The seahorse genome and the evolution of its specialized morphology

Nature. 2016 Dec 14;540(7633):395-399. doi: 10.1038/nature20595.


Seahorses have a specialized morphology that includes a toothless tubular mouth, a body covered with bony plates, a male brood pouch, and the absence of caudal and pelvic fins. Here we report the sequencing and de novo assembly of the genome of the tiger tail seahorse, Hippocampus comes. Comparative genomic analysis identifies higher protein and nucleotide evolutionary rates in H. comes compared with other teleost fish genomes. We identified an astacin metalloprotease gene family that has undergone expansion and is highly expressed in the male brood pouch. We also find that the H. comes genome lacks enamel matrix protein-coding proline/glutamine-rich secretory calcium-binding phosphoprotein genes, which might have led to the loss of mineralized teeth. tbx4, a regulator of hindlimb development, is also not found in H. comes genome. Knockout of tbx4 in zebrafish showed a 'pelvic fin-loss' phenotype similar to that of seahorses.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animal Fins / anatomy & histology
  • Animal Fins / metabolism
  • Animals
  • Biological Evolution*
  • Conserved Sequence / genetics
  • Fish Proteins / deficiency
  • Fish Proteins / genetics*
  • Gene Deletion
  • Genome / genetics*
  • Genomics
  • Hindlimb / anatomy & histology
  • Hindlimb / metabolism
  • Male
  • Molecular Sequence Annotation
  • Multigene Family / genetics
  • Mutation Rate
  • Phylogeny
  • Reproduction / physiology
  • Smegmamorpha / anatomy & histology*
  • Smegmamorpha / genetics*
  • T-Box Domain Proteins / deficiency
  • T-Box Domain Proteins / genetics
  • Time Factors
  • Zebrafish Proteins / deficiency
  • Zebrafish Proteins / genetics


  • Fish Proteins
  • T-Box Domain Proteins
  • Zebrafish Proteins
  • tbx4 protein, zebrafish