An Independent Genome Duplication Inferred from Hox Paralogs in the American Paddlefish—A Representative Basal Ray-Finned Fish and Important Comparative Reference

Crow, K.D., Smith, C.D., Cheng, J.F., Wagner, G.P., and Amemiya, C.T.
Genome biology and evolution   4(9): 937-953 (Journal)
Registered Authors
Amemiya, Chris, Smith, Christopher
Polyodon spathula, whole genome duplication, WGD, rate asymmetry, paralog retention, fin-limb transition
MeSH Terms
  • Animals
  • Chromosomes, Artificial, Bacterial/genetics
  • Chromosomes, Artificial, Bacterial/metabolism
  • Cloning, Molecular
  • Evolution, Molecular
  • Fishes/classification
  • Fishes/genetics*
  • Gene Duplication*
  • Genes, Homeobox/genetics*
  • Genome*
  • Models, Genetic
  • Molecular Sequence Annotation
  • Multigene Family
  • Phylogeny
  • Sequence Analysis, DNA
  • Synteny
22851613 Full text @ Genome Biol. Evol.

Vertebrates have experienced two rounds of whole genome duplication in the stem lineages of deep nodes within the group, and a subsequent duplication event in the stem lineage of the teleosts-a highly diverse group of ray-finned fishes. Here we present the first full Hox gene sequences for any member of the Acipenseriformes, the American paddlefish, and confirm that an independent whole genome duplication occurred in the paddlefish lineage, approximately 42 million years ago based on sequences spanning the entire HoxA cluster and eight genes on the HoxD gene cluster. These clusters comprise different HOX loci, and maintain conserved synteny relative to bichir, zebrafish, stickleback and pufferfish, as well as human, mouse, and chick. We also provide a gene genealogy for the duplicated fzd8 gene in paddlefish and present evidence for the first Hox14 gene in any ray-finned fish. Taken together, these data demonstrate that the American paddlefish has an independently duplicated genome. Substitution patterns of the “beta” paralogs on both the HoxA and HoxD gene clusters suggest transcriptional inactivation-consistent with functional diploidization. Further, there are similarities in the pattern of sequence divergence among duplicated Hox genes in paddlefish and teleost lineages, even though they occurred independently approximately 200 million years apart. We highlight implications on comparative analyses in the study of the “fin-limb transition” as well as gene and genome duplication in bony fishes, which includes all ray-finned fishes as well as the lobe-finned fishes and tetrapod vertebrates.

Genes / Markers
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Engineered Foreign Genes
Errata and Notes