Editing Chloroplast (section)

==== 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" />