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The seahorse genome and the evolution of its specialized morphology

Author

Listed:
  • Qiang Lin

    (CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences)

  • Shaohua Fan

    (Chair in Zoology and Evolutionary Biology, University of Konstanz
    † Present addresses: Department of Genetics, University of Pennsylvania, Pennsylvania 19104, USA (S.F.); Bioprocessing Technology Institute, Biopolis, Singapore 138668, Singapore (A.P.L.); Institute of Evolutionary Biology, the University of Edinburgh EH9 3FL, UK (H.M.G.); School of Material Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore (Z.W.L.).)

  • Yanhong Zhang

    (CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences)

  • Meng Xu

    (BGI-Shenzhen)

  • Huixian Zhang

    (CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences
    Institute of Molecular and Cell Biology)

  • Yulan Yang

    (BGI-Shenzhen)

  • Alison P. Lee

    (Institute of Molecular and Cell Biology
    † Present addresses: Department of Genetics, University of Pennsylvania, Pennsylvania 19104, USA (S.F.); Bioprocessing Technology Institute, Biopolis, Singapore 138668, Singapore (A.P.L.); Institute of Evolutionary Biology, the University of Edinburgh EH9 3FL, UK (H.M.G.); School of Material Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore (Z.W.L.).)

  • Joost M. Woltering

    (Chair in Zoology and Evolutionary Biology, University of Konstanz)

  • Vydianathan Ravi

    (Institute of Molecular and Cell Biology)

  • Helen M. Gunter

    (Chair in Zoology and Evolutionary Biology, University of Konstanz
    † Present addresses: Department of Genetics, University of Pennsylvania, Pennsylvania 19104, USA (S.F.); Bioprocessing Technology Institute, Biopolis, Singapore 138668, Singapore (A.P.L.); Institute of Evolutionary Biology, the University of Edinburgh EH9 3FL, UK (H.M.G.); School of Material Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore (Z.W.L.).)

  • Wei Luo

    (CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences)

  • Zexia Gao

    (College of Fisheries, Huazhong Agricultural University)

  • Zhi Wei Lim

    (Institute of Molecular and Cell Biology
    † Present addresses: Department of Genetics, University of Pennsylvania, Pennsylvania 19104, USA (S.F.); Bioprocessing Technology Institute, Biopolis, Singapore 138668, Singapore (A.P.L.); Institute of Evolutionary Biology, the University of Edinburgh EH9 3FL, UK (H.M.G.); School of Material Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore (Z.W.L.).)

  • Geng Qin

    (CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences
    University of Chinese Academy of Science)

  • Ralf F. Schneider

    (Chair in Zoology and Evolutionary Biology, University of Konstanz)

  • Xin Wang

    (CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences
    University of Chinese Academy of Science)

  • Peiwen Xiong

    (Chair in Zoology and Evolutionary Biology, University of Konstanz)

  • Gang Li

    (CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences)

  • Kai Wang

    (School of Agriculture, Ludong University)

  • Jiumeng Min

    (BGI-Shenzhen)

  • Chi Zhang

    (BGI-Shenzhen)

  • Ying Qiu

    (Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI)

  • Jie Bai

    (Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI)

  • Weiming He

    (BGI-Shenzhen)

  • Chao Bian

    (Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI)

  • Xinhui Zhang

    (Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI)

  • Dai Shan

    (BGI-Shenzhen)

  • Hongyue Qu

    (CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences
    University of Chinese Academy of Science)

  • Ying Sun

    (Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI)

  • Qiang Gao

    (BGI-Shenzhen)

  • Liangmin Huang

    (CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences
    University of Chinese Academy of Science)

  • Qiong Shi

    (CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences
    Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI)

  • Axel Meyer

    (Chair in Zoology and Evolutionary Biology, University of Konstanz)

  • Byrappa Venkatesh

    (Institute of Molecular and Cell Biology
    Yong Loo Lin School of Medicine, National University of Singapore)

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.

Suggested Citation

  • Qiang Lin & Shaohua Fan & Yanhong Zhang & Meng Xu & Huixian Zhang & Yulan Yang & Alison P. Lee & Joost M. Woltering & Vydianathan Ravi & Helen M. Gunter & Wei Luo & Zexia Gao & Zhi Wei Lim & Geng Qin , 2016. "The seahorse genome and the evolution of its specialized morphology," Nature, Nature, vol. 540(7633), pages 395-399, December.
    • Handle: RePEc:nat:nature:v:540:y:2016:i:7633:d:10.1038_nature20595
    DOI: 10.1038/nature20595
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    Cited by:

    1. Krista R. B. Gert & Karin Panser & Joachim Surm & Benjamin S. Steinmetz & Alexander Schleiffer & Luca Jovine & Yehu Moran & Fyodor Kondrashov & Andrea Pauli, 2023. "Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Francesco Cicconardi & Edoardo Milanetti & Erika C. Pinheiro de Castro & Anyi Mazo-Vargas & Steven M. Van Belleghem & Angelo Alberto Ruggieri & Pasi Rastas & Joseph Hanly & Elizabeth Evans & Chris D. , 2023. "Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies," Nature Communications, Nature, vol. 14(1), pages 1-24, December.
    3. Yali Liu & Meng Qu & Han Jiang & Ralf Schneider & Geng Qin & Wei Luo & Haiyan Yu & Bo Zhang & Xin Wang & Yanhong Zhang & Huixian Zhang & Zhixin Zhang & Yongli Wu & Yingyi Zhang & Jianping Yin & Si Zha, 2022. "Immunogenetic losses co-occurred with seahorse male pregnancy and mutation in tlx1 accompanied functional asplenia," Nature Communications, Nature, vol. 13(1), pages 1-12, December.

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