Advanced search
1 file | 238.61 KB Add to list

Comparative genomics provides evidence for an ancient genome duplication event in fish

Author
Organization
Abstract
There are approximately 25 000 species in the division Teleostei and most arc believed to have arisen during a relatively short period of time ca. 200 Myr ago. The discovery of 'extra' Hox gene clusters in zebrafish (Danio rerio), medaka (Oryzias latipes), and pufferfish (Fugu rubripes), has led to the hypothesis that genome duplication provided the genetic raw material necessary for the telcost radiation. We identified 27 groups of orthologous genes which included one gene from man, mouse and chicken, one or two genes from tetraploid Xenopus and two genes from zebrafish. A genome duplication in the ancestor of teleost fishes is the most parsimonious explanation for the observations that for 15 of these genes, the two zebrafish orthologues are sister sequences in phylogenies that otherwise match the expected organismal tree, the zebrafish gene pairs appear to have been formed at approximately the same time, and are unlinked. Phylogenies of nine genes differ a little from the tree predicted by the fish-specific genome duplication hypothesis: one tree shows a sister sequence relationship for the zebrafish genes but differs slightly from the expected organismal tree and in eight trees, one zebrafish gene is the sister sequence to a clade which includes the second zebrafish gene and orthologues from Xenopus, chicken, mouse and man. For these nine gene trees, deviations from the predictions of the fish-specific genome duplication hypothesis are poorly supported. The two zebrafish orthologues for each of the three remaining genes are tightly linked and are, therefore, unlikely to have been formed during a genome duplication event. We estimated that the unlinked duplicated zebrafish genes are between 300 and 450 Myr. Thus, genome duplication could have provided the genetic raw material for teleost radiation. Alternatively, the loss of different duplicates in different populations (i.e. 'divergent resolution') may have promoted speciation in ancient teleost populations.
Keywords
Genome duplication, speciation, phylogenetics, zebrafish (Danto rerio), comparative genomics, VERTEBRATE EVOLUTION, TREE TOPOLOGIES, COMPARATIVE MAP, LINKAGE MAP, GENES, PROTEINS, ZEBRAFISH, PHYLOGENIES, HYPOTHESIS, SEQUENCES

Downloads

  • (...).pdf
    • full text
    • |
    • UGent only
    • |
    • PDF
    • |
    • 238.61 KB

Citation

Please use this url to cite or link to this publication:

MLA
Taylor, John S., et al. “Comparative Genomics Provides Evidence for an Ancient Genome Duplication Event in Fish.” PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, vol. 356, no. 1414, 2001, pp. 1661–79, doi:10.1098/rstb.2001.0975.
APA
Taylor, J. S., Van de Peer, Y., Braasch, I., & Meyer, A. (2001). Comparative genomics provides evidence for an ancient genome duplication event in fish. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 356(1414), 1661–1679. https://doi.org/10.1098/rstb.2001.0975
Chicago author-date
Taylor, John S, Yves Van de Peer, Ingo Braasch, and Axel Meyer. 2001. “Comparative Genomics Provides Evidence for an Ancient Genome Duplication Event in Fish.” PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 356 (1414): 1661–79. https://doi.org/10.1098/rstb.2001.0975.
Chicago author-date (all authors)
Taylor, John S, Yves Van de Peer, Ingo Braasch, and Axel Meyer. 2001. “Comparative Genomics Provides Evidence for an Ancient Genome Duplication Event in Fish.” PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 356 (1414): 1661–1679. doi:10.1098/rstb.2001.0975.
Vancouver
1.
Taylor JS, Van de Peer Y, Braasch I, Meyer A. Comparative genomics provides evidence for an ancient genome duplication event in fish. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES. 2001;356(1414):1661–79.
IEEE
[1]
J. S. Taylor, Y. Van de Peer, I. Braasch, and A. Meyer, “Comparative genomics provides evidence for an ancient genome duplication event in fish,” PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, vol. 356, no. 1414, pp. 1661–1679, 2001.
@article{8535844,
  abstract     = {{There are approximately 25 000 species in the division Teleostei and most arc believed to have arisen during a relatively short period of time ca. 200 Myr ago. The discovery of 'extra' Hox gene clusters in zebrafish (Danio rerio), medaka (Oryzias latipes), and pufferfish (Fugu rubripes), has led to the hypothesis that genome duplication provided the genetic raw material necessary for the telcost radiation. We identified 27 groups of orthologous genes which included one gene from man, mouse and chicken, one or two genes from tetraploid Xenopus and two genes from zebrafish. A genome duplication in the ancestor of teleost fishes is the most parsimonious explanation for the observations that for 15 of these genes, the two zebrafish orthologues are sister sequences in phylogenies that otherwise match the expected organismal tree, the zebrafish gene pairs appear to have been formed at approximately the same time, and are unlinked. Phylogenies of nine genes differ a little from the tree predicted by the fish-specific genome duplication hypothesis: one tree shows a sister sequence relationship for the zebrafish genes but differs slightly from the expected organismal tree and in eight trees, one zebrafish gene is the sister sequence to a clade which includes the second zebrafish gene and orthologues from Xenopus, chicken, mouse and man. For these nine gene trees, deviations from the predictions of the fish-specific genome duplication hypothesis are poorly supported. The two zebrafish orthologues for each of the three remaining genes are tightly linked and are, therefore, unlikely to have been formed during a genome duplication event. We estimated that the unlinked duplicated zebrafish genes are between 300 and 450 Myr. Thus, genome duplication could have provided the genetic raw material for teleost radiation. Alternatively, the loss of different duplicates in different populations (i.e. 'divergent resolution') may have promoted speciation in ancient teleost populations.}},
  author       = {{Taylor, John S and Van de Peer, Yves and Braasch, Ingo and Meyer, Axel}},
  issn         = {{0962-8436}},
  journal      = {{PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES}},
  keywords     = {{Genome duplication,speciation,phylogenetics,zebrafish (Danto rerio),comparative genomics,VERTEBRATE EVOLUTION,TREE TOPOLOGIES,COMPARATIVE MAP,LINKAGE MAP,GENES,PROTEINS,ZEBRAFISH,PHYLOGENIES,HYPOTHESIS,SEQUENCES}},
  language     = {{eng}},
  number       = {{1414}},
  pages        = {{1661--1679}},
  title        = {{Comparative genomics provides evidence for an ancient genome duplication event in fish}},
  url          = {{http://dx.doi.org/10.1098/rstb.2001.0975}},
  volume       = {{356}},
  year         = {{2001}},
}

Altmetric
View in Altmetric
Web of Science
Times cited: