Editing Chloroplast (section)

=== Red algal derived chloroplasts ===
Secondary chloroplasts derived from [[red algae]] appear to have only been taken up only once, which then diversified into a large group called [[chromist]]s or chromalveolates. Today they are found in the [[Haptophyte|haptophytes]], [[Cryptomonad|cryptomonads]], [[Stramenopile|heterokonts]], [[Dinoflagellate|dinoflagellates]] and [[Apicomplexa|apicomplexans]] (the CASH lineage).<ref name="Keeling-2010" /> Red algal secondary chloroplasts usually contain chlorophyll c and are surrounded by four membranes.<ref name="Kim-2009" />

However, chromist [[monophyly]] has been rejected, and it is considered more likely that some chromists acquired their plastids by incorporating another chromist instead of inheriting them from a common ancestor. [[Cryptophyte]]s seem to have acquired plastids from red algae, which were then transmitted from them to both the [[Ochrophyte|Heterokontophyte]]s and the [[Haptophyte]]s, and then from these last to the [[Myzozoa]].<ref name="Strassert Irisarri Williams Burki 2021">{{Cite journal |last1=Strassert |first1=Jürgen F. H. |last2=Irisarri |first2=Iker |last3=Williams |first3=Tom A. |last4=Burki |first4=Fabien |date=2021-03-25 |title=A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids |journal=Nature Communications |volume=12 |issue=1 |pages=1879 |doi=10.1038/s41467-021-22044-z |pmid=33767194 |pmc=7994803 |bibcode=2021NatCo..12.1879S |issn=2041-1723}}</ref>

==== Cryptophytes ====
{{See also|Cryptomonad}}
[[File:CSIRO ScienceImage 6743 SEM Cryptophyte.jpg|thumb|Cryptophytes under [[Scanning electron microscope|SEM]].]]

[[Cryptomonad|Cryptophytes]], or cryptomonads, are a group of algae that contain a red-algal derived chloroplast. Cryptophyte chloroplasts contain a [[nucleomorph]] that superficially resembles that of the [[chlorarachniophytes]].<ref name="Keeling-2004" /> Cryptophyte chloroplasts have four membranes. The outermost membrane is continuous with the [[rough endoplasmic reticulum]]. They synthesize ordinary [[starch]], which is stored in granules found in the periplastid space—outside the original double membrane, in the place that corresponds to the ancestral red alga's cytoplasm. Inside cryptophyte chloroplasts is a [[pyrenoid]] and [[thylakoid]]s in stacks of two.<ref name="Kim-2009" /> Cryptophyte chloroplasts do not have [[phycobilisome]]s,<ref name="Kim-2009" /> but they do have [[Phycobilin|phycobilin pigments]] which they keep in the thylakoid space, rather than anchored on the outside of their thylakoid membranes.<ref name="Kim-2009" /><ref name="Keeling-2004" />

Cryptophytes may have played a key role in the spreading of red algal based chloroplasts.<ref>{{Cite thesis|last=Toledo|first=Rafael Isaac Ponce| name-list-style=vanc |title=Origins and early evolution of photosynthetic eukaryotes|date=5 March 2018|publisher=Université Paris-Saclay|url=https://tel.archives-ouvertes.fr/tel-01760725|language=en}}</ref><ref>{{cite journal | vauthors=Bodył A | title=Did some red alga-derived plastids evolve via kleptoplastidy? A hypothesis | journal=Biological Reviews of the Cambridge Philosophical Society | volume=93 | issue=1 | pages=201–222 | date=February 2018 | pmid=28544184 | doi=10.1111/brv.12340 | s2cid=24613863 }}</ref>

==== Haptophytes ====
{{See also|Haptophyte}}
[[File:Gephyrocapsa oceanica brighter.jpg|thumb|left|[[Scanning electron micrograph]] of ''[[Gephyrocapsa oceanica]]'', a haptophyte.]]

[[Haptophytes]] are similar and closely related to cryptophytes or heterokontophytes.<ref name="Keeling-2010" /> Their chloroplasts lack a nucleomorph,<ref name="Kim-2009" /><ref name="Keeling-2004" /> their thylakoids are in stacks of three, and they synthesize [[chrysolaminarin]] sugar, which are stored in granules completely outside of the chloroplast, in the cytoplasm of the haptophyte.<ref name="Kim-2009" />

==== Stramenopiles <span style="font-weight: 400;">(heterokontophytes)</span> ====
{{See also|Stramenopile}}[[File:20110123 185042 Diatom.jpg|thumb|upright=0.8|The photosynthetic pigments present in their chloroplasts make [[diatoms]] greenish-brown.]]

The [[stramenopile]]s, also known as heterokontophytes, are a very large and diverse group of eukaryotes. It inlcludes [[Ochrophyta]]—which includes [[diatoms]], [[brown algae]] (seaweeds), and [[golden algae]] (chrysophytes)<ref name="Campbell-2009f" />— and [[Yellow-green algae|Xanthophyceae]] (also called yellow-green algae).<ref name="Keeling-2010" />

Heterokont chloroplasts are very similar to haptophyte chloroplasts. They have a [[pyrenoid]], triplet thylakoids, and, with some exceptions,<ref name="Kim-2009" /> four layer plastidic envelope with the outermost membrane connected to the [[endoplasmic reticulum]]. Like haptophytes, stramenopiles store sugar in [[chrysolaminarin]] granules in the cytoplasm.<ref name="Kim-2009" /> Stramenopile chloroplasts contain [[chlorophyll a|chlorophyll ''a'']] and, with a few exceptions,<ref name="Kim-2009" /> [[Chlorophyll c|chlorophyll ''c'']].<ref name="Keeling-2004" /> They also have [[carotenoid]]s which give them their many colors.<ref name="Campbell-2009f" />

==== Apicomplexans, chromerids, and dinophytes ====
{{See also|Alveolate|Myzozoa}}
The alveolates are a major clade of unicellular eukaryotes of both [[Autotroph|autotrophic]] and [[Heterotroph|heterotrophic]] members. Many members contain a red-algal derived plastid. One notable characteristic of this diverse group is the frequent loss of photosynthesis. However, a majority of these heterotrophs continue to process a non-photosynthetic plastid.<ref name="Janouškovec-2017">{{cite journal | vauthors=Janouškovec J, Gavelis GS, Burki F, Dinh D, Bachvaroff TR, Gornik SG, Bright KJ, Imanian B, Strom SL, Delwiche CF, Waller RF, Fensome RA, Leander BS, Rohwer FL, Saldarriaga JF | display-authors=6 | title=Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics | journal=Proceedings of the National Academy of Sciences of the United States of America | volume=114 | issue=2 | pages=E171–E180 | date=January 2017 | pmid=28028238 | pmc=5240707 | doi=10.1073/pnas.1614842114 | bibcode=2017PNAS..114E.171J | doi-access=free }}</ref>

===== Apicomplexans =====
[[File:Plasmodium.png|thumb|Diagram of Plasmodium, including its apicoplast.]]

[[Apicomplexans]] are a group of alveolates. Like the [[helicosproidia]], they're parasitic, and have a nonphotosynthetic chloroplast.<ref name="Keeling-2010" /> They were once thought to be related to the helicosproidia, but it is now known that the helicosproida are green algae rather than part of the CASH lineage.<ref name="Keeling-2010" /> The apicomplexans include ''[[Plasmodium]]'', the [[malaria]] parasite. Many apicomplexans keep a [[vestigial]] red algal derived chloroplast<ref name="Nair-2011" /><ref name="Keeling-2010" /> called an [[apicoplast]], which they inherited from their ancestors. Apicoplasts have lost all photosynthetic function, and contain no photosynthetic pigments or true thylakoids. They are bounded by four membranes, but the membranes are not connected to the [[endoplasmic reticulum]].<ref name="Kim-2009" /> Other apicomplexans like ''[[Cryptosporidium]]'' have lost the chloroplast completely.<ref name="Nair-2011" /> Apicomplexans store their energy in [[amylopectin]] granules that are located in their cytoplasm, even though they are nonphotosynthetic.<ref name="Kim-2009" />

The fact that apicomplexans still keep their nonphotosynthetic chloroplast around demonstrates how the chloroplast carries out important functions other than [[photosynthesis]]. [[Plant]] chloroplasts provide plant cells with many important things besides sugar, and apicoplasts are no different—they synthesize [[fatty acid]]s, [[isopentenyl pyrophosphate]], [[iron-sulfur clusters]], and carry out part of the [[heme]] pathway.<ref name="Nair-2011" /> The most important apicoplast function is [[isopentenyl pyrophosphate]] synthesis—in fact, apicomplexans die when something interferes with this apicoplast function, and when apicomplexans are grown in an isopentenyl pyrophosphate-rich medium, they dump the organelle.<ref name="Nair-2011" />

===== Chromerids =====
[[File:Vitrella brassicaformis LM Michalek 2020.png|thumb|Typical life cycle stages of [[Vitrella brassicaformis]], a chromerid.]]

The [[chromerid]]s are a group of algae known from Australian corals which comprise some close photosynthetic relatives of the apicomplexans. The first member, ''[[Chromera velia]]'', was discovered and first isolated in 2001. The discovery of ''Chromera velia'' with similar structure to the apicomplexans, provides an important link in the evolutionary history of the apicomplexans and dinophytes. Their plastids have four membranes, lack chlorophyll c and use the type II form of [[RuBisCO]] obtained from a horizontal transfer event.<ref>{{cite journal | vauthors=Quigg A, Kotabová E, Jarešová J, Kaňa R, Setlík J, Sedivá B, Komárek O, Prášil O | display-authors=6 | title=Photosynthesis in Chromera velia represents a simple system with high efficiency | journal=PLOS ONE | volume=7 | issue=10 | pages=e47036 | date=10 October 2012 | pmid=23071705 | pmc=3468483 | doi=10.1371/journal.pone.0047036 | bibcode=2012PLoSO...747036Q | doi-access=free }}</ref>

===== Dinophytes =====
[[File:Ceratium furca.jpg|thumb|''[[Ceratium furca]]'', a [[peridinin]]-containing dinophyte.<ref>{{cite journal  |vauthors=Meeson BW, Chang SS, Sweeney BM |doi=10.1515/botm.1982.25.8.347 |title=Characterization of Peridinin-Chlorophyll α-Proteins from the Marine Dinoflagellate Ceratium furca |year=1982 |journal=Botanica Marina |volume=25 |issue=8 |pages=347–50|bibcode=1982BoMar..25..347M |s2cid=83867103 }}</ref>]]

The [[dinoflagellates]] are yet another very large and diverse group, around half of which are at least partially photosynthetic (i.e. [[Mixotroph|mixotrophic]]).<ref name="Campbell-2009f" /><ref name="Hackett-2004">{{cite journal | vauthors=Hackett JD, Anderson DM, Erdner DL, Bhattacharya D | title=Dinoflagellates: a remarkable evolutionary experiment | journal=American Journal of Botany | volume=91 | issue=10 | pages=1523–34 | date=October 2004 | pmid=21652307 | doi=10.3732/ajb.91.10.1523 }}</ref> Dinoflagellate chloroplasts have relatively complex history. Most dinoflagellate chloroplasts are secondary [[red algae|red algal]] derived chloroplasts. Many dinoflagellates have lost the chloroplast (becoming nonphotosynthetic), some of these have replaced it though ''tertiary'' endosymbiosis.<ref name="Dorrell-2011">{{cite journal | vauthors=Dorrell RG, Smith AG | title=Do red and green make brown?: perspectives on plastid acquisitions within chromalveolates | journal=Eukaryotic Cell | volume=10 | issue=7 | pages=856–68 | date=July 2011 | pmid=21622904 | pmc=3147421 | doi=10.1128/EC.00326-10 }}</ref> Others replaced their original chloroplast with a [[green algae|green algal]] derived chloroplast.<ref name="Keeling-2004" /><ref name="Keeling-2010" /><ref name="Hackett-2004" /> The peridinin chloroplast is thought to be the dinophytes' "original" chloroplast,<ref name="Hackett-2004" /> which has been lost, reduced, replaced, or has company in several other dinophyte lineages.<ref name="Keeling-2010" />

The most common dinophyte chloroplast is the [[peridinin]]-type chloroplast, characterized by the [[carotenoid]] pigment [[peridinin]] in their chloroplasts, along with [[chlorophyll a|chlorophyll ''a'']] and [[chlorophyll c2|chlorophyll ''c''<sub>2</sub>]].<ref name="Keeling-2004" /><ref name="Hackett-2004" /> Peridinin is not found in any other group of chloroplasts.<ref name="Hackett-2004" /> The peridinin chloroplast is bounded by three membranes (occasionally two),<ref name="Kim-2009" /> having lost the red algal endosymbiont's original cell membrane.<ref name="Keeling-2004" /><ref name="Keeling-2010" /> The outermost membrane is not connected to the endoplasmic reticulum.<ref name="Kim-2009" /><ref name="Hackett-2004" /> They contain a [[pyrenoid]], and have triplet-stacked thylakoids. Starch is found outside the chloroplast.<ref name="Kim-2009" /> Peridinin chloroplasts also have DNA that is highly [[genome reduction|reduced]] and fragmented into many small circles.<ref name="Hackett-2004" /> Most of the genome has migrated to the nucleus, and only critical photosynthesis-related genes remain in the chloroplast. 

Most dinophyte chloroplasts contain form II RuBisCO, at least the [[photosynthetic pigments]] [[chlorophyll a|chlorophyll ''a'']], [[chlorophyll c2|chlorophyll ''c<sub>2</sub>'']], [[beta-carotene|''beta''-carotene]], and at least one dinophyte-unique [[xanthophyll]] ([[peridinin]], [[dinoxanthin]], or [[diadinoxanthin]]), giving many a golden-brown color.<ref name="Janouškovec-2017" /><ref name="Hackett-2004" /> All dinophytes store starch in their cytoplasm, and most have chloroplasts with thylakoids arranged in stacks of three.<ref name="Kim-2009" />