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Front. Immunol. | doi: 10.3389/fimmu.2018.00251

High-throughput sequencing of the expressed torafugu (Takifugu rubripes) antibody sequences distinguishes IgM and IgT repertoires and reveals evidence of convergent evolution

 Xi Fu1,  Jianqiang Sun2, Engkong Tan3,  Kentaro Shimizu2,  Md. Shaheed Reza4, Shugo Watabe4 and Shuichi Asakawa3*
  • 1Sichuan University, China
  • 2Department of Biotechnology, The University of Tokyo, Japan
  • 3Department of Aquatic Bioscience, The University of Tokyo, Japan
  • 4School of Marine Bioscience, Kitasato University, Japan

B cell antigen receptor (BCR) or antibody diversity arises from somatic recombination of immunoglobulin (Ig) gene segments and is concentrated within the Ig heavy (H) chain complementarity-determining region 3 (CDR-H3). We performed high-throughput sequencing of the expressed antibody heavy chain repertoire from adult torafugu. We found that torafugu use between 70% and 82% of all possible V (variable) D (diversity) J (joining) gene segment combinations and that they share a similar frequency distribution of these VDJ combinations. The CDR-H3 sequence repertoire observed in individuals is biased with the preferential use of a small number of VDJ, dominated by sequences containing inserted nucleotides. We uncovered the common CDR-H3 amino acid (aa) sequences shared by individuals. Common CDR-H3 sequences feature highly convergent nucleic acid recombination compared with private ones. Finally, we observed differences in repertoires between IgM and IgT, including the unequal usage frequencies of V gene segment and the biased number of nucleotides insertion/deletion at VDJ junction regions that leads to distinct distributions of CDR-H3 lengths.

Keywords: Antibody repertoire, CDR-H3, teleost fish, convergent evolution, IgM, IGT

Received: 06 Nov 2017; Accepted: 29 Jan 2018.

Edited by:

Victoriano Mulero, Universidad de Murcia, Spain

Reviewed by:

Pierre Boudinot, Institut National de la Recherche Agronomique, France
Yuko Ota, University of Maryland, Baltimore, United States  

Copyright: © 2018 Fu, Sun, Tan, Shimizu, Reza, Watabe and Asakawa. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Shuichi Asakawa, The University of Tokyo, Department of Aquatic Bioscience, Bunkyō, 113-8657, Japan, asakawa@mail.ecc.u-tokyo.ac.jp