Differential evolution of the 13 Atlantic salmon hox clusters

Molecular Biology and Evolution

Volumn 25, Issue 7, 2008, Pages 1333-1343

  Mungpakdee, Sutada ^a   Seo, Hee Chan ^a   Angotzi, Anna Rita ^a   Dong, Xianjun ^a   Akalin, Altuna ^a   Chourrout, Daniel ^a  

^a UNIVERSITY OF BERGEN   (Norway)

Author keywords

Genome duplication; Hox cluster; Pseudogene; Ray finned fish; Subfunctionalization

Indexed keywords

COMPLEMENTARY DNA;

ARTICLE; ATLANTIC SALMON; CONTROLLED STUDY; GENE AMPLIFICATION; GENE DUPLICATION; GENE IDENTIFICATION; GENETIC VARIABILITY; HOX GENE; MALE; MOLECULAR EVOLUTION; NONHUMAN; POLYMERASE CHAIN REACTION;

ANIMALS; BASE SEQUENCE; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENES, HOMEOBOX; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PHYLOGENY; SALMO SALAR; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, NUCLEIC ACID;

ACTINOPTERYGII; MYA; SALMO SALAR; SALMONIDAE; TELEOSTEI; VERTEBRATA;

EID: 45849106430     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msn097     Document Type: Article

References (38)

1. Allendorf FW, Stahl G, Ryman N. 1984. Silencing of duplicate genes: a null allele polymorphism for lactate dehydrogenase in brown trout (Salmo trutta). Mol Biol Evol. 1:238-248.
2. Allendorf FW, Thorgaard GH. 1984. Tetraploidy and the evolution of salmonid fishes. In: Turner BJ, editor. Evolutionary genetics of fishes. New York: Plenum Press. p. 1-46.
3. 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.
4. Aparicio S, Chapman J, Stupka E, et al. (41 co-authors). 2002. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science. 297:1301-1310.
5. Chain FJ, Evans BJ. 2006. Multiple mechanisms promote the retained expression of gene duplicates in the tetraploid frog Xenopus laevis. PLoS Genet. 2:e56.
6. 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.
7. Conant GC, Wagner A. 2003. Asymmetric sequence divergence of duplicate genes. Genome Res. 9:2052-2058.
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. 1:121-136.
9. Duboule D. 2007. The rise and fall of Hox gene clusters. Development. 134:2549-2560.
10. Fares MA, Bezemer D, Moya A, Marin I. 2003. Selection on coding regions determined Hox7 genes evolution. Mol Biol Evol. 20:2104-2112.
11. Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics. 151:1531-1545.
12. He X, Zhang J. 2005. Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics. 169:1157-1164.
13. 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.
14. Holland PW, Garcia-Fernandez J, Williams NA, Sidow A. 1994. Gene duplications and the origins of vertebrate development. Dev Suppl. 125-133.
15. Hughes AL. 1994. The evolution of functionally novel proteins after gene duplication. Proc Biol Sci. 256:119-124.
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. Jaillon O, Aury JM, Brunet F, et al. (62 co-authors). 2004. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature. 431:946-957.
18. Kellis M, Birren BW, Lander ES. 2004. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature. 428:617-624.
19. Kmita M, Duboule D. 2003. Organizing axes in time and space; 25 years of colinear tinkering. Science. 301:331-333.
20. Kondrashov FA, Rogozinm IB, Wolf I, Koonin EV. 2002. Selection in the evolution of gene duplications. Genome Biol. 3:research0008.
21. Kurosawa G, Takamatsu N, Takahashi M, et al. (15 co-authors). 2006. Organization and structure of hox gene loci in medaka genome and comparison with those of pufferfish and zebrafish genomes. Gene. 370:75-82.
22. Lercher MJ, Chamary JV, Hurst LD. 2004. Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile. Genome Res. 14:1002-1013.
23. Lynch VJ, Roth JJ, Wagner GP. 2006. Adaptive evolution of Hox-gene homeodomains after cluster duplications. BMC Evol Biol. 6:86.
24. Moghadam HK, Ferguson MM, Danzmann RG. 2005. Evolution of Hox clusters in Salmonidae: a comparative analysis between Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). J Mol Evol. 61:636-649.
25. Naruse K, Tanaka M, Mita K, Shima A, Postlethwait J, Mitani H. 2004. A medaka gene map: the trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping. Genome Res. 14:820-828.
26. Nelson JS. 1994. Fishes of the world, 3rd ed. New York: John Wiley & Son Inc.
27. Ohno S. 1970. Evolution by gene duplication. New York: Springer.
28. Phillips RB, Nichols KM, DeKoning JJ, Morasch MR, Keatley KA, Rexroad C 3rd, Gahr SA, Danzmann RG, Drew RE, Thorgaard GH. 2006. Assignment of rainbow trout linkage groups to specific chromosomes. Genetics. 174:1661-1670.
29. Pond SL, Frost SD, Muse SV. 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics. 21:676-679.
30. Powers TP, Amemiya CT. 2004. Evidence for a Hox 14 paralog group in vertebrates. Curr Biol. 14:R183-R184.
31. Rastogi S, Liberles DA. 2005. Subfunctionalization of duplicated genes as a transition state to neofunctionalization. BMC Evol Biol. 5:28-35.
32. Ruddle FH, Bentley KL, Murtha MT, Risch N. 1994. Gene loss and gain in the evolution of the vertebrates. Dev Suppl. 155-161.
33. 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.
34. Van de Peer Y, Taylor JS, Braasch I, Meyer A. 2001. The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes. J Mol Evol. 4-5:436-446.
35. Wagner GP, Takahashi K, Lynch V, Prohaska SJ, Fried C, Stadler PF, Amemiya C. 2005. Molecular evolution of duplicated ray finned fish HoxA clusters: increased synonymous substitution rate and asymmetrical co-divergence of coding and non-coding sequences. J Mol Evol. 5:665-676.
36. Woltering JM, Durston AJ. 2006. The zebrafish hoxDb cluster has been reduced to a single microRNA. Nat Genet. 6:601-602.
37. Woods IG, Wilson C, Friedlander B, Chang P, Reyes DK, Nix R, Kelly PD, Chu F, Postlethwait JH, Talbot WS. 2005. The zebrafish gene map defines ancestral vertebrate chromosomes. Genome Res. 15:1307-1314.
38. Zhang P, Gu Z, Li WH. 2003. Different evolutionary patterns between young duplicate genes in the human genome. Genome Biol. 9:R56.