Evidence for independent Hox gene duplications in the hagfish lineage: A PCR-based gene inventory of Eptatretus stoutii

Molecular Phylogenetics and Evolution

Volumn 32, Issue 3, 2004, Pages 686-694

  Stadler, Peter F ^a,d   Fried, Claudia ^a   Prohaska, Sonja J ^a   Bailey, Wendy J ^b,e   Misof, Bernhard Y ^c,e   Ruddle, Frank H ^e   Wagner, Günter P ^e  

^a UNIVERSITY OF LEIPZIG   (Germany)

^b MERCK RESEARCH LABORATORIES   (United States)

^c ZOOLOGISCHES FORSCHUNGSMUSEUM ALEXANDER KOENIG   (Germany)

^d UNIVERSITY OF VIENNA   (Austria)

^e YALE UNIVERSITY   (United States)

Author keywords

Eptatretus stoutii; Hox genes; PCR survey; Vertebrate evolution

Indexed keywords

PRIMER DNA;

ANIMAL; ARTICLE; CLUSTER ANALYSIS; COMPARATIVE STUDY; DNA SEQUENCE; GENE DUPLICATION; GENETICS; HAGFISH; HOMEOBOX; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY;

ANIMALS; BASE SEQUENCE; CLUSTER ANALYSIS; DNA PRIMERS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENES, HOMEOBOX; HAGFISHES; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

AGNATHA; ANIMALIA; BRANCHIOSTOMA LANCEOLATUM; EPTATRETUS; EPTATRETUS STOUTII; HAGFISH; INVERTEBRATA; MYXINIDAE; PETROMYZONTIDAE; PISCES; VERTEBRATA;

EID: 1842838629     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2004.03.015     Document Type: Article

References (54)

1. Amores A., Force A., Yan Y.L., Joly L., Amemiya C., Fritz A., Ho R.K., Langeland J., Prince V., Wang Y.L., Westerfield M., Ekker M., Postlethwait J.H. Zebrafish hox clusters and vertebrate genome evolution. Science. 282:1998;1711-1714
2. Amores A., Suzuki T., Yan Y.-L., Pomeroy J., Singer A., Amemiya C., Postlethwait J. Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish. Genome Res. 14:2004;1-10
3. Bandelt H.J., Dress A.W.M. A canonical decomposition theory for metrics on a finite set. Adv. Math. 92:1992;47
4. Bartels J.L., Murtha M.T., Ruddle F.H. Multiple Hox/HOM-class homeoboxes in plathelminthes. Mol. Phylogenet. Evol. 2:1993;143-151
5. Cartwright P., Dick M.H., Buss L.W. HOM/Hox type homeoboxes in the chelicerate Limulus polyphemus. Mol. Phylogenet. Evol. 2:1993;185-192
6. Chiu C.-H., Amemiya C., Dewar K., Kim C.-B., Ruddle F.H., Wagner G.P. Molecular evolution of the HoxA cluster in the three major gnathostome lineages. Proc. Natl. Acad. Sci. USA. 99:2002;5492-5497
7. Delabre C., Gallut C., Barriel V., Janvier P., Gachelin G. Complete mitochondrial DNA of the hagfish, Eptatretus burgerie: the comparative analysis of mitochondrial DNA sequences strongly supports cyclostome monophyly. Mol. Phylogenet. Evol. 22:2002;184-192
8. Dick M.H., Buss L.W. A PCR-based survey of homeobox genes in Ctenodrilus serratus (annelida: polychaeta). Mol. Phylogenet. Evol. 3:1994;146-158
9. Escriva H., Manzon L., Youson J., Laudet V. Analysis of lamprey and hagfish genes reveals a complex history of gene duplications during early vertebrate evolution. Mol. Biol. Evol. 19:2002;1440-1450
10. Felsenstein J. Phylip - phylogeny inference package (version 3.2). Cladistics. 5:1989;164-166
11. Ferrier D.E.K., Minguillón C., Holland P.W.H., Garcia-Fernàndez J. The amphioxus Hox cluster: deuterostome posterior flexibility and Hox14. Evol. Dev. 2:2000;284-293
12. Force A., Amores A., Postlethwait J.H. Hox cluster organization in the jawless vertebrate Petromyzon marinus. J. Exp. Zool. (Mol. Dev. Evol.). 294:2002;30-46
13. Forey P., Janvier P. Agnathans and the origin of jawed vertebrates. Nature. 361:1993;129-134
14. Fried C., Prohaska S.J., Stadler P.F. Independent Hox-cluster duplications in lampreys. J. Exp. Zool., Mol. Dev. Evol. B. 299:2003;18-25
15. Furlong R.F., Holland P.W. Bayesian phylogenetic analysis supports monophyly of ambulacria and cyclostomes. Zool. Sci. 19:2002;593-599
16. Garcia-Fernandez J., Holland P.W. Archetypal organization of the amphioxus hox gene cluster. Nature. 370:1994;563-566
17. Germot A., Lecointre G., Plouhinec J.-L., Le Mentec C., Girardot F., Mazan S. Structural evolution of Otx genes in craniates. Mol. Biol. Evol. 18:2001;1668-1678
18. Gursoy H.-C., Koper D., Benecke B.-J. The vertebrate 7S K RNA separates hagfish (Myxine glutinosa) and lamprey (Lampetra fluviatilis). J. Mol. Evol. 50:2000;456-464
19. Holland P.W., Garcia-Fernandez J. Hox genes and chordate evolution. Dev. Biol. 173:1996;382-395
20. Holland P.W., Williams N.A. Conservation of engrailed-like homeobox sequences during vertebrate evolution. FEBS Lett. 277:1990;250-252
21. Holland P.W.H., Garcia-Fernández J., Williams N.A., Sidow A. Gene duplication and the origins of vertebrate development. Development. (Suppl.):1994;125-133
22. Huson D.H. Splitstree: analyzing and visualizing evolutionary data. Bioinformatics. 14:1998;68-73
23. Irvine S.Q., Carr J.L., Bailey W.J., Kawasaki K., Shimizu N., Amemiya C.T., Ruddle F.H. Genomic analysis of Hox clusters in the sea lamprey, Petromyzon marinus. J. Exp. Zool. (Mol. Dev. Evol.). 294:2002;47-62
24. Janvier P. Early Vertebrates. 1996;Clarendon Press, Oxford
25. Kappen C., Schughart K., Ruddle F.H. Two steps in the evolution of antennapedia-class vertebrate homeobox genes. Proc. Natl. Acad. Sci. USA. 86:1989;5459-5463
26. Koh E.G.L., Lam K., Christoffels A., Erdmann M.V., Brenner S., Venkatesh B. Hox gene clusters in the indonesian coelacanth, Latimeria menadoensis. Proc. Natl. Acad. Sci. USA. 100:2003;1084-1088
27. Kuraku S., Hoshiyama D., Katoh K., Suga H., Miyata T. Monophyly of lampreys and hagfishes supported by nuclear DNA-coded sequences. J. Mol. Evol. 49:1999;729-735
28. Ledje C., Kim C.-B., Ruddle F.H. Characterization of Hox genes in the bichir, Polypterus palmas. J. Exp. Zool. Mol. Dev. Evol. 294:2002;107-111
29. Lynch M., Conery J.S. The evolutionary fate and consequences of duplicate genes. Science. 290:2000;1151-1155
30. Maisey J.G. Heads and tails: a chordate phylogeny. Cladistics. 2:1986;201-256
31. Málaga-Trillo E., Meyer A. Genome duplications and accelerated evolution of Hox genes and cluster architecture in teleost fishes. Am. Zool. 41:2001;676-686
32. Mallatt J., Sullivan J. 28S and 18S rDNA sequences support the monophyly of lampreys and hagfishes. Mol. Biol. Evol. 15:1998;1706-1718
33. Martinez P., Amemiya C.T. Genomics of the HOX gene cluster. Comp. Biochem. Physiol. Part B. 133:2002;571-580
34. Meyer A., Schartl M. Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. Curr. Opin. Cell Biol. 11:1999;699-704
35. Misof B.Y., Wagner G.P. Evidence for four Hox clusters in the killifish Fundulus heteroclitus (teleostei). Mol. Phylogenet. Evol. 5:1996;309-322
36. Misof B.Y., Blanco M.J., Wagner G.P. A PCR-survey of Hox genes of the zebrafish: new sequences and evolutionary implications. J. Exp. Zool. 274:1996;193-206
37. Murtha M.T., Lechman J.F., Ruddle F.H. Detection of homeobox genes in development and evolution. Proc. Natl. Acad. Sci. USA. 88:1991;10711-10715
38. Nelson J.S. Fishes of the World. 1994;Wiley, New York
39. Nieselt-Struwe K., von Haeseler A. Quartet-mapping, a generalization of the likelihood mapping procedure. Mol. Biol. Evol. 18:2001;1204-1219
40. Ohno S. Evolution by Gene Duplication. 1970;Springer Verlag, New York
41. Pendleton J., Nagai B.K., Murtha M.T., Ruddle F.H. Expansion of the Hox gene family and the evolution of chordates. Proc. Natl. Acad. Sci. USA. 90:1993;6300-6304
42. Prohaska S., Fried C., Flamm C., Wagner G., Stadler P.F. Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications. Mol. Phyl. Evol. 31:2004;581-604 10.1016/j.ympev.2003.08.009
43. Prohaska S.J., Fried C., Amemiya C.T., Ruddle F.H., Wagner G.P., Stadler P.F. The shark HoxN cluster is homologous to the human HoxD cluster. J. Mol. Evol. 58:2004;212-217
44. Rasmussen A.-S., Janke A., Arnason U. The mitochondrial DNA molecule of the hagfish Myxine glutinosa and vertebrate phylogeny. J. Mol. Evol. 46:1998;382-388
45. Ruddle F.H., Bartels J.L., Bentley K.L., Kappen C., Murta M.T., Pendleton J.W. Evolution of Hox genes. Annu. Rev. Genet. 28:1994;423-442
46. Ruddle F.H., Bentley K.L., Murtha M.T., Risch N. Gene loss and gain in the evolution of the vertebrates. Development. (Supplement):1994;155-161
47. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:1987;406-425
48. Sarkar I.N., Thornton J.W., Planet P.J., Figurski D.H., Schierwater B., DeSalle R. An automated phylogenetic key for classifying homeoboxes. Mol. Phylogenet. Evol. 24:2002;388-399
49. Schughart K., Kappen C., Ruddle F.H. Mammalian homeobox-containing genes: genomic organization, structure, expression and evolution. Br. J. Cancer. 58:1987;9-13
50. Sharman A.C., Holland P.W. Estimation of Hox gene cluster number in lampreys. Int. J. Dev. Biol. 42:1998;617-620
51. Shashikant C.S., Utset M.F., Violette S.M., Wise T.L., Einat P., Einat M., Pendleton J.W., Schughart K., Ruddle F.H. Homeobox genes in mouse development. Crit. Rev. Eukaryot. Gene Expr. 1:1991;207-245
52. Stellwag E.J. Hox gene duplications in fish. Cell Dev. Biol. 10:1999;531-540
53. Stock D.W., Whitt G.S. Evidence from 18S ribosomal RNA sequences that lampreys and hagfish form a natural group. Science. 257:1992;787-789
54. Takezaki N., Figueroa F., Zelska-Rutcynska Z., Klein J. Molecular phylogeny of early vertebrates: monophyly of the agnathans as revealed by sequences of 35 genes. Mol. Biol. Evol. 20:2003;287-292