Eukaryote genome duplication - Where's the evidence?

Current Opinion in Genetics and Development

Volumn 8, Issue 6, 1998, Pages 694-700

  Skrabanek, Lucy ^b   Wolfe, Kenneth H ^a  

^a TRINITY COLLEGE DUBLIN   (Ireland)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

AMPHIBIA; ANIMAL CELL; EUKARYOTE; FISH; GENE DUPLICATION; GENE MAPPING; GENE NUMBER; GENE SEQUENCE; GENOME; MAIZE; NONHUMAN; POLYPLOIDY; PRIORITY JOURNAL; REVIEW; VERTEBRATE; XENOPUS; YEAST;

AMPHIBIA; ANIMALIA; EUKARYOTA; MAMMALIA; VERTEBRATA; XENOPUS; ZEA MAYS;

EID: 0031795610     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-437X(98)80039-7     Document Type: Article

References (60)

1. Ohno S. Evolution by Gene Duplication. 1970;George Allen and Unwin, London.
2. Ohno S. Ancient linkage groups and frozen accidents. Nature. 244:1973;259-262.
3. Henikoff S, Greene EA, Pietrokovski S, Bork P, Attwood TK, Hood L. Gene families: the taxonomy of protein paralogs and chimeras. Science. 278:1997;609-614.
4. Nadeau JH, Sankoff D. Comparable rates of gene loss and functional divergence after genome duplications early in vertebrate evolution. Genetics. 147:1997;1259-1266.
5. Wolfe KH, Shields DC. Molecular evidence for an ancient duplication of the entire yeast genome. Nature. 387:1997;708-713.
6. Coissac E, Maillier E, Netter P. A comparative study of duplications in bacteria and eukaryotes: the importance of telomeres. Mol Biol Evol. 14:1997;1062-1074.
7. Mewes HW, Albermann K, Bähr M, Frishman D, Gleissner A, Hani J, Heumann K, Kleine K, Maierl A, Oliver SG, et al. Overview of the yeast genome. Nature. 387:1997;7-65. (Suppl).
8. Helentjaris T, Weber D, Wright S. Identification of the genomic locations of duplicate nucleotide sequences in maize by analysis of restriction fragment length polymorphisms. Genetics. 118:1988;353-363.
9. Ahn S, Tanksley SD. Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci USA. 90:1993;7980-7984.
10. Moore G, Devos KM, Wang Z, Gale MD. Cereal genome evolution: grasses, line up and form a circle. Curr Biol. 5:1995;737-739.
11. Gale MD, Devos KM. Comparative genetics in the grasses. of special interest Proc Natl Acad Sci USA. 95:1998;1971-1974 In our opinion, although there is strong evidence both that the maize genome is an ancient tetraploid and that there is substantial conservation of gene order among grasses, the 'Lego' model of Gale and co-workers is misleading and questionable. The circular representation of the aligned genomes of different species (including two putative sub-genomes from maize) implies that either there have been no chromosomal fusions or translocations during grass evolution - in which case the ancestor of the grasses must have had just a single, giant, chromosome; [12] - or else that chromosomal fusions occur but each chromosome is only permitted to fuse with a particular designated partner. Neither of these seems plausible.
12. Moore G, Foote T, Helentjaris T, Devos K, Kurata N, Gale M. Was there a single ancestral cereal chromosome? Trends Genet. 11:1995;81-82.
13. Kowalski SP, Lan TH, Feldmann KA, Paterson AH. Comparative mapping of Arabidopsis thaliana and Brassica oleracea chromosomes reveals islands of conserved organization. Genetics. 138:1994;499-510.
14. Seoighe C, Wolfe KH. Extent of genomic rearrangement after genome duplication in yeast. Proc Natl Acad Sci USA. 95:1998;4447-4452.
15. Gaut BS, Doebley JF. DNA sequence evidence for the segmental allotetraploid origin of maize. of outstanding interest Proc Natl Acad Sci USA. 94:1997;6809-6814 The authors propose that the duplicated regions of the maize genome arose from segmental allotetraploidy and they provide a very clear and reasoned explanation of their model. Moleculr clock analysis of 14 maize gene pairs yielded two non-overlapping groups of date estimates centred on 11.4 and 20.5 Mya. An allotetraploid ancestor is proposed to have gone through a phase of tetrasomic inheritance - each locus has four alleles - before becoming 'diploidised' (disomic). At each locus, genetic drift during the tetrasomic phase might result in the loss of alleles inherited from one of the progenitor species, or alleles from both progenitors might be retained. Consequently, after diploidisation, the divergence time between the two sequences at a duplicated locus could correspond either to the speciation time between the two progenitors (20.5 Mya), or to the time of establishment of disomy (11.4 Mya). It would be impossible to predict the outcome for any particular locus.
16. Keogh RS, Seoighe C, Wolfe KH. Evolution of gene order and chromosome number in Saccharomyces, Kluyveromyces and related fungi. Yeast. 14:1998;443-457.
17. Sharp PM, Li WH. An evolutionary perspective on synonymous codon usage in unicellular organisms. J Mol Evol. 24:1986;28-38.
18. Bailey GS, Poulter RT, Stockwell PA. Gene duplication in tetraploid fish: model for gene silencing at unlinked duplicated loci. Proc Natl Acad Sci USA. 75:1978;5575-5579.
19. Walsh JB. How often do duplicated genes evolve new functions? Genetics. 139:1995;421-428.
20. Sidow A. Gen(om)e duplications in the evolution of early vertebrates. Curr Opin Genet Dev. 6:1996;715-722.
21. Hughes MK, Hughes AL. Evolution of duplicate genes in a tetraploid animal, Xenopus laevis. Mol Biol Evol. 10:1993;1360-1369.
22. Nowak MA, Boerlijst MC, Cooke J, Smith JM. Evolution of genetic redundancy. of special interest Nature. 388:1997;167-171 Four models are proposed here for how genetic redundancy could be evolutionarily stable but these require different mutation rates in different genes - which seems unlikely for genes with, initially, identical DNA sequences - or are only applicable to multicellular organisms.
23. Cooke J, Nowak MA, Boerlijst M, Maynard-Smith J. Evolutionary origins and maintenance of redundant gene expression during metazoan development. of special interest Trends Genet. 13:1997;360-364 Building on their earlier results [22], the authors here point out that developmental genes are much more likely to acquire new functions than are housekeeping genes with metabolic functions. Redundancy generated by gene duplication may increase fitness, or it may be retained if the duplicated genes have different efficiencies and different mutation rates which interact in such a way as to keep the two copies in a dynamic equilibrium.
24. Gibson TJ, Spring J. Genetic redundancy in vertebrates: polyploidy and persistence of genes encoding multidomain proteins. of special interest Trends Genet. 14:1998;46-49 Point mutations in developmental genes often have dominant deleterious phenotypes, whereas complete deletion of these genes often has no phenotype. Gibson and Spring argue that this is to be expected for genes encoding multidomain proteins and that this may prevent these genes from decaying into pseudogenes.
25. Iwabe N, Kuma K, Miyata T. Evolution of gene families and relationship with organismal evolution: rapid divergence of tissue-specific genes in the early evolution of chordates. Mol Biol Evol. 13:1996;483-493.
26. Ohno S. The notion of the Cambrian pananimalla genome and a genomic difference that separated vertebrates from invertebrates. Müller WE, Kuchino Y, Jeanteur P, Paine PL. Molecular Evolution: Evidence for Monophyly of Metazoa (Progress in Molecular and Subcellular Biology, vol. 19). 1998;Springer-Verlag, New York. in press.
27. Simmen MW, Leitgeb S, Clark VH, Jones SJ, Bird A. Gene number in an invertebrate chordate, Ciona intestinalis. of outstanding interest Proc Natl Acad Sci USA. 95:1998;4437-4440 A method for estimating the number of genes in any eukaryote on the basis of BLAST searches with random genomic and cDNA sequences. The method was tested using subsets of the data from the Caenorhabditis elegans genome project, and was then applied to the tunicate Ciona intestinalis. Its apparent accuracy, simplicity, and low cost - only 76 EST and 1487 genomic single-pass sequencing runs were made - make it attractive to apply to other organisms such as amphioxus and lamprey.
28. Fields C, Adams MD, White O, Venter JC. How many genes in the human genome? Nat Genet. 7:1994;345-346.
29. Spring J. Vertebrate evolution by interspecific hybridisation - are we polyploid? FEBS Lett. 400:1997;2-8.
30. Baker ME. Steroid receptor phylogeny and vertebrate origins. Mol Cell Endocrinol. 135:1997;101-107.
31. Escriva H, Safi R, Hanni C, Langlois MC, Saumitou-Laprade P, Stehelin D, Capron A, Pierce R, Laudet V. Ligand binding was acquired during evolution of nuclear receptors. Proc Natl Acad Sci USA. 94:1997;6803-6808.
32. Comings DE. Evidence for ancient tetraploidy and conservation of linkage groups in mammalian chromosomes. Nature. 238:1972;455-457.
33. Carver EA, Stubbs L. Zooming in on the human-mouse comparative map: genome conservation re-examined on a high-resolution scale. Genome Res. 7:1997;1123-1137.
34. Lundin LG. Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse. Genomics. 16:1993;1-19.
35. Ruddle FH, Bentley KL, Murtha MT, Risch N. Gene loss and gain in the evolution of the vertebrates. Development. 1994;155-161. Suppl.
36. Katsanis N, Fitzgibbon J, Fisher EMC. Paralogy mapping: identification of a region in the human MHC triplicated onto human chromosomes 1 and 9 allows the prediction and isolation of novel PBX and NOTCH loci. Genomics. 35:1996;101-108.
37. Kasahara M, Hayashi M, Tanaka K, Inoko H, Sugaya K, Ikemura T, Ishibashi T. Chromosomal localization of the proteasome Z subunit gene reveals an ancient chromosomal duplication involving the major histocompatibility complex. Proc Natl Acad Sci USA. 93:1996;9096-9101.
38. Kasahara M. New insights into the genomic organization and origin of the major histocompatibility complex: role of chromosomal (genome) duplication in the emergence of the adaptive immune system. Hereditas. 127:1997;59-65.
39. Endo T, Imanishi T, Gojobori T, Inoko H. Evolutionary significance of intra-genome duplication of human chromosomes. of outstanding interest Gene. 205:1997;19-27 See annotation [40].
40. Hughes AL. Phylogenetic tests of the hypothesis of block duplication of homologous genes on human chromosomes 6, 9, and 1. of outstanding interest Mol Biol Evol. 15:1998;854-870 The combined results from this study and that of Endo et al. [39] show that, of the 11 gene pairs on HSA6/HSA9 that have previously been proposed, a simultaneous origin seems possible for six: RXRA/RXRB, COL5A1/COL11A2. ORFX/RING3, PBX3/PBX2, C5/C4A and TNC/TNX. Gene order for these pairs is conserved except for one inversion of C5 and TNC. Other gene pairs are either much older (ABC2/TAP1, NOTCH1/INT3, PSMB7/PSMB8 and HSPA5/HSPA1A) or much younger (VARS1/VARS2). Despite their similar conclusions, the use of different molecular clock calibrations in the two studies causes them to disagree on the absolute date of the block duplication: 579-696 Mya in Hughes' study, but 161-580 Mya in Endo et al.'s. The latter group also put forward a convoluted hypothesis involving two round of duplication to explain the presence of older gene pairs in the region, whereas Hughes proposes that there may be some sort of selective constraint causing clustering of the ancient paralogues.
41. Kappen C, Schughart K, Ruddle FH. Two steps in the evolution of Antennapedia-class vertebrate homeobox genes. Proc Natl Acad Sci USA. 86:1989;5459-5463.
42. Holland PW, Garcia-Fernandez J, Williams NA, Sidow A. Gene duplications and the origins of vertebrate development. Development. 1994;125-133. Suppl.
43. Bailey WJ, Kim J, Wagner GP, Ruddle FH. Phylogenetic reconstruction of vertebrate Hox cluster duplications. Mol Biol Evol. 14:1997;843-853.
44. Sharman AC, Holland PW. Estimation of Hox gene cluster number in lampreys. Int J Dev Biol. 42:1998;617-620.
45. Aparicio S, Hawker K, Cottage A, Mikawa Y, Zuo L, Venkatesh B, Chen E, Krumlauf R, Brenner S. Organization of the Fugu rubripes Hox clusters: evidence for continuing evolution of vertebrate Hox complexes. Nat Genet. 16:1997;79-83.
46. Prince VE, Joly L, Ekker M, Ho RK. Zebrafish hox genes: genomic organization and modified colinear expression patterns in the trunk. Development. 125:1998;407-420.
47. Postlethwait JH, Yan YL, Gates MA, Horne S, Amores A, Brownlie A, Donovan A, Egan ES, Force A, Gong Z, et al. Vertebrate genome evolution and the zebrafish gene map. of outstanding interest Nat Genet. 18:1998;345-349 Duplicated genes linked to the four Hox clusters in mammals - the HSA 2/7/12/17 region - are also linked to them in zebrafish, and parts of the HSA 1/6/9/19 region are conserved. This implies that the duplications producing these regions occurred prior to the bony fish/tetrapod divergence, contrary to Lundin's proposal ([34]; Figure 1). As noted in the commentary by Aparicio [49], although zebrafish and mammals show conservation of synteny, gene order is often rearranged in these examples. Postlethwait et al. also report some examples where a pair of linked genes in a mammal seems to correspond to two linked pairs in zebrafish and propose that additional duplications (either of chromosomal fragments or of the whole genome) may have occurred in this species.
48. Meyer A. Hox gene variation and evolution. Nature. 391:1998;225-228.
49. Aparicio S. Exploding vertebrate genomes. Nat Genet. 18:1998;301-303.
50. Brooke NM, Garcia-Fernandez J, Holland PW. The ParaHox gene cluster is an evolutionary sister of the Hox gene cluster. of outstanding interest Nature. 392:1998;920-922 Three homebox genes, Gsx, Xlox (Pdx) and Cdx, are clustered in the amphioxus genome and may also be clustered in mammals. These genes are similar to three of the Hox paralogy groups in terms of their sequence, expression, and order on the chromosome. ParaHox and Hox arose by duplication 520 Mya, before Hox duplicated further to produce the four clusters found in mammals.
51. Pébusque M-J, Coulier F, Birnbaum D, Pontarotti P. Ancient large scale genome duplications: phylogenetic and linkage analyses shed light on chordate genome evolution. Mol Biol Evol. 15:1998;1145-1159.
52. Rowen L, Mahairas G, Hood L. Sequencing the human genome. of special interest Science. 278:1997;605-607 The human genome sequence should be completed by 2005.
53. Sharman AC, Holland PWH. Conservation, duplication, and divergence of developmental genes during chordate evolution. Neth J Zool. 46:1996;47-67.
54. Koop BF, Nadeau JH. Pufferfish and new paradigm for comparative genome analysis. Proc Natl Acad Sci USA. 93:1996;1363-1365.
55. Nadeau JH. Genome duplication and comparative gene mapping. Adolph KW. Advanced Techniques in Chromosome Research. 1991;269-296 Marcel Dekker, New York.
56. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 215:1990;403-410.
57. NCBI Entrez Database on World Wide Web URL: http://www.ncbi.nlm.nih.gov.
58. Tatusov R: DUST sequence filter on the internet at ftp://ncbi.nlm.nih.gov/pub/tatusov/dust.
59. Claverie JM, States DJ. Information enhancement methods for large scale sequence analysis. Computers Chem. 17:1993;191-201.
60. Jurka J: REPBASE database of human repetitive DNA on the internet at ftp://ncbi.nlm.nih.gov/repository/repbase/REF/humrep.ref.