Journal Article

The seahorse genome and the evolution of its specialized morphology

Sun, Ying, Shan, Dai, Bian, Chao, Gunter, Helen M., Zhang, Xinhui, Li, Gang, Wang, Xin, Qin, Geng, Yang, Yulan, Zhang, Yanhong, Qu, Hongyue, Meyer, Axel, Luo, Wei, Zhang, Chi, He, Weiming, Gao, Qiang, Gao, Zexia, Huang, Liangmin, Zhang, Huixian, Woltering, Joost M., Xu, Meng, Venkatesh, Byrappa, Shi, Qiong, Qiu, Ying, Lin, Qiang, Lim, Zhi Wei, Fan, Shaohua, Xiong, Peiwen, Min, Jiumeng, Schneider, Ralf F., Ravi, Vydianathan, Bai, Jie, Wang, Kai, Lee, Alison P.

2016

Overview

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. Here, the genome sequence of the tiger tail seahorse is reported and comparative genomic analyses with other ray-finned fishes are used to explore the genetic basis of the unique morphology and reproductive system of the seahorse. Evolution at a gallop Seahorses are prime examples of the exuberance of evolution and are unique among bony fish on several counts, including their equine body shape and male brood pouch. An international collaboration reporting in this issue of Nature has determined the genome sequence of a seahorse ( Hippocampus comes , the tiger tail seahorse). They find it to be the most rapidly evolving fish genome studied so far. H. comes is among the most commonly traded seahorse species—dried for traditional medicines and live for the aquarium trade—and is on the IUCN Red List as a 'vulnerable' species. Analysis of the genomic sequence provides insights into the evolution of its unique morphology. Of note is the absence of a master control gene, tbx4 , which functions in the development of hindlimbs and pelvic fins. Pelvic fins are missing in seahorses, and tbx4 -knockout mutant zebrafish also lack pelvic fins.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/181/2806 / 631/208/726 / Animal Fins - anatomy & histology / Animal Fins - metabolism / Animals / Biological Evolution / Conserved Sequence - genetics / Evolution / Fish / Fish Proteins - deficiency / Fish Proteins - genetics / Gene Deletion / Gene expression / Genes / Genetic aspects / Genome - genetics / Genomes / Genomics / Hindlimb - anatomy & histology / Hindlimb - metabolism / Humanities and Social Sciences / Male / Mineralization / Molecular Sequence Annotation / Morphology / Morphology (Animals) / multidisciplinary / Multigene Family - genetics / Mutation Rate / Natural history / Observations / Phylogenetics / Phylogeny / Proteins / Reproduction - physiology / Science / Sea horses / Smegmamorpha - anatomy & histology / Smegmamorpha - genetics / T-Box Domain Proteins - deficiency / T-Box Domain Proteins - genetics / Teeth / Time Factors / Zebrafish Proteins - deficiency / Zebrafish Proteins - genetics