High-Throughput Sequencing of the Expressed Torafugu (Takifugu rubripes) Antibody Sequences Distinguishes IgM and IgT Repertoires and Reveals Evidence of Convergent Evolution.

Engkong Tan,Md Shaheed Reza,Jianqiang Sun,Kentaro Shimizu,Shuichi Asakawa,Xi Fu,Shugo Watabe

doi:10.3389/fimmu.2018.00251

Abstract

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), and 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 nucleotide insertion/deletion at VDJ junction regions that leads to distinct distributions of CDR-H3 lengths.

Highlights

The adaptive immune system (AIS) is fundamentally reliant on a highly diverse set of antigen receptors. These receptors are generated through somatic recombination of tandemly arranged variable (V), diversity (D), and joining (J) segments of the B-cell antigen receptor [BCR, the membranebound form of antibodies or immunoglobulins (Igs)] and T-cell receptor (TCR) genes, and the insertion and deletion of nucleotides at the junctions between ligated segments [1]
We found evidence that the repertoire of individual fish is highly biased toward sequences with specific VDJ combinations, in addition to the convergent evolution of CDR-H3 sequences in both IgM and IgT
We found that on an average, 180,062 and 24,933 distinct CDR-H3 clusters were presented in the naïve IgM and IgT repertoires, respectively

Summary

Introduction

The adaptive immune system (AIS) is fundamentally reliant on a highly diverse set of antigen receptors. For the human BCRs, for example, the potential diversity of Ig molecules is estimated to be >1013 [9], while this number exceeds the total number of B cells in the human body (approximately 1–2 × 1011) [10]. This excess of potential Ig diversity leads to the expectation that different individuals could seldom share the same segment rearrangement. Several studies have demonstrated overlap among the Ig repertoires of different individuals occurring, i.e., in the naïve human and zebrafish IgH repertoires [8, 11], and in the B-cell responses to virus infection in the rainbow trout [12]

Methods

Results

Conclusion