloroplast lineage, and the [[chloroplastidan]] ("green") chloroplast lineage, the amoeboid ''Paulinella chromatophora'' lineage.<ref name="Ball-2011" /> The glaucophyte, rhodophyte, and chloroplastidian lineages are all descended from the same ancestral endosymbiotic event and are all within the group [[Archaeplastida]].<ref name="Keeling-2004" />

=== Glaucophyte chloroplasts ===
{{See also|Glaucophyte|}}{{Plain image with caption|image=Woelfib cyanphoraparadoxa teilungsfigur 1 0632002 img 54414492 ude 20131024233254 small.jpg|caption=The glaucophyte ''[[Cyanophora paradoxa]]'' with two chloroplasts in the process of dividing.|align=right}}
The glaucophyte chloroplast group is the smallest of the three primary chloroplast lineages as there are only 25 described glaucophyte species.<ref>{{Cite journal |last=Guiry |first=Michael D. |date=2 January 2024 |title=How many species of algae are there? A reprise. Four kingdoms, 14 phyla, 63 classes and still growing |journal=Journal of Phycology |language=en |volume=60 |issue=2 |pages=214–228 |doi=10.1111/jpy.13431 |pmid=38245909 |bibcode=2024JPcgy..60..214G |issn=0022-3646|doi-access=free }}</ref> Glaucophytes diverged first before the red and green chloroplast lineages diverged.<ref>{{Cite journal |last=Archibald |first=John M. |date=27 January 2009 |title=The Puzzle of Plastid Evolution |url=https://linkinghub.elsevier.com/retrieve/pii/S0960982208014851 |journal=Current Biology |language=en |volume=19 |issue=2 |pages=R81–R88 |doi=10.1016/j.cub.2008.11.067|pmid=19174147 |bibcode=2009CBio...19..R81A }}</ref> Because of this, they are sometimes considered intermediates between cyanobacteria and the red and green chloroplasts.<ref name="Miyagishima-2011">{{Cite journal |last=Miyagishima |first=Shin-ya |date=1 March 2011 |title=Mechanism of Plastid Division: From a Bacterium to an Organelle |journal=Plant Physiology |language=en |volume=155 |issue=4 |pages=1533–1544 |doi=10.1104/pp.110.170688 |issn=1532-2548 |pmc=3091088 |pmid=21311032}}</ref> This early divergence is supported by both [[Phylogenetics|phylogenetic]] studies and physical features present in glaucophyte chloroplasts and cyanobacteria, but not the red and green chloroplasts. First, glaucophyte chloroplasts have a [[peptidoglycan]] wall, a type of cell wall otherwise only in bacteria (including cyanobacteria).<ref group="Note">For this reason, glaucophyte chloroplasts are also known as 'muroplasts' from the Latin ''muro'' meaning wall.</ref> Second, glaucophyte chloroplasts contain [[concentric]] unstacked [[thylakoid]]s which surround a [[carboxysome]] – an [[icosahedral]] structure that contains the enzyme [[RuBisCO]] responsible for [[carbon fixation]]. Third, starch created by the chloroplast is collected outside the chloroplast.<ref name="Wise-2006">{{Cite book |url=http://link.springer.com/10.1007/978-1-4020-4061-0 |title=The Structure and Function of Plastids |date=2006 |publisher=Springer Netherlands |isbn=978-1-4020-4060-3 |editor-last=Wise |editor-first=Robert R. |series=Advances in Photosynthesis and Respiration |volume=23 |location=Dordrecht |doi=10.1007/978-1-4020-4061-0 |editor-last2=Hoober |editor-first2=J. Kenneth}}</ref> Additionally, like cyanobacteria, both glaucophyte and rhodophyte thylakoids are studded with light collecting structures called [[phycobilisome]]s. 

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=== Rhodophyta (red chloroplasts) ===
{{See also|Red algae}}
{{plain image with caption|File:Cyanidium O5A.jpg|'''Diversity of red algae''' Clockwise from top left: ''[[Bornetia secundiflora]]'', ''[[Peyssonnelia squamaria]]'', ''[[Cyanidium]]'', ''[[Laurencia]]'', ''[[Callophyllis laciniata]]''. Red algal chloroplasts are characterized by [[phycobilin]] pigments which often give them their reddish color.|400px|right|top|triangle|#ca004d|image override=
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The rhodophyte, or [[red algae]], group is a large and diverse lineage.<ref name="Keeling-2004" /> Rhodophyte chloroplasts are also called ''rhodoplasts'',<ref name="Wise-2006b" /> literally "red chloroplasts".<ref>{{cite web|url=http://www.thefreedictionary.com/rhodo-|title=rhodo-|work=The Free Dictionary|publisher=Farlex|access-date=7 June 2013}}</ref> Rhodoplasts have a double membrane with an intermembrane space and [[phycobilin]] pigments organized into [[phycobilisome]]s on the thylakoid membranes, preventing their thylakoids from stacking.<ref name="Kim-2009" /> Some contain [[pyrenoid]]s.<ref name="Wise-2006b" /> Rhodoplasts have [[chlorophyll a|chlorophyll ''a'']] and phycobilins<ref name="Keeling-2010" /> for photosynthetic pigments; the phycobilin [[phycoerythrin]] is responsible for giving many red algae their distinctive [[red]] color.<ref name="Campbell-2009f">{{cite book | vauthors=Campbell NA, Reece JB, Urry LA, Cain ML, Wasserman, Minorsky PV, Jackson RB |title=Biology | edition=8th | year=2009 |publisher=Benjamin Cummings (Pearson) | pages=582–92 | isbn=978-0-8053-6844-4 }}</ref> However, since they also contain the blue-green [[chlorophyll a|chlorophyll ''a'']] and other pigments, many are reddish to purple from the combination.<ref name="Wise-2006b" />{{dubious|date=January 2022|Subtractive pigments won't give purple}} The red phycoerytherin pigment is an adaptation to help red algae catch more sunlight in deep water<ref name="Wise-2006b" />—as such, some red algae that live in shallow water have less phycoerythrin in their rhodoplasts, and can appear more greenish.<ref name="Campbell-2009f" /> Rhodoplasts synthesize a form of starch called [[floridean starch]],<ref name="Wise-2006b" /> which collects into granules outside the rhodoplast, in the cytoplasm of the red alga.<ref name="Kim-2009" />

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=== Chloroplastida (green chloroplasts) ===
{{See also|Chloroplastida}}
{{plain image with caption|File:Micrasterias .jpg|'''Diversity of green algae''' Clockwise from top left: ''[[Scenedesmus]]'', ''[[Micrasterias]]'', ''[[Hydrodictyon]]'', ''[[Volvox]]'', ''[[Stigeoclonium]]''. Green algal chloroplasts are characterized by their pigments [[chlorophyll a|chlorophyll ''a'']] and [[chlorophyll b|chlorophyll ''b'']] which give them their green color.|425px|right|top|triangle|#3cca48|image override=
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The [[chloroplastida]] group is another large, highly diverse lineage that includes both [[green algae]] and [[land plants]].<ref name="Lewis-2004">{{cite journal | vauthors=Lewis LA, McCourt RM | title=Green algae and the origin of land plants | journal=American Journal of Botany | volume=91 | issue=10 | pages=1535–56 | date=October 2004 | pmid=21652308 | doi=10.3732/ajb.91.10.1535 | bibcode=2004AmJB...91.1535L }}</ref> This group is also called [[Viridiplantae]], which includes two core clades—[[Chlorophyta]] and [[Streptophyta]].

Most green chloroplasts are [[green]] in color, though some aren't due to accessory pigments that override the green from chlorophylls, such as in the resting cells of ''[[Haematococcus pluvialis]]''. Green chloroplasts differ from glaucophyte and red algal chloroplasts in that they have lost their [[phycobilisome]]s, and contain [[chlorophyll b|chlorophyll ''b'']].<ref name="Kim-2009" /> They have also lost the [[peptidoglycan]] wall between their double membrane, leaving an intermembrane space.<ref name="Kim-2009" /> Some [[plant]]s have kept some [[gene]]s required the synthesis of peptidoglycan, but have repurposed them for use in [[#Division|chloroplast division]] instead.<ref name="Machida-2006">{{cite journal | vauthors=Machida M, Takechi K, Sato H, Chung SJ, Kuroiwa H, Takio S, Seki M, Shinozaki K, Fujita T, Hasebe M, Takano H | display-authors=6 | title=Genes for the peptidoglycan synthesis pathway are essential for chloroplast division in moss | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=103 | issue=17 | pages=6753–8 | date=April 2006 | pmid=16618924 | pmc=1458953 | doi=10.1073/pnas.0510693103 | bibcode=2006PNAS..103.6753M | doi-access=free }}</ref> Chloroplastida lineages also keep their [[starch]] ''inside'' their chloroplasts.<ref name="Kim-2009" /><ref name="Keeling-2010" /><ref name="Lewis-2004" /> In plants and some algae, the chloroplast thylakoids are arranged in grana stacks. Some green algal chloroplasts, as well as those of [[hornworts]], contain a structure called a [[pyrenoid]],<ref name="Kim-2009" /> that concentrate [[RuBisCO]] and CO{{sub|2}} in the chloroplast, functionally similar to the glaucophyte [[carboxysome]].<ref name="Moroney-1999">{{cite journal | vauthors=Moroney JV, Somanchi A | title=How Do algae concentrate CO2 to increase the efficiency of photosynthetic carbon fixation? | journal=Plant Physiology | volume=119 | issue=1 | pages=9–16 | date=January 1999 | pmid=9880340 | pmc=1539202 | doi=10.1104/pp.119.1.9 }}</ref><ref>{{cite journal | vauthors=((Robison, T. A.)), ((Oh, Z. G.)), ((Lafferty, D.)), ((Xu, X.)), ((Villarreal, J. C. A.)), ((Gunn, L. H.)), ((Li, F.-W.)) | journal=Nature Plants | title=Hornworts reveal a spatial model for pyrenoid-based CO2-concentrating mechanisms in land plants | pages=63–73 | publisher=Nature Publishing Group | date=3 January 2025 | volume=11 | issn=2055-0278 | doi=10.1038/s41477-024-01871-0| pmid=39753956 }}
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There are some lineages of non-photosynthetic parasitic green algae that have lost their chloroplasts entirely, such as ''[[Prototheca]],''<ref name="Keeling-2010" /> or have no chloroplast while retaining the separate chloroplast genome, as in ''[[Helicosporidium]].''<ref name="Tartar-2004">{{cite journal |vauthors=Tartar A, Boucias DG |date=April 2004 |title=The non-photosynthetic, pathogenic green alga Helicosporidium sp. has retained a modified, functional plastid genome |journal=FEMS Microbiology Letters |volume=233 |issue=1 |pages=153–7 |doi=10.1016/j.femsle.2004.02.006 |pmid=15043882 |doi-access=free}}</ref> Morphological and physiological similarities, as well as [[phylogenetics]], confirm that these are lineages that ancestrally had chloroplasts but have since lost them.<ref name="Tartar-2004" /><ref>{{Cite journal |last1=Ueno |first1=Ryohei |last2=Urano |first2=Naoto |last3=Suzuki |first3=Motofumi |date=2003-06-01 |title=Phylogeny of the non-photosynthetic green micro-algal genus Prototheca (Trebouxiophyceae, Chlorophyta) and related taxa inferred from SSU and LSU ribosomal DNA partial sequence data |url=https://academic.oup.com/femsle/article-abstract/223/2/275/499272?redirectedFrom=fulltext |journal=FEMS Microbiology Letters |volume=223 |issue=2 |pages=275–280 |doi=10.1016/s0378-1097(03)00394-x |pmid=12829298 |issn=0378-1097}}</ref>

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=== ''Paulinella chromatophora'' ===
{{See also|Paulinella|}}
{{Plain image with caption|image=File:Paulinella-chromatophora-fig1ab.jpg|caption=Light micrograph of the amoeboid ''Paulinella chromatophora''|align=left}}

The photosynthetic amoeboids in the genus ''[[Paulinella]]—P. chromatophora, P. micropora,'' and marine ''P. longichromatophora—''have the only known independently evolved chloroplast, often called a '''chromatophore'''.<ref name=":0" group="Note" /> While all other chloroplasts originate from a single ancient endosymbiotic event, ''Paulinella'' independently acquired an endosymbiotic cyanobacterium from the genus ''[[Synechococcus]]'' around 90 – 140 million years ago.<ref name="Macorano-2021" /><ref name="Keeling-2004" /> Each ''Paulinella'' cell contains one or two sausage-shaped chloroplasts;<ref name="Nakayama-2012" /><ref name="Nowack-2011">{{cite journal |vauthors=Nowack EC, Vogel H, Groth M, Grossman AR, Melkonian M, Glöckner G |date=January 2011 |title=Endosymbiotic gene transfer and transcriptional regulation of transferred genes in Paulinella chromatophora |journal=Molecular Biology and Evolution |volume=28 |issue=1 |pages=407–22 |doi=10.1093/molbev/msq209 |pmid=20702568 |doi-access=free}}</ref> they were first described in 1894 by German biologist Robert Lauterborn.<ref>{{Cite journal |last=Archibald |first=John M. |date=25 September 2017 |title=Evolution: Protein Import in a Nascent Photosynthetic Organelle |url=https://linkinghub.elsevier.com/retrieve/pii/S0960982217310229 |journal=Current Biology |volume=27 |issue=18 |pages=R1004–R1006 |doi=10.1016/j.cub.2017.08.013 |pmid=28950079 |bibcode=2017CBio...27R1004A |issn=0960-9822}}</ref> 

The chromatophore is highly reduced compared to its free-living cyanobacterial relatives and has limited functions. For example, it has a genome of about 1 million [[base pair]]s, one third the size of ''Synechococcus'' genomes, and only encodes around 850 proteins.<ref name="Nakayama-2012" /> However, this is still much larger than other chloroplast genomes, which are typically around 150,000 base pairs. Chromatophores have also transferred much less of their DNA to the nucleus of their hosts. About 0.3–0.8% of the nuclear DNA in ''Paulinella'' is from the chromatophore, compared with 11–14% from the chloroplast in plants.<ref name="Nowack-2011" /> Similar to other chloroplasts, ''Paulinella'' provides specific proteins to the chromatophore using a specific targeting sequence.<ref>{{Cite journal |last1=Singer |first1=Anna |last2=Poschmann |first2=Gereon |last3=Mühlich |first3=Cornelia |last4=Valadez-Cano |first4=Cecilio |last5=Hänsch |first5=Sebastian |last6=Hüren |first6=Vanessa |last7=Rensing |first7=Stefan A. |last8=Stühler |first8=Kai |last9=Nowack |first9=Eva C.M. |date=25 September 2017 |title=Massive Protein Import into the Early-Evolutionary-Stage Photosynthetic Organelle of the Amoeba Paulinella chromatophora |url=https://linkinghub.elsevier.com/retrieve/pii/S0960982217310199 |journal=Current Biology |volume=27 |issue=18 |pages=2763–2773.e5 |doi=10.1016/j.cub.2017.08.010 |pmid=28889978 |bibcode=2017CBio...27E2763S |issn=0960-9822}}</ref> Because chromatophores are much younger compared to the canoncial chloroplasts, ''Paulinella chromatophora'' is studied to understand how early chloroplasts evolved.<ref name="Nakayama-2012" />

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