Hox genes of the Japanese eel Anguilla japonica and Hox cluster evolution in teleosts

Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

Volumn 314 B, Issue 2, 2010, Pages 135-147

  Guo, Baocheng ^a,b   Gan, Xiaoni ^a   He, Shunping ^a  

^a INSTITUTE OF HYDROBIOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

HOMEODOMAIN PROTEIN; PRIMER DNA;

ANIMAL; ARTICLE; EEL; FEMALE; GENETICS; GENOMICS; HOMEOBOX; MOLECULAR EVOLUTION; POLYMERASE CHAIN REACTION;

ANGUILLA; ANIMALS; DNA PRIMERS; EVOLUTION, MOLECULAR; FEMALE; GENES, HOMEOBOX; GENOMICS; HOMEODOMAIN PROTEINS; POLYMERASE CHAIN REACTION;

ANGUILLA JAPONICA; DANIO RERIO; EUTELEOSTEI; OTOCEPHALA; TELEOSTEI; TETRAODONTIDAE;

EID: 76749169889     PISSN: 15525007     EISSN: 15525015     Source Type: Journal    
DOI: 10.1002/jez.b.21318     Document Type: Article

References (46)

1. Amores A, Force A, Yan YL, Joly L, Amemiya C, Fritz A, Ho RK, Langeland J, Prince V, Wang YL, Westerfield M, Ekker M, Postlethwait JH. 1998. Zebrafish hox clusters and vertebrate genome evolution. Science 282:1711-1714.
2. Amores A, Suzuki T, Yan YL, Pomeroy J, Singer A, Amemiya C, Postlethwait JH. 2004. Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish. Genome Res 14:1-10.
3. Aparicio S, Hawker K, Cottage A, Mikawa Y, Zuo L, Venkatesh B, Chen E, Krumlauf R, Brenner S. 1997. Organization of the Fugu rubripes Hox clusters: evidence for continuing evolution of vertebrate Hox complexes. Nat Genet 16:79-83.
4. Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, Gelpke MD, Roach J, Oh T, Ho IY, Wong M, Detter C, Verhoef F, Predki P, Tay A, Lucas S, Richardson P, Smith SF, Clark MS, Edwards YJ, Doggett N, Zharkikh A, Tavtigian SV, Pruss D, Barnstead M, Evans C, Baden H, Powell J, Glusman G, Rowen L, Hood L, Tan YH, Elgar G, Hawkins T, Venkatesh B, Rokhsar D, Brenner S. 2002. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297:1301-1310.
5. Bryant D, Moulton V. 2004. Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol 21:255-265.
6. Chambers KE, McDaniell R, Raincrow JD, Deshmukh M, Stadler PF, Chiu CH. 2009. Hox cluster duplication in the basal teleost Hiodon alosoides (Osteoglossomorpha). Theory Biosci 128:109-121.
7. Christoffels A, Koh EG, Chia JM, Brenner S, Aparicio S, Venkatesh B. 2004. Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. Mol Biol Evol 21:1146-1151.
8. Crow KD, Stadler PF, Lynch VJ, Amemiya C, Wagner GP. 2006. The ''fish-specific'' Hox cluster duplication is coincident with the origin of teleosts. Mol Biol Evol 23:121-136.
9. Garcia-Fernandez J, Holland PW. 1994. Archetypal organization of the amphioxus Hox gene cluster. Nature 370:563-566.
10. Hinegardner R, Rosen DE. 1972. Cellular DNA content and the evolution of teleostean fishes. Am Nat 160:621-644.
11. Hoegg S, Brinkmann H, Taylor JS, Meyer A. 2004. Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish. J Mol Evol 59:190-203.
12. Hoegg S, Boore J, Kuehl J, Meyer A. 2007. Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni. BMC genomics 8:317.
13. Holland LZ, Albalat R, Azumi K, Benito-Gutierrez E, Blow MJ, Bronner- Fraser M, Brunet F, Butts T, Candiani S, Dishaw LJ, Ferrier DE, Garcia- Fernandez J, Gibson-Brown JJ, Gissi C, Godzik A, Hallbook F, Hirose D, Hosomichi K, Ikuta T, Inoko H, Kasahara M, Kasamatsu J, Kawashima T, Kimura A, Kobayashi M, Kozmik Z, Kubokawa K, Laudet V, Litman GW, McHardy AC, Meulemans D, Nonaka M, Olinski RP, Pancer Z, Pennacchio LA, Pestarino M, Rast JP, Rigoutsos I, Robinson-Rechavi M, Roch G, Saiga H, Sasakura Y, Satake M, Satou Y, Schubert M, Sherwood N, Shiina T, Takatori N, Tello J, Vopalensky P, Wada S, Xu A, Ye Y, Yoshida K, Yoshizaki F, Yu JK, Zhang Q, Zmasek CM, de Jong PJ, Osoegawa K, Putnam NH, Rokhsar DS, Satoh N, Holland PW. 2008. The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res 18:1100-1111.
14. Huelsenbeck JP, Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
15. Huson DH. 1998. SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14:68-73.
16. Inoue JG, Miya M, Tsukamoto K, Nishida M. 2003. Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the ''ancient fish''. Mol Phylogenet Evol 26:110-120.
17. Ishiguro NB, Miya M, Nishida M. 2003. Basal euteleostean relation- ships: a mitogenomic perspective on the phylogenetic reality of the Protacanthopterygii. Mol Phylogenet Evol 27:476-488.
18. Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, Nicaud S, Jaffe D, Fisher S, Lutfalla G, Dossat C, Segurens B, Dasilva C, Salanoubat M, Levy M, Boudet N, Castellano S, Anthouard V, Jubin C, Castelli V, Katinka M, Vacherie B, Biemont C, Skalli Z, Cattolico L, Poulain J, De Berardinis V, Cruaud C, Duprat S, Brottier P, Coutanceau JP, Gouzy J, Parra G, Lardier G, Chapple C, McKernan KJ, McEwan P, Bosak S, Kellis M, Volff JN, Guigo R, Zody MC, Mesirov J, Lindblad-Toh K, Birren B, Nusbaum C, Kahn D, Robinson-Rechavi M, Laudet V, Schachter V, Quetier F, Saurin W, Scarpelli C, Wincker P, Lander ES, Weissenbach J, Roest Crollius H. 2004. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431:946-957.
19. Kurosawa G, Takamatsu N, Takahashi M, Sumitomo M, Sanaka E, Yamada K, Nishii K, Matsuda M, Asakawa S, Ishiguro H, Miura K, Kurosawa Y, Shimizu N, Kohara Y, Hori H. 2006. Organization and structure of hox gene loci in medaka genome and comparison with those of pufferfish and zebrafish genomes. Gene 370:75-82.
20. Li C, Lu G, Ortí G. 2008. Optimal data partitioning and a test case for ray-finned fishes (Actinopterygii) based on ten nuclear loci. Syst Biol 57:519-539.
21. McGinnis W, Krumlauf R. 1992. Homeobox genes and axial patterning. Cell 68:283-302.
22. Meyer A, van de Peer Y. 2005. From 2R to 3R: evidence for a fish- specific genome duplication (FSGD). Bioessays 27:937-945.
23. Miya M, Takeshima H, Endo H, Ishiguro NB, Inoue JG, Mukai T, Satoh TP, Yamaguchi M, Kawaguchi A, Mabuchi K, Shirai SM, Nishida M. 2003. Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol Phylogenet Evol 26:121-138.
24. Mungpakdee S, Seo H-C, Angotzi AR, Dong X, Akalin A, Chourrout D. 2008. Differential evolution of the thirteen atlantic salmon hox clusters. Mol Biol Evol:msn097.
25. Nelson JS. 2006. Fishes of the World. Hoboken, New Jersey: John Wiley & Sons.
26. Nieselt-Struwe K, von Haeseler A. 2001. Quartet-mapping, a generalization of the likelihood-mapping procedure. Mol Biol Evol 18:1204-1219.
27. Ohno S. 1970. Evolution by Gene Duplication. New York: Springer.
28. Park EH, Kang YS. 1976. Karyotype conservation and difference in DNA amount in anguilloid fishes. Science (New York, NY) 193:64-66.
29. Posada D, Crandall KA. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817-818.
30. Prohaska SJ, Stadler PF. 2004. The duplication of the Hox gene clusters in teleost fishes. Theory Biosci 123:89-110.
31. Saitoh K, Miya M, Inoue JG, Ishiguro NB, Nishida M. 2003. Mitochondrial genomics of ostariophysan fishes: perspectives on phylogeny and biogeography. J Mol Evol 56:464-472.
32. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425.
33. Sansom IJ, Donoghue PC, Albanesi G. 2005. Histology and affinity of the earliest armoured vertebrate. Biol Lett 1:446-449.
34. Santini S, Bernardi G. 2005. Organization and base composition of tilapia Hox genes: implications for the evolution of Hox clusters in fish. Gene 346:51-61.
35. Schughart K, Kappen C, Ruddle FH. 1989. Duplication of large genomic regions during the evolution of vertebrate homeobox genes. Proc Natl Acad Sci USA 86:7067-7071.
36. Stadler PF, Fried C, Prohaska SJ, Bailey WJ, Misof BY, Ruddle FH, Wagner GP. 2004. Evidence for independent Hox gene duplications in the hagfish lineage: a PCR-based gene inventory of Eptatretus stoutii. Mol Phylogenet Evol 32:686-694.
37. Steinke D, Salzburger W, Meyer A. 2006. Novel relationships among ten fish model species revealed based on a phylogenomic analysis using ESTs. J Mol Evol 62:772-784.
38. Stephens SG. 1951. Possible significance of duplication in evolution. Adv Genet 4:247-265.
39. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599.
40. Taylor JS, van de Peer Y, Braasch I, Meyer A. 2001. Comparative genomics provides evidence for an ancient Genome duplication event in fish. Philos Trans R Soc Lond B Biol Sci 356:1661-1679.
41. Thomas-Chollier M, Ledent V. 2008. Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni: comment. BMC genomics 9:35.
42. Thomas-Chollier M, Leyns L, Ledent V. 2007. HoxPred: automated classification of Hox proteins using combinations of generalised profiles. BMC Bioinformatics 8:247.
43. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 25:4876-4882.
44. Vandepoele K, De Vos W, Taylor JS, Meyer A, van de Peer Y. 2004. Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates. Proc Natl Acad Sci USA 101:1638-1643.
45. Woltering JM, Durston AJ. 2006. The zebrafish hoxDb cluster has been reduced to a single microRNA. Nat Genet 38:601-602.
46. Zou SM, Jiang XY, He ZZ, Yuan J, Yuan XN, Li SF. 2007. Hox gene clusters in blunt snout bream, Megalobrama amblycephala and comparison with those of zebrafish, fugu and medaka genomes. Gene 400:60-70.