Polymorphism of MHC class IIB in an acheilognathid species, Rhodeus sinensis shaped by historical selection and recombination

Hyung-Bae Jeon,Hari Won,Ho Young Suk

doi:10.1186/s12863-019-0775-3

Hyung-Bae Jeon, Hari Won + Show 1 more

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https://doi.org/10.1186/s12863-019-0775-3

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Journal: BMC genetics	Publication Date: Sep 13, 2019
Citations: 4	License type: open-access

Affiliation: Concordia University, Yeungnam University

Abstract

BackgroundRhodeus sinensis is a bitterling species occurring throughout the numerous freshwater systems on the East Asia. Here, we analyzed the diversity of the MHC class IIB (DAB) genes from this species, which may offer meaningful insights into evolutionary processes in this species as well as other bitterlings.ResultsUsing cDNA and gDNA samples from 50 individuals, we discovered classical 140 allelic sequences that could be allocated into either DAB1 (Rhsi-DAB1) or DAB3 (Rhsi-DAB3). DAB sequences completely lacking the intron, but identical or similar to Rhsi-DAB1, were also discovered from our gDNA samples, and this intron loss likely originated from the retrotransposition events of processed mDNA. The β1 domain was the most polymorphic in both Rhsi-DAB1 and -DAB3. Putative peptide biding residues (PBRs) in Rhsi-DAB1, but not in Rhsi-DAB3, exhibited a significant dN/dS, presumably indicating that different selection pressures have acted on those two DABs. Recombination between different alleles seemed to have contributed to the increase of diversity in Rhsi-DABs. Upon phylogenetic analysis, Rhsi-DAB1 and -DAB3 formed independent clusters. Several alleles from other species of Cypriniformes were embedded in the clade of Rhsi-DAB1, whereas Rhsi-DAB3 clustered with alleles from the wider range of taxa (Cyprinodontiformes), indicating that these two Rhsi-DABs have taken different historical paths.ConclusionsA great deal of MHC class IIB allelic diversity was found in R. sinensis, and gene duplication, selection and recombination may have contributed to this diversity. Based on our data, it is presumed that such historical processes have commonly or differently acted on the polymorphism of Rhsi-DAB1 and -DAB3.

Highlights

Rhodeus sinensis is a bitterling species occurring throughout the numerous freshwater systems on the East Asia
The primary aim of this study was to identify the signature of evolutionary forces that have acted on the major histocompatibility complex (MHC) class IIB (DAB) sequences of Korean Rhodeus sinensis, one of the most widely distributed bitterling species (Acheilognathidae)
Based on the blasting search and comparison with diversity of the MHC class IIB (DAB) sequences of other cypriniform species, the alleles were allocated into either DAB1 (Rhsi-DAB1; N = 104) or DAB3 (Rhsi-DAB3; N = 36; Additional file 8: Figure S1 and Additional file 9: Figure S2)

Summary

Introduction

Rhodeus sinensis is a bitterling species occurring throughout the numerous freshwater systems on the East Asia. Three major evolutionary forces are known to contribute to the enormous levels of polymorphism observed in the β1 domain [9]: (i) negative frequency-dependent selection [10,11,12], (ii) heterozygote advantage [13, 14] and (iii) preferences for MHC dissimilar mates [15,16,17] Another well-known evolutionary signature of MHC genes is transspecies polymorphism (TSP), which refers to genetic variants whose origin predates speciation, resulting in the occurrence of shared or similar alleles between different, but related, taxa [18,19,20,21,22]. To learn if TSP exist in a family or order and to infer the related evolutionary factors, information about a very certain phylogenetic structure among species in the taxa should be available

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