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The gain and loss of genes during 600 million years of vertebrate evolution

Tine Blomme (UGent) , Klaas Vandepoele (UGent) , Stefanie De Bodt (UGent) , Cedric Simillion (UGent) , Steven Maere (UGent) and Yves Van de Peer (UGent)
(2006) GENOME BIOLOGY. 7(5).
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Organization
Abstract
Background: Gene duplication is assumed to have played a crucial role in the evolution of vertebrate organisms. Apart from a continuous mode of duplication, two or three whole genome duplication events have been proposed during the evolution of vertebrates, one or two at the dawn of vertebrate evolution, and an additional one in the fish lineage, not shared with land vertebrates. Here, we have studied gene gain and loss in seven different vertebrate genomes, spanning an evolutionary period of about 600 million years. Results: We show that: first, the majority of duplicated genes in extant vertebrate genomes are ancient and were created at times that coincide with proposed whole genome duplication events; second, there exist significant differences in gene retention for different functional categories of genes between fishes and land vertebrates; third, there seems to be a considerable bias in gene retention of regulatory genes towards the mode of gene duplication ( whole genome duplication events compared to smaller-scale events), which is in accordance with the so-called gene balance hypothesis; and fourth, that ancient duplicates that have survived for many hundreds of millions of years can still be lost. Conclusion: Based on phylogenetic analyses, we show that both the mode of duplication and the functional class the duplicated genes belong to have been of major importance for the evolution of the vertebrates. In particular, we provide evidence that massive gene duplication ( probably as a consequence of entire genome duplications) at the dawn of vertebrate evolution might have been particularly important for the evolution of complex vertebrates.
Keywords
WHOLE-GENOME DUPLICATION, MULTIPLE SEQUENCE ALIGNMENT, RAY-FINNED FISHES, ANIMAL GENOMES, HOX CLUSTERS, 2 ROUNDS, FAMILIES, AGE, NEOFUNCTIONALIZATION, SUBFUNCTIONALIZATION

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Chicago
Blomme, Tine, Klaas Vandepoele, Stefanie De Bodt, Cedric Simillion, Steven Maere, and Yves Van de Peer. 2006. “The Gain and Loss of Genes During 600 Million Years of Vertebrate Evolution.” Genome Biology 7 (5).
APA
Blomme, T., Vandepoele, K., De Bodt, S., Simillion, C., Maere, S., & Van de Peer, Y. (2006). The gain and loss of genes during 600 million years of vertebrate evolution. GENOME BIOLOGY, 7(5).
Vancouver
1.
Blomme T, Vandepoele K, De Bodt S, Simillion C, Maere S, Van de Peer Y. The gain and loss of genes during 600 million years of vertebrate evolution. GENOME BIOLOGY. 2006;7(5).
MLA
Blomme, Tine, Klaas Vandepoele, Stefanie De Bodt, et al. “The Gain and Loss of Genes During 600 Million Years of Vertebrate Evolution.” GENOME BIOLOGY 7.5 (2006): n. pag. Print.
@article{371611,
  abstract     = {Background: Gene duplication is assumed to have played a crucial role in the evolution of vertebrate organisms. Apart from a continuous mode of duplication, two or three whole genome duplication events have been proposed during the evolution of vertebrates, one or two at the dawn of vertebrate evolution, and an additional one in the fish lineage, not shared with land vertebrates. Here, we have studied gene gain and loss in seven different vertebrate genomes, spanning an evolutionary period of about 600 million years. 
Results: We show that: first, the majority of duplicated genes in extant vertebrate genomes are ancient and were created at times that coincide with proposed whole genome duplication events; second, there exist significant differences in gene retention for different functional categories of genes between fishes and land vertebrates; third, there seems to be a considerable bias in gene retention of regulatory genes towards the mode of gene duplication ( whole genome duplication events compared to smaller-scale events), which is in accordance with the so-called gene balance hypothesis; and fourth, that ancient duplicates that have survived for many hundreds of millions of years can still be lost. 
Conclusion: Based on phylogenetic analyses, we show that both the mode of duplication and the functional class the duplicated genes belong to have been of major importance for the evolution of the vertebrates. In particular, we provide evidence that massive gene duplication ( probably as a consequence of entire genome duplications) at the dawn of vertebrate evolution might have been particularly important for the evolution of complex vertebrates.},
  articleno    = {R43},
  author       = {Blomme, Tine and Vandepoele, Klaas and De Bodt, Stefanie and Simillion, Cedric and Maere, Steven and Van de Peer, Yves},
  issn         = {1474-760X},
  journal      = {GENOME BIOLOGY},
  language     = {eng},
  number       = {5},
  pages        = {12},
  title        = {The gain and loss of genes during 600 million years of vertebrate evolution},
  url          = {http://dx.doi.org/10.1186/gb-2006-7-5-r43},
  volume       = {7},
  year         = {2006},
}

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