Editing Chloroplast (section)

=== Molecular structure ===

With few exceptions, most chloroplasts have their entire chloroplast genome combined into a single large circular DNA molecule,<ref name="Sandelius-2009" /> typically 120,000–170,000 [[base pair]]s long<ref name="Dann-2002">{{cite book |last=Dann |first=Leighton |url=http://www.bioscience-explained.org/ENvol1_2/pdf/ctDNAEN.pdf |title=Bioscience—Explained |publisher=BIOSCIENCE EXPLAINED |year=2002 |location=Green DNA |archive-url=https://web.archive.org/web/20101214102105/http://www.bioscience-explained.org/ENvol1_2/pdf/ctDNAEN.pdf |archive-date=14 December 2010 |url-status=live |name-list-style=vanc}}</ref><ref name="Clegg-1994" /><ref name="Shaw-2007" /><ref name="Milo">{{cite web | vauthors=Milo R, Phillips R |url=http://book.bionumbers.org/how-large-are-chloroplasts/|title=Cell Biology by the Numbers: How large are chloroplasts?|website =book.bionumbers.org |access-date=7 February 2017}}</ref> and a mass of about 80–130&nbsp;million [[dalton (unit)|daltons]].<ref name="Burgess-1989b">{{cite book |last=Burgess |first=Jeremy | name-list-style=vanc |title=An introduction to plant cell development |year=1989 |publisher=Cambridge university press |location=Cambridge |isbn=0-521-31611-1 |page=62 |url=https://books.google.com/books?id=r808AAAAIAAJ&pg=PA62}}</ref> While chloroplast genomes can almost always be assembled into a circular map, the physical DNA molecules inside cells take on a variety of linear and branching forms.<ref name="Sandelius-2009" /><ref>{{Cite journal |last=Green |first=Beverley R. |date=28 April 2011 |title=Chloroplast genomes of photosynthetic eukaryotes |url=https://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2011.04541.x |journal=The Plant Journal |language=en |volume=66 |issue=1 |pages=34–44 |doi=10.1111/j.1365-313X.2011.04541.x |pmid=21443621 |issn=0960-7412}}</ref> New chloroplasts may contain up to 100 copies of their genome,<ref name="Dann-2002" /> though the number of copies decreases to about 15–20 as the chloroplasts age.<ref name="PlantBiochem-2005">{{cite book|title=Plant Biochemistry |edition=3rd |year=2005|publisher=Academic Press|page=[https://archive.org/details/isbn_9788131200032/page/517 517]|url=https://archive.org/details/isbn_9788131200032|url-access=registration |quote=number of copies of ctDNA per chloroplast. |isbn=978-0-12-088391-2}}</ref>

Chloroplast DNA is usually condensed into [[nucleoid]]s, which can contain multiple copies of the chloroplast genome. Many nucleoids can be found in each chloroplast.<ref name="Burgess-1989b" /> In primitive [[red algae]], the chloroplast DNA nucleoids are clustered in the center of the chloroplast, while in green plants and [[green algae]], the nucleoids are dispersed throughout the [[stroma (fluid)|stroma]].<ref name="Kobayashi-2002" /> Chloroplast DNA is not associated with true [[histone]]s, proteins that are used to pack DNA molecules tightly in eukaryote nuclei.<ref name="Campbell-2009c" /> Though in [[red algae]], similar proteins tightly pack each chloroplast DNA ring in a [[nucleoid]].<ref name="Kobayashi-2002">{{cite journal | vauthors=Kobayashi T, Takahara M, Miyagishima SY, Kuroiwa H, Sasaki N, Ohta N, Matsuzaki M, Kuroiwa T | display-authors=6 | title=Detection and localization of a chloroplast-encoded HU-like protein that organizes chloroplast nucleoids | journal=The Plant Cell | volume=14 | issue=7 | pages=1579–89 | date=July 2002 | pmid=12119376 | pmc=150708 | doi=10.1105/tpc.002717 | bibcode=2002PlanC..14.1579K }}</ref>

Many chloroplast genomes contain two [[inverted repeat]]s, which separate a long single copy section (LSC) from a short single copy section (SSC).<ref name="Shaw-2007">{{cite journal | vauthors=Shaw J, Lickey EB, Schilling EE, Small RL | s2cid=30501148 | title=Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III | journal=American Journal of Botany | volume=94 | issue=3 | pages=275–88 | date=March 2007 | pmid=21636401 | doi=10.3732/ajb.94.3.275 }}</ref> A given pair of inverted repeats are rarely identical, but they are always very similar to each other, apparently resulting from [[concerted evolution]].<ref name="Sandelius-2009" /> The inverted repeats vary wildly in length, ranging from 4,000 to 25,000 [[base pair]]s long each and containing as few as four or as many as over 150 genes.<ref name="Sandelius-2009" /> The inverted repeat regions are highly [[Conserved sequence|conserved]] in land plants, and accumulate few mutations.<ref name="Shaw-2007" /><ref name="Kolodner-1979">{{cite journal |vauthors=Kolodner R, Tewari KK |date=January 1979 |title=Inverted repeats in chloroplast DNA from higher plants |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=76 |issue=1 |pages=41–5 |bibcode=1979PNAS...76...41K |doi=10.1073/pnas.76.1.41 |pmc=382872 |pmid=16592612 |doi-access=free}}</ref>

Similar inverted repeats exist in the genomes of cyanobacteria and the other two chloroplast lineages ([[glaucophyta]] and [[rhodophyceae]]), suggesting that they predate the chloroplast.<ref name="Sandelius-2009" /> Some chloroplast genomes have since lost<ref name="Kolodner-1979" /><ref name="Palmer-1982" /> or flipped the inverted repeats (making them [[direct repeat]]s).<ref name="Sandelius-2009" /> It is possible that the inverted repeats help stabilize the rest of the chloroplast genome, as chloroplast genomes which have lost some of the inverted repeat segments tend to get rearranged more.<ref name="Palmer-1982">{{cite journal | vauthors=Palmer JD, Thompson WF | title=Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost | journal=Cell | volume=29 | issue=2 | pages=537–50 | date=June 1982 | pmid=6288261 | doi=10.1016/0092-8674(82)90170-2 | s2cid=11571695 }}</ref>