Abstract
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.Supplementary informationThe online version of this article (doi:10.1038/nature20595) contains supplementary material, which is available to authorized users.
Highlights
It is becoming recognized that evolutionary changes in cis-regulatory elements, the loss and gain of enhancers, might play a major part in the evolution of morphological innovations and phenotypic changes across species[21,36,37,40]
Of the six duplicated genes in seahorse, five are highly expressed in the male brood pouch, suggesting that they may be involved in male pregnancy, possibly through rewiring of their r egulatory network
By combining comparative genomics and gene-knockout experiments in zebrafish, we suggest that loss of tbx[4] may have a role in this phenotype in s eahorse
Summary
Qiang Lin1*§, Shaohua Fan2†*, Yanhong Zhang1*, Meng Xu3*, Huixian Zhang1,4*, Yulan Yang3*, Alison P. 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. Members of the teleost family Syngnathidae (seahorses, pipefishes and seadragons) (Extended Data Fig. 1), comprising approximately 300 species, display a complex array of morphological innovations and reproductive behaviours. This includes specialized morphological phenotypes such as an elongated snout with a small terminal mouth, fused jaws, absent pelvic and caudal fins, and an extended body covered with an armour of bony plates instead of scales[1] (Fig. 1a). The phylogenetic analysis (Fig. 1b) showed that H. comes is a sister group to other percomorph fishes a nalysed
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