Editing Mitochondrial DNA (section)

== Genome structure and diversity ==
Across all organisms, there are six main mitochondrial genome types, classified by structure (i.e. circular versus linear), size, presence of [[intron]]s or [[Plasmid|plasmid like structures]], and whether the genetic material is a singular molecule or collection of [[Homogeneity and heterogeneity|homogeneous]] or [[Homogeneity and heterogeneity|heterogeneous]] molecules.<ref name="Kolesnikov, A. A. 2012">{{Cite journal |vauthors=Kolesnikov AA, Gerasimov ES |date=December 2012 |title=Diversity of mitochondrial genome organization |journal=Biochemistry. Biokhimiia |volume=77 |issue=13 |pages=1424–1435 |doi=10.1134/S0006297912130020 |pmid=23379519 |s2cid=14441187}}</ref>

In many unicellular organisms (e.g., the [[ciliate]] ''[[Tetrahymena]]'' and the [[green alga]] ''[[Chlamydomonas reinhardtii]]''), and in rare cases also in multicellular organisms (e.g. in some species of [[Cnidaria]]), the mtDNA is linear [[DNA]]. Most of these linear mtDNAs possess [[telomerase]]-independent [[telomere]]s (i.e., the ends of the linear [[DNA]]) with different modes of replication, which have made them interesting objects of research because many of these unicellular organisms with linear mtDNA are known [[pathogen]]s.<ref>{{Cite journal |vauthors=Nosek J, Tomáska L, Fukuhara H, Suyama Y, Kovác L |date=May 1998 |title=Linear mitochondrial genomes: 30 years down the line |journal=Trends in Genetics |volume=14 |issue=5 |pages=184–188 |doi=10.1016/S0168-9525(98)01443-7 |pmid=9613202}}</ref>

=== Animals ===
Most ([[bilateria]]n) animals have a circular mitochondrial genome. [[Medusozoa]] and [[Calcareous sponge|calcarea]] [[clade]]s however include species with linear mitochondrial chromosomes.<ref>{{Cite journal |vauthors=Lavrov DV, Pett W |date=September 2016 |title=Animal Mitochondrial DNA as We Do Not Know It: mt-Genome Organization and Evolution in Nonbilaterian Lineages |journal=Genome Biology and Evolution |volume=8 |issue=9 |pages=2896–2913 |doi=10.1093/gbe/evw195 |pmc=5633667 |pmid=27557826}}</ref> With a few exceptions, animals have 37 genes in their mitochondrial DNA: 13 for [[protein]]s, 22 for [[transfer RNA|tRNAs]], and 2 for [[ribosomal RNA|rRNAs]].<ref name="Boore1999">{{Cite journal |last=Boore |first=J. L. |date=1 April 1999 |title=Animal mitochondrial genomes |journal=Nucleic Acids Research |volume=27 |issue=8 |pages=1767–1780 |doi=10.1093/nar/27.8.1767 |pmc=148383 |pmid=10101183}}</ref>

Mitochondrial genomes for animals average about 16,000 base pairs in length.<ref name="Boore1999" /> The anemone ''Isarachnanthus nocturnus'' has the largest mitochondrial genome of any animal at 80,923 bp.<ref>{{Cite journal |vauthors=Stampar SN, Broe MB, Macrander J, Reitzel AM, Brugler MR, Daly M |date=April 2019 |title=Linear Mitochondrial Genome in Anthozoa (Cnidaria): A Case Study in Ceriantharia |journal=Scientific Reports |volume=9 |issue=1 |page=6094 |bibcode=2019NatSR...9.6094S |doi=10.1038/s41598-019-42621-z |pmc=6465557 |pmid=30988357}}</ref> The smallest known mitochondrial genome in animals belongs to the comb jelly ''[[Vallicula multiformis]]'', which consist of 9,961 bp.<ref>[https://www.biorxiv.org/content/10.1101/366880v1.full Polymorphism within the mitochondrial genome of the ctenophore, Pleurobrachia bachei and its ongoing rapid evolution - bioRxiv]</ref>

In February 2020, a jellyfish-related parasite – ''[[Henneguya salminicola]]'' – was discovered that lacks a mitochondrial genome but retains structures deemed mitochondrion-related organelles. Moreover, nuclear DNA genes involved in aerobic respiration and mitochondrial DNA replication and transcription were either absent or present only as [[pseudogene]]s. This is the first multicellular organism known to have this absence of aerobic respiration and live completely free of oxygen dependency.<ref>{{Cite journal |display-authors=6 |vauthors=Yahalomi D, Atkinson SD, Neuhof M, Chang ES, Philippe H, Cartwright P, Bartholomew JL, Huchon D |date=March 2020 |title=A cnidarian parasite of salmon (Myxozoa: ''Henneguya'') lacks a mitochondrial genome |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=117 |issue=10 |pages=5358–5363 |bibcode=2020PNAS..117.5358Y |doi=10.1073/pnas.1909907117 |pmc=7071853 |pmid=32094163 |doi-access=free}}</ref><ref>{{Cite web |date=25 February 2020 |title=Scientists Find The First-Ever Animal That Doesn't Need Oxygen to Survive |url=https://www.sciencealert.com/this-is-the-first-known-animal-that-doesn-t-need-oxygen-to-survive |url-status=live |archive-url=https://web.archive.org/web/20200225075450/https://www.sciencealert.com/this-is-the-first-known-animal-that-doesn-t-need-oxygen-to-survive |archive-date=25 February 2020 |access-date=2020-02-25 |website=ScienceAlert |language=en-gb |vauthors=Starr M}}</ref>

=== Plants and fungi ===
There are three different mitochondrial genome types in plants and fungi. The first type is a circular genome that has introns (type 2) and may range from 19 to 1000 kbp in length. The second genome type is a circular genome (about 20–1000 kbp) that also has a plasmid-like structure (1 kb) (type 3). The final genome type found in plants and fungi is a linear genome made up of homogeneous DNA molecules (type 5).<ref>{{Cite journal |last1=de Queiroz |first1=Casley Borges |last2=Santana |first2=Mateus Ferreira |last3=Pereira Vidigal |first3=Pedro M. |last4=de Queiroz |first4=Marisa Vieira |date=2018-03-15 |title=Comparative analysis of the mitochondrial genome of the fungus Colletotrichum lindemuthianum, the causal agent of anthracnose in common beans |url=http://www.locus.ufv.br/handle/123456789/19132 |journal=Applied Microbiology & Biotechnology |volume=102 |issue=6 |pages=2763–2778 |doi=10.1007/s00253-018-8812-0 |pmid=29453633 |s2cid=3341230}}</ref><ref>{{Cite journal |last1=Masutani |first1=Bansho |last2=Arimura |first2=Shin-ichi |last3=Morishita |first3=Shinichi |date=2021-01-12 |title=Investigating the mitochondrial genomic landscape of Arabidopsis thaliana by long-read sequencing |journal=PLOS Computational Biology |volume=17 |issue=1 |pages=e1008597 |bibcode=2021PLSCB..17E8597M |doi=10.1371/journal.pcbi.1008597 |pmc=7833223 |pmid=33434206 |doi-access=free}}</ref><ref>{{Cite journal |last1=Kozik |first1=Alexander |last2=Rowan |first2=Beth A. |last3=Lavelle |first3=Dean |last4=Berke |first4=Lidija |last5=Schranz |first5=M. Eric |last6=Michelmore |first6=Richard W. |last7=Christensen |first7=Alan C. |date=2019-08-30 |title=The alternative reality of plant mitochondrial DNA: One ring does not rule them all |journal=PLOS Genetics |volume=15 |issue=8 |pages=e1008373 |doi=10.1371/journal.pgen.1008373 |pmc=6742443 |pmid=31469821 |doi-access=free}}</ref>

Great variation in mtDNA gene content and size exists among fungi and plants, although there appears to be a core subset of genes present in all eukaryotes (except for the few that have no mitochondria at all).<ref name="Johnston, I. G. and Williams, B. P. 2016" /> In Fungi, however, there is no single gene shared among all mitogenomes.<ref>{{Cite journal |display-authors=6 |vauthors=Fonseca PL, De-Paula RB, Araújo DS, Tomé LM, Mendes-Pereira T, Rodrigues WF, Del-Bem LE, Aguiar ER, Góes-Neto A |date=2021 |title=Global Characterization of Fungal Mitogenomes: New Insights on Genomic Diversity and Dynamism of Coding Genes and Accessory Elements |journal=Frontiers in Microbiology |volume=12 |page=787283 |doi=10.3389/fmicb.2021.787283 |pmc=8672057 |pmid=34925295 |doi-access=free}}</ref>
Some plant species have enormous mitochondrial genomes, with ''[[Silene conica]]'' mtDNA containing as many as 11,300,000 base pairs.<ref>{{Cite journal |vauthors=Sloan DB, Alverson AJ, Chuckalovcak JP, Wu M, McCauley DE, Palmer JD, Taylor DR |date=January 2012 |title=Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates |journal=PLOS Biology |volume=10 |issue=1 |pages=e1001241 |doi=10.1371/journal.pbio.1001241 |pmc=3260318 |pmid=22272183 |doi-access=free}}</ref> Surprisingly, even those huge mtDNAs contain the same number and kinds of genes as related plants with much smaller mtDNAs.<ref>{{Cite journal |vauthors=Ward BL, Anderson RS, Bendich AJ |date=September 1981 |title=The mitochondrial genome is large and variable in a family of plants (cucurbitaceae) |journal=Cell |volume=25 |issue=3 |pages=793–803 |doi=10.1016/0092-8674(81)90187-2 |pmid=6269758 |s2cid=45090891}}</ref>
The genome of the mitochondrion of the cucumber (''[[Cucumis sativus]]'') consists of three circular chromosomes (lengths 1556, 84 and 45 kilobases), which are entirely or largely autonomous with regard to their [[DNA replication|replication]].<ref name="Alverson2011">{{Cite journal |vauthors=Alverson AJ, Rice DW, Dickinson S, Barry K, Palmer JD |date=July 2011 |title=Origins and recombination of the bacterial-sized multichromosomal mitochondrial genome of cucumber |journal=The Plant Cell |volume=23 |issue=7 |pages=2499–2513 |doi=10.1105/tpc.111.087189 |jstor=41433488 |pmc=3226218 |pmid=21742987|bibcode=2011PlanC..23.2499A }}</ref>

=== Protists ===
[[Protist]]s contain the most diverse mitochondrial genomes, with five different types found in this kingdom. Type 2, type 3, and type 5 of the plant and fungal genomes also exist in some protists, as do two unique genome types. One of these unique types is a heterogeneous collection of circular DNA molecules (type 4) while the other is a heterogeneous collection of linear molecules (type 6). Genome types 4 and 6 each range from 1–200 kbp in size.{{citation needed|date=April 2023}}

The smallest mitochondrial genome sequenced to date is the 5,967 bp mtDNA of the parasite ''[[Plasmodium falciparum]]''.<ref>{{Cite web |title=Mitochondrial DNA (mtDNA) |url=https://www.idtdna.com/pages/docs/educational-resources/mitochondrial-dna.pdf?sfvrsn=4 |archive-url=https://web.archive.org/web/20160729031823/https://www.idtdna.com/pages/docs/educational-resources/mitochondrial-dna.pdf?sfvrsn=4 |archive-date=29 July 2016 |access-date=25 February 2016 |publisher=Integrated DNA Technologies}}</ref><ref>{{Cite journal |vauthors=Tyagi S, Pande V, Das A |date=February 2014 |title=Whole mitochondrial genome sequence of an Indian Plasmodium falciparum field isolate |journal=The Korean Journal of Parasitology |volume=52 |issue=1 |pages=99–103 |doi=10.3347/kjp.2014.52.1.99 |pmc=3949004 |pmid=24623891}}</ref>

[[Endosymbiotic]] gene transfer, the process by which genes that were coded in the mitochondrial genome are transferred to the cell's main genome, likely explains why more complex organisms such as humans have smaller mitochondrial genomes than simpler organisms such as protists.{{cn|date=November 2024}}

{| class="wikitable"
!Genome Type<ref name="Kolesnikov, A. A. 2012" />
!Kingdom
!Introns
!Size
!Shape
!Description
|-
|1
|Animal
|No
|11–28 kbp
|Circular
|Single molecule
|-
|2
|Fungi, Plant, Protista
|Yes
|19–1000 kbp
|Circular
|Single molecule
|-
|3
|Fungi, Plant, Protista
|No
|20–1000 kbp
|Circular
|Large molecule and small plasmid-like structures
|-
|4
|Protista
|No
|1–200 kbp
|Circular
|Heterogeneous group of molecules
|-
|5
|Fungi, Plant, Protista
|No
|1–200 kbp
|Linear
|Homogeneous group of molecules
|-
|6
|Protista
|No
|1–200 kbp
|Linear
|Heterogeneous group of molecules
|}