A census of nuclear mitochondrial pseudogenes (numts)

Created: November 2000

Last Update: January 2004

If you have more information, comments, changes, improvements, contact Douda Bensasson, douda@pseudogene.net

All numts in this list (note: this list is not complete).
	Fungi
	Plants
	Metazoa	Cnidaria
		Onychophora
		Echinodermata
		Arthropoda
		Chordata

Key to abbreviations used in the table
References

For more information:
Checking for numts and avoiding them
Using numts

Review:
Bensasson, D., Zhang, D-X., Hartl, D. and Hewitt G.M. 2001. Trends Ecol. Evol. 16:314-321. "Mitochondrial pseudogenes: evolution's misplaced witnesses".


Organisms	References	Xtra-NM-N	Size (kb)	copy no. (ratio of Numts in PCR)	ind-amp	divergence from mtDNA	GenBank Accession number(s)
FUNGI
Neurospora crassa	(van den Boogart et al, 1982)	N
Saccharomyces cerevisiae	(Farrelly and Butow, 1983) . (Louis and Haber, 1991) .	N
PLANTS
Zea mays (maize)	(Kemble et al, 1983) .	N
Oryza sativa (rice)	(Blanchard and Schmidt, 1995) . (Fukuchi et al, 1991) . (Kubo et al, 2001)	N	0.03 - > 0.79	>11	ind.	0-7%
Oenothera	(Grohmann et al, 1992) .
Nicotiana alata	(Bernatzky et al, 1989) . (Blanchard and Schmidt, 1995) .	N	0.06	1	-	4%
Nicotiana tabacum (tobacco)	(Blanchard and Schmidt, 1995) . (Knoop and Brennicke, 1994) . (Hua et al, 1993) .	N	0.07-0.19	5	ind.	12-28%
Lycopersicon esculentum (tomato)	(Blanchard and Schmidt, 1995) .	N	0.12	1	-	30%
Arabidopsis thaliana	(Sun and Callis, 1993) . (Blanchard and Schmidt, 1995) . (Stupar et al, 2001) (Lin et al, 1999) (Intitiative, 2000)	N	0.1- 620	>17	ind. & amp	0-29%
Dolichos biflourus (bean)	(Knoop and Brennicke, 1991) . (Blanchard and Schmidt, 1995) .	N	0.12	1	-	13%
Petunia inflata (petunia)	(Blanchard and Schmidt, 1995) .	N	0.05	1	-	4%
Petunia hydrida (petunia)	(Blanchard and Schmidt, 1995) .	N	0.09	1	-	19%
Cologania lemmonii	(Adams et al, 1999)	N, NF	> 0.3		-		AF181943-4
Pueraria phaseoloides	(Adams et al, 1999)	N, NF			-
Teramnus uncinatus	(Adams et al, 1999)	N, NF			-
METAZOA
Cnidaria
Lophelia pertusa (deep-sea coral)	(Le Goff-Vitry, submitted)	Xtra	> 0.3
Onychophora
Peripatoides sympatrica (velvet worm)	Steve Trewick, Natural History Museum, London, UK	NM	> 0.8	-	-	~ 2%	-
Echinodermata
Strongylocentrotus purpuratus (sea urchin)	(Jacobs et al, 1983) .		2.8	low		9 - 17% (30 Mya)
Arthropoda
Crustacea
Menippe (stone crabs)	(SchneiderBroussard and Neigel, 1997) .	N	> 0.5	1 (1/10)	-	3%	U20740/42/45/48/50
planktonic copepods	(Bucklin et al, 1999) .
Alpheus (snapping shrimp) 10 species.	(Williams and Knowlton, 2001)	N	> 0.7	> 37	> 21	0.2 – 19%	AF321325–AF321360
Orthoptera
Locusta migratoria	(Gellissen et al, 1983; Gellissen and Michaelis, 1987) .	N	3.5	hundreds	?	< 10%
Schistocerca gregaria	(Zhang and Hewitt, 1996; Bensasson et al, 2000b) .	N	> 1	>> 13	> 3	0.5 - 1.5%	AF085581-93
Podisma pedestris	(Bensasson, 1999; Bensasson et al, 2000a; Bensasson et al, 2000b)	NM, NF, N-like	> 0.6	>> 37 (37/65)	> 13 ind. & amp	0 - 15%	AF085539-74
Italopodisma sp.	(Bensasson, 1999; Vaughan et al, 1999; Bensasson et al, 2000a; Bensasson et al, 2000b)	N	> 0.6	>> 50 (42/49)	> 2 ind. & amp	0.2 - 7%	AF085508-38, AF085575-78
Chorthippus parallelus	(Bensasson, 1999; Vaughan et al, 1999; Bensasson et al, 2000b)	N	> 0.6	>> 4 (>4/5)	> 2 ind.		AF085594-99
Parapodisma mikado	(Bensasson, 1999; Bensasson et al, 2000b)	Xtra, NF, N-like	> 0.6	>> 3 (2/5)	> 2 ind.	5 - 9%	AF085579-80
Cophopodisma pyrenea	(Bensasson, 1999; Bensasson et al, 2000b)	Xtra	> 0.6	> 6	-	-	-
Ognevia longipennis	(Bensasson, 1999; Bensasson et al, 2000b)	Xtra	> 0.6				-
Primnoa hayachinensis	(Bensasson, 1999; Bensasson et al, 2000b)	Xtra	> 0.6				-
Calliptamus sp.	(Bensasson, 1999; Bensasson et al, 2000b)	Xtra	> 0.6	> 4			-
Arcyptera sp	(Bensasson, 1999; Bensasson et al, 2000b)	Xtra	> 0.6	> 2			-
Alpinacris crassicauda Alpinacris tumicauda	Steve Trewick, Natural History Museum, London, UK	NM	> 0.8	-	-	-	-
Hemideina femorata (cricket)	Steve Trewick, Natural History Museum, London, UK	Xtra	-	-	-	-	-
Homoptera
Sitobion (aphid)	(Sunnucks and Hales, 1996)	N	> 0.9	at least 8-10	many ind.	0.6 - 2.9%	U41114-U41132
Hymenoptera
Cynipidae: Andricus kollari, A. lignicola, A. corruptrix, A. quercustozae (gall wasp), Synergus nervosum, Barbotinia oraniensis	Antonis Rokas (pers. comm.) (Rokas et al, 2003)	Xtra	> 0.4	multiple	-	recent
Braconidae: Microctonus aethiopoides (solitary, arrhenotokous endoparasitoid)	(Vink et al, 2003)	Xtra
Chordata
Reptiles
Cuora galbinifrons (turtle)	(Stuart and Parham, in press) doi:10.1016/S0006-8993(00)02382-9	Xtra	> 0.89
Aves
Anser caerulescens (snow goose)	(Quinn and White, 1987)		0.2			9 -11.8%
Aythyini (diving ducks)	(Sorenson and Fleischer, 1996)				>6 ind.
Somateria mollissima (eider duck)	(Tiedemann and von Kistowski, 1998)
Cepphus (diving sea birds)	(Kidd and Friesen, 1998)	N		1
Charadriformes and Pelecaniformes (murres, murreletes, guillemots, kittiwakes, shags, gannets)	Vicki Friesen, Queens University, Ontario, Canada	Xtra, N-like, N	> 0.3	1	-	0.02 - 10%	AF027234-49
Dendrocygna arcuata (Wandering Whistling-Duck)	(Sorenson and Quinn, 1998)	Xtra NF	> 0.4	1	-	11.6%	-
Cygnus (swans)	Nick Harvey, pers. comm.
Scytalopus and Myornis senilis	(Arctander, 1995)		> 0.3			~ 16 - 19% > 5 Mya
Oeromanes, Conirostrum	Kirstine Nielsen, pers. comm.
Motacilla cinerea cinerea (grey wagtail)	(Odeen and Bjorklund, 2003)	Xtra	> 0.5
Parus	(Kvist et al, 1996)
Sporophila, Oryzoborus, Diglossa, Catamenia, Sicalis, Poospiza, Volatina, Coereba Loxigilla, Tiaris, Melanopiza, Certhidea, Platyspiza, Geospiza, Pinaroloxias, Cactospiza, Coryphospingus, Ramphocelus, Cyanocomposa Pheucticus (Darwin’s finches)	(Sato et al, 1999; Sato et al, 2001)	N	> 0.1 - > 0.9	at least 4	-	-	AF310020-40
Mammalia
Didelphis (opossum)	(Lemos et al, 1999)	Xtra, NF, N-like	> 0.6	multiple	ind.	-	AF089796-805
Homo sapiens	(Tsuzuki et al, 1983; Nomiyama et al, 1984; Fukuda et al, 1985; Nomiyama et al, 1985; Kamimura et al, 1989; Hu and Thilly, 1994; Hu and Thilly, 1995; van der Kuyl et al, 1995; Zischler et al, 1995a; Zischler et al, 1995b; Zischler, 2000) (Thomas et al, 1996; Mourier et al, 2001; Tourmen et al, 2002; Woischnik and Moraes, 2002; Bensasson et al, 2003) (Hazkani-Covo et al, 2003) (Wallace et al, 1997)	N	0.2 – 14.7	350 - 612	ind. & amp	0 - 33% (recent - 58 Mya)	see references
	(Herrnstadt et al, 1999)	N	5.8	1	-	1.9%	AF134583
	(Yuan et al, 1999)	N	> 0.1	estimate> 570 kb of Numts total	-	-	L27602-3 AF055271AF055272 AF029308 AC004035 U66061
hominoids (human, chimpanzee, gorilla, orangutan, gibbons)	(Zischler et al, 1998)	N	0.4	1	-	17-30 Mya	AF035463-7
orangutan	(Collura and Stewart, 1995)			at least 2
Gorilla (G. gorilla & G. beringei)	(Jensen-Seaman, 2000)	Xtra	> 0.4	at least 5 (Xtra > mt)	> 5 ind.	in the last 2-3 My	-
proboscis monkeys	(Collura et al, 1996) .			multiple
Saguinus (tamarins)	(Vallinoto et al, 2000) .
Saguinus, Saimiri, Leontopithecus	(Mundy et al, 2000)	Xtra	> 0.3	multiple	ind.	-	AF245046-95
Callithrix (marmosets), Callimico	(Mundy et al, 2000)	Xtra, NF	0.3 - 2.2	2-5	ind.	11-25%	AF245046-95
Macaca mulatta (rhesus macaques)	(Vartanian and Wain-Hobson, 2002)	N	> 0.1	> 102	ind & amp	up to 30%	AF502296–AF502367
primates	(van der Kuyl et al, 1995)
cats	(Lopez et al, 1994)	N	7.9	38-76	amp	3 - 8%
Panthera tigris (tigers)	(Cracraft et al, 1998)
rats	(Hadler et al, 1983; Corral et al, 1989; Zullo et al, 1991; Zullo and Upender, 1995; Blanchard and Schmidt, 1996; Hadler et al, 1998)	Xtra NF	0.5	repetitive		20% (13.6 Mya)
Microtus (vole)	(DeWoody et al, 1999)	Xtra, NF	> 1.1	- (1/127)	-	17.6% (~6 Mya)	AF057139
Cavis sp.	(Blanchard and Schmidt, 1996)	N	0.22	1	-	> 28%	X13537
Ctenomys (tuco-tuco)	(Mirol et al, 2000)	Xtra, NF, N-like	> 0.2	at least 3	2 ind. & amp	10 - 37%	AF210389-97, AF221718-45
Chroeomys jelskii (akodontines)	(Smith et al, 1992) .
Elephas maximus (Asian elephant)	(Greenwood and Paabo, 1999)	Xtra	> 0.2	at least 3	-	-	AF071099-102
Loxodonta africana (African elephant)	(Greenwood and Paabo, 1999)	Xtra	> 0.2	-	-	-	AF155041
Mammuthus primigenius (mammoths)	(Greenwood et al, 1999) .	Xtra	> 0.08	-	-	-	AF155040
bovids	(Arctander, 1995)	-	-	-	-	-	-
whales	(Arctander, 1995)	-	-	-	-	-	-
Odontocetes and Mysticete cetaceans (whales and dolphins)	Matthew Hare, University of Maryland, MD	NM	> 0.3	-	-	-	-

Abbreviations:


Xtra	Extra copies:	more than one type of mtDNA-like is found within individuals, but the location of the extra sequences has not been established
NM	Not Mitochondrial:	it has been established that there are extra mtDNA-like sequences which are not mitochondrial
N	Nuclear:	it has been established that there are extra mtDNA-like sequences which are nuclear
NF	Non-Functional	there are extra non-functional mtDNA like sequences
N-like	Nuclear-like	analysis of extra mtDNA-like sequences suggests that the mutations theyhave accumulated resemble those expected under conditions in the nucleus and not under those in mitochondria
ind.	Independent transfers	Numts were generated by >1 independent transfer from mitochondrion to the nucleus
amp.	Amplified	there are groups Numts that closely resemble each other; these may have been amplified from a single type of pseudogene (e.g. by segmental DNA duplication)

References

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A census of nuclear mitochondrial pseudogenes (numts)

Abbreviations:

References

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