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Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates

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Abstract
It has been suggested that fish have more genes than humans. Whether most of these additional genes originated through a complete (fish-specific) genome duplication or through many lineage-specific tandem gene or smaller block duplications and family expansions continues to be debated. We analyzed the complete genome of the pufferfish Takifugu rubripes (Fugu) and compared it with the paranome of humans. We show that most paralogous genes of Fugu are the result of three complete genome duplications. Both relative and absolute dating of the complete predicted set of protein-coding genes suggest that initial genome duplications, estimated to have occurred at least 600 million years ago, shaped the genome of all vertebrates, In addition, analysis of >150 block duplications in the Fugu genome clearly supports a fish-specific genome duplication (approximate to320 million years ago) that coincided with the vast radiation of most modern ray-finned fishes. Unlike the human genome, Fugu contains very few recently duplicated genes; hence, many human genes are much younger than fish genes. This lack of recent gene duplication, or, alternatively, the accelerated rate of gene loss, is possibly one reason for the drastic reduction of the genome size of Fugu observed during the past 100 million years or so, subsequent to the additional genome duplication that ray-finned fishes but not land vertebrates experienced.
Keywords
FUGU-RUBRIPES, HUMAN GENE FAMILIES, ANIMAL GENOMES, DUPLICATION, ARABIDOPSIS, CHROMOSOMES, HYPOTHESIS, SUPPORT, ORIGINS, RULE

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Chicago
Vandepoele, Klaas, Wouter De Vos, John S Taylor, Axel Meyer, and Yves Van de Peer. 2004. “Major Events in the Genome Evolution of Vertebrates: Paranome Age and Size Differ Considerably Between Ray-finned Fishes and Land Vertebrates.” Proceedings of the National Academy of Sciences of the United States of America 101 (6): 1638–1643.
APA
Vandepoele, K., De Vos, W., Taylor, J. S., 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. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 101(6), 1638–1643.
Vancouver
1.
Vandepoele K, De Vos W, Taylor JS, Meyer A, Van de Peer Y. Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2004;101(6):1638–43.
MLA
Vandepoele, Klaas, Wouter De Vos, John S Taylor, et al. “Major Events in the Genome Evolution of Vertebrates: Paranome Age and Size Differ Considerably Between Ray-finned Fishes and Land Vertebrates.” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101.6 (2004): 1638–1643. Print.
@article{298770,
  abstract     = {It has been suggested that fish have more genes than humans. Whether most of these additional genes originated through a complete (fish-specific) genome duplication or through many lineage-specific tandem gene or smaller block duplications and family expansions continues to be debated. We analyzed the complete genome of the pufferfish Takifugu rubripes (Fugu) and compared it with the paranome of humans. We show that most paralogous genes of Fugu are the result of three complete genome duplications. Both relative and absolute dating of the complete predicted set of protein-coding genes suggest that initial genome duplications, estimated to have occurred at least 600 million years ago, shaped the genome of all vertebrates, In addition, analysis of {\textrangle}150 block duplications in the Fugu genome clearly supports a fish-specific genome duplication (approximate to320 million years ago) that coincided with the vast radiation of most modern ray-finned fishes. Unlike the human genome, Fugu contains very few recently duplicated genes; hence, many human genes are much younger than fish genes. This lack of recent gene duplication, or, alternatively, the accelerated rate of gene loss, is possibly one reason for the drastic reduction of the genome size of Fugu observed during the past 100 million years or so, subsequent to the additional genome duplication that ray-finned fishes but not land vertebrates experienced.},
  author       = {Vandepoele, Klaas and De Vos, Wouter and Taylor, John S and Meyer, Axel and Van de Peer, Yves},
  issn         = {0027-8424},
  journal      = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA},
  language     = {eng},
  number       = {6},
  pages        = {1638--1643},
  title        = {Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates},
  url          = {http://dx.doi.org/10.1073/pnas.0307968100},
  volume       = {101},
  year         = {2004},
}

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