Coelacanth genomes reveal signatures for evolutionary transition from water to land

Genome Research

Volumn 23, Issue 10, 2013, Pages 1740-1748

  Nikaido, Masato ^a   Noguchi, Hideki ^a,b   Nishihara, Hidenori ^a   Toyoda, Atsushi ^b   Suzuki, Yutaka ^c   Kajitani, Rei ^a   Suzuki, Hikoyu ^a   Okuno, Miki ^a   Aibara, Mitsuto ^a   Ngatunga, Benjamin P ^d   Mzighani, Semvua I ^d   Kalombo, Hassan W J ^e   Masengi, Kawilarang W A ^f   Tuda, Josef ^f   Nogami, Sadao ^g   Maeda, Ryuichiro ^h   Iwata, Masamitsu ⁱ   Abe, Yoshitaka ⁱ   Fujimura, Koji ^j   Okabe, Masataka ^j   Amano, Takanori ^b   Maeno, Akiteru ^b   Shiroishi, Toshihiko ^b   Itoh, Takehiko ^a   Sugano, Sumio ^c   Kohara, Yuji ^b   Fujiyama, Asao ^b   Okada, Norihiro ^a,k,l   more..

^a Tokyo Institute of Technology ^*  (Japan)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

^d TANZANIA FISHERIES RESEARCH INSTITUTE   (Tanzania)

^e Regional Commissioner's Office Tanga   (Tanzania)

^f SAM RATULANGI UNIVERSITY   (Indonesia)

^g NIHON UNIVERSITY   (Japan)

^h OBIHIRO UNIVERSITY OF AGRICULTURE AND VETERINARY MEDICINE   (Japan)

ⁱ Marine Science Museum   (Japan)

^j JIKEI UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^k NATIONAL CHENG KUNG UNIVERSITY   (Taiwan)

^l NAGAHAMA INSTITUTE OF BIO SCIENCE AND TECHNOLOGY   (Japan)

more..

Author keywords

[No Author keywords available]

Indexed keywords

OSTEOGENIC PROTEIN 1; TRANSCRIPTION FACTOR GLI3; WATER;

AMINO ACID SUBSTITUTION; ANIMAL TISSUE; ARTICLE; BREEDING; COMOROS; DNA BASE COMPOSITION; GENE SEQUENCE; GENETIC VARIABILITY; GENOME; GENOME SIZE; HETEROZYGOSITY; INDONESIA; LATIMERIA; LATIMERIA CHALUMNAE; LATIMERIA MENADOENSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHASE TRANSITION; POPULATION SIZE; POPULATION STRUCTURE; PRIORITY JOURNAL; TANZANIA; TETRAPOD; TRANSPOSON;

ADAPTATION, BIOLOGICAL; AFRICA; ANIMALS; AQUATIC ORGANISMS; BASE SEQUENCE; BIODIVERSITY; BONE MORPHOGENETIC PROTEIN 7; EVOLUTION, MOLECULAR; EXTREMITIES; FISHES; GENETIC SPECIATION; GENETIC VARIATION; GENOME; MOLECULAR SEQUENCE DATA; NERVE TISSUE PROTEINS; PHYLOGENY; RECEPTORS, ODORANT; RECEPTORS, PHEROMONE; SEQUENCE ANALYSIS, DNA; VERTEBRATES; WATER;

EID: 84885040878     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.158105.113     Document Type: Article

References (51)

1. Abbasi AA, Paparidis Z, Malik S, Bangs F, Schmidt A, Koch S, Lopez-Rios J, Grzeschik KH. 2010. Human intronic enhancers control distinct sub-domains of Gli3 expression during mouse CNS and limb development. BMC Dev Biol 10: 44.
2. Adams D, Karolak M, Robertson E, Oxburgh L. 2007. Control of kidney, eye and limb expression of Bmp7 by an enhancer element highly conserved between species. Dev Biol 311: 679-690.
3. Agassiz L. 1844. Recherches sur les Poissons Fossiles, Vol. 2. Imprimerie de Petitpierre, Neuchâtel.
4. Amemiya CT, Powers TP, Prohaska SJ, Grimwood J, Schmutz J, Dickson M, Miyake T, Schoenborn MA, Myers RM, Ruddle FH, et al. 2010. Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome. Proc Natl Acad Sci 107: 3622-3627.
5. Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, MacCallum I, Braasch I, Manousaki T, Schneider I, Rohner N, et al. 2013. The African coelacanth genome provides insights into tetrapod evolution. Nature 496: 311-316.
6. Bogart JP, Balon EK, Bruton MN. 1994. The chromosomes of the living coelacanth and their remarkable similarity to those of one of the most ancient frogs. J Hered 85: 322-325.
7. Coates MI, Jeffery JE, Rut M. 2002. Fins to limbs: What the fossils say. Evol Dev 4: 390-401.
8. De Vos L, Oyugi D. 2002. First capture of a coelacanth, Latimeria chalumnae Smith, 1939 (Pisces: Latimeriidae), off Kenya. S Afr J Sci 98: 345-347.
9. Erdmann MV, Caldwell RL, Moosa MK. 1998. Indonesian king of the sea discovered. Nature 395: 335.
10. Forey PL. 1988. Golden jubilee for the coelacanth Latimeria chalumnae. Nature 336: 727-732.
11. Fricke H, Hissmann K, Froese R, Schauer J, Plante R, Fricke S. 2011. The population biology of the living coelacanth studied over 21 years. Mar Biol 158: 1511-1522.
12. Friedman M, Coates MI, Anderson P. 2007. First discovery of a primitive coelacanth fin fills amajor gap in the evolution of lobed fins and limbs. Evol Dev 9: 329-337.
13. Geraudie J, Meunier FJ. 1980. Elastoidin actinotrichia in Coelacanth fins: A comparison with teleosts. Tissue Cell 12: 637-645.
14. Gregory TR, Nicol JA, Tamm H, Kullman B, Kullman K, Leitch IJ, Murray BG, Kapraun DF, Greilhuber J, Bennett MD. 2007. Eukaryotic genome size databases. Nucleic Acids Res 35: D332-D338.
15. Hay JM, Subramanian S, Millar CD, Mohandesan E, Lambert DM. 2008. Rapid molecular evolution in a living fossil. Trends Genet 24: 106-109.
16. Heemstra PC, Freeman AL, Wong HY, Hensley DA, Rabesandratana HD. 1996.First authentic capture of a coelacanth, Latimeria chalumnae (Pisces: Latimeriidae), off Madagascar. S Afr J Sci 92: 150-151.
17. Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, et al. 2010. The genome of the Western clawed frog Xenopus tropicalis. Science 328: 633-636.
18. Higasa K, Nikaido M, Saito TL, Yoshimura J, Suzuki Y, Suzuki H, Nishihara H, Aibara M, Ngatunga BP, KalomboHW, et al. 2012. Extremely slow rate of evolution in the HOX cluster revealed by comparison between Tanzanian and Indonesian coelacanths. Gene 505: 324-332.
19. Hillier LW, Miller W, Birney E, Warren W, Hardison RC, Ponting CP, Bork P, Burt DW, Groenen MA, Delany ME, et al. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716.
20. Hinegardner R, Rosen DE. 1972. Cellular DNA content and the evolution of teleostean fishes. Am Nat 106: 621-644.
21. Hissmann K, Fricke H, Schauer J. 1998. Population monitoring of the coelacanth (Latimeria chalumnae). Conserv Biol 12: 759-765.
22. Inoue JG, Miya M, Venkatesh B, Nishida M. 2005. The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanths. Gene 349: 227-235.
23. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409: 806-921.
24. Kapitonov VV, Jurka J. 2004. Harbinger transposons and an ancient HARBI1 gene derived from a transposase. DNA Cell Biol 23: 311-324.
25. Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, et al. 2007. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447: 167-177.
26. Millot J, Anthony J. 1958. Anatomie de Latimeria chalumnae. Tome I. Squelette, Muscles, et Formations du Soutien. É ditions du Centre National de la Recherche Scientifique, Paris, France.
27. Miyata T, Suga H. 2001. Divergence pattern of animal gene families and relationship with the Cambrian explosion. Bioessays 23: 1018-1027.
28. Nei M, Niimura Y, NozawaM. 2008. The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity. Nat Rev Genet 9: 951-963.
29. Niimura Y, Nei M. 2005. Evolutionary dynamics of olfactory receptor genes in fishes and tetrapods. Proc Natl Acad Sci 102: 6039-6044.
30. Nikaido M, Sasaki T, Emerson JJ, Aibara M, Mzighani SI, Budeba YL, Ngatunga BP, Iwata M, Abe Y, Li WH, et al. 2011. Genetically distinct coelacanth population off the northern Tanzanian coast. Proc Natl Acad Sci 108: 18009-18013.
31. Noonan JP, Grimwood J, Danke J, Schmutz J, Dickson M, Amemiya CT, Myers RM. 2004. Coelacanth genome sequence reveals the evolutionary history of vertebrate genes. Genome Res 14: 2397-2405.
32. Piskurek O, Nishihara H, Okada N. 2009. The evolution of two partner LINE/ SINE families and a full-length chromodomain-containing Ty3/Gypsy LTR element in the first reptilian genome of Anolis carolinensis. Gene 441: 111-118.
33. Saitoh K, Sado T, Doosey MH, Bart HLJ, Inoue JG, Nishida M, Mayden RL, Nishida M, Miya M. 2011. Evidence from mitochondrial genomics supports the lowerMesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi). Zool J Linn Soc 161: 633-662.
34. Saraiva LR, Korsching SI. 2007. A novel olfactory receptor gene family in teleost fish. Genome Res 17: 1448-1457.
35. Sasaki T, Sato T, Miura S, Bwathondi PO, Ngatunga BP, Okada N. 2007. Mitogenomic analysis for coelacanths (Latimeria chalumnae) caught in Tanzania. Gene 389: 73-79.
36. Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, et al. 2012. Insights into hominid evolution from the gorilla genome sequence. Nature 483: 169-175.
37. Schliewen U, Fricke H, Schartl M, Epplen JT, Pääbo S. 1993. Which home for coelacanth? Nature 363: 405.
38. Schneider I, Aneas I, Gehrke AR, Dahn RD, Nobrega MA, Shubin NH. 2011. Appendage expression driven by the Hoxd Global Control Region is an ancient gnathostome feature. Proc Natl Acad Sci 108: 12782-12786.
39. Shedlock AM, Okada N. 2000. SINE insertions: Powerful tools for molecular systematics. Bioessays 22: 148-160.
40. Smith JLB. 1939. A living fish of Mesozonic type. Nature 143: 455-456.
41. Smith JLB. 1953. The second Coelacanth. Nature 171: 99-101.
42. Smith JLB. 1963. The atomic bomb and the coelacanth. The Daily Dispatch, 10 Dec.
43. Smith JJ, Sumiyama K, Amemiya CT. 2012. A living fossil in the genome of a living fossil: Harbinger transposons in the coelacanth genome. Mol Biol Evol 29: 985-993.
44. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, et al. 2002. The generic genome browser: A building block for a model organism system database. Genome Res 12: 1599-1610.
45. Takezaki N, Figueroa F, Zaleska-Rutczynska Z, Takahata N, Klein J. 2004. The phylogenetic relationship of tetrapod, coelacanth, and lungfish revealed by the sequences of forty-four nuclear genes. Mol Biol Evol 21: 1512-1524.
46. Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Guo Y, et al. 2008. The diploid genome sequence of an Asian individual. Nature 456: 60-65.
47. Watanabe H, Fujiyama A, Hattori M, Taylor TD, Toyoda A, Kuroki Y, Noguchi H, BenKahla A, Lehrach H, Sudbrak R, et al. 2004. DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature 429: 382-388.
48. Zardoya R, Meyer A. 1996. Evolutionary relationships of the coelacanth, lungfishes, and tetrapods based on the 28S ribosomal RNA gene. Proc Natl Acad Sci 93: 5449-5454.
49. Zeller R, López-Ríos J, Zuniga A. 2009. Vertebrate limb bud development: Moving towards integrative analysis of organogenesis. Nat Rev Genet 10: 845-858.
50. Zhang J, Wagh P, Guay D, Sanchez-Pulido L, Padhi BK, Korzh V, Andrade- Navarro MA, Akimenko MA. 2010. Loss of fish actinotrichia proteins and the fin-to-limb transition. Nature 466: 234-237.
51. Zuniga A, Laurent F, Lopez-Rios J, Klasen C, Matt N, Zeller R. 2012. Conserved cis-regulatory regions in a large genomic landscape control SHH and BMP-regulated Gremlin1 expression in mouse limb buds. BMC Dev Biol 12: 23. Technology