Characterization of 40 full-length MHC class IIA functional alleles in miiuy croaker: Polymorphism and positive selection

Xu, Tianjun; Liu, Jiang; Sun, Yueyan; Zhu, Zhihuang; Liu, Tianxing

doi:10.1016/j.dci.2015.10.019

Cited by 11 publications

(7 citation statements)

References 41 publications

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“…In this study, 25 alleles were found from 459 valid sequences. The polymorphisms of mcaIIa have been reported in many fish species (Bracamonte et al ., ; Liu et al ., ; Liu, Liu, Wang, et al ., ; Liu, Liu, Zhao, et al ., ; Shen et al ., ; Wynne et al ., ; Xu et al ., , ; Yang et al ., ). For example, 37 different mcaIIa alleles were found from the E. coioides (Yang et al ., ).…”

Section: Discussionmentioning

confidence: 97%

“…For example, 37 different mcaIIa alleles were found from the E. coioides (Yang et al ., ). In M. miiuy , 40 mcaIIa alleles were found, encoding 30 amino acid sequences (Xu et al ., ). These results indicate that the mcaIIa gene is highly polymorphic in fishes.…”

Section: Discussionmentioning

confidence: 97%

“…MHC gene polymorphisms lead to the combination and presentation of a variety of peptide ligands for each individual, which affects the peptide binding ability of the MHC locus and the recognition of the pathogen. Association between mcaIIa polymorphisms and disease resistance has been reported in miiuy croaker Miichthys miiuy (Basilewsky 1855) (Xu et al ., ), orange‐spotted grouper Epinephelus coioides (Hamilton 1822) (Yang et al ., ), common carp Cyprinus carpio L. 1758 (Liu, Liu, Wang, et al ., ; Liu, Liu, Zhao, et al . ), Japanese flounder Paralichthys olivaceus (Temminck & Schlegel 1846) (Xu et al ., ), gilthead sea bream Sparus aurata L. 1758 (Karaiskou et al ., ) trout and salmons Oncorhynchus spp.…”

Section: Introductionmentioning

confidence: 99%

“…Association between mcaIIa polymorphisms and disease resistance has been reported in miiuy croaker Miichthys miiuy (Basilewsky 1855) (Xu et al, 2016), orange-spotted grouper Epinephelus coioides (Hamilton 1822) (Yang et al, 2016), common carp Cyprinus carpio L. 1758 Liu, Liu, Zhao, et al 2014), Japanese flounder Paralichthys olivaceus (Temminck & Schlegel 1846) (Xu et al, 2010), gilthead sea bream Sparus aurata L. 1758 (Karaiskou et al, 2010) trout and salmons Oncorhynchus spp. (Glover et al, 2007;Grimholt et al, 2003;Kjøglum et al, 2006Kjøglum et al, , 2008Liu et al, 2013;Palti et al, 2001;Stet et al, 2002;Wynne et al, 2007).…”

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confidence: 97%

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MHC class IIA polymorphisms and their association with resistance–susceptibility to Streptococcus agalactiae in Nile tilapia, Oreochromis niloticus

Gao

Zhao

et al. 2018

Journal of Fish Biology

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The association between major histocompatibility complex (MHC) class IIA polymorphisms and the severity of infection by Streptococcus agalactiae was investigated using 40 susceptible and 40 resistant individuals of Nile tilapia Oreochromis niloticus. Twenty‐five alleles were identified from 80 individuals, which belong to 22 major allele types. High polymorphism of mhcIIa gene and at least two loci were discovered in O. niloticus. In peptide‐binding region (PBR) and non‐PBR, the ratio of nonsynonymous substitution (dN) to synonymous substitution (dS) was 1.294 (>1) and 1.240 (>1), suggesting that the loci are evolving under positive balancing selection. Association analysis showed that the allele, orni‐daa*0501, was significantly associated with resistance to S. agalactiae, while the alleles, orni‐daa*1101, orni‐daa*1301, orni‐daa*1401 and orni‐daa*1201, were associated with susceptibility to S. agalactiae. To confirm these correlations, another independent challenge experiment was performed in the Huizhou population of the O. niloticus. The frequency distribution showed that the orni‐daa*1101 allele was significantly more frequent in the Huizhou‐Susceptible group (HZ‐SG) than in the Huizhou‐Resistant group (HZ‐RG) (P < 0.05), which was consistent with the first challenge. However, orni‐daa*0501 did not present in HZ‐SG and HZ‐RG and the distribution frequencies of the orni‐daa*1201, orni‐daa*1301 and orni‐daa*1401 alleles were not significantly more frequent in HZ‐SG than in HZ‐RG. These results indicate that the orni‐daa*1101 allele confers susceptibility to S. agalactia infection. These results suggest that the diversity of exon 2 of mcaIIa alleles could be used to explore the association between disease susceptibility or resistance and the multiformity of mcaIIa and to achieve the molecular‐assisted selection of O. niloticus with enhanced disease resistance.

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Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

mentioning

confidence: 97%

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MHC class IIA polymorphisms and their association with resistance–susceptibility to Streptococcus agalactiae in Nile tilapia, Oreochromis niloticus

Gao

Zhao

et al. 2018

Journal of Fish Biology

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“…All other groups of alleles and the ungrouped alleles showed classic MHC class II gene patterns. They all displayed sites subjected to strong positive selection, suggesting that they might have evolved under strong parasite-mediated balancing selection [ 95 , 96 ]. However, the results of the selection tests have to be taken with caution since we cannot allocate alleles to specific loci and alleles within groups could potentially belong to different evolutionary lineages.…”

Section: Discussionmentioning

confidence: 99%

Molecular characterization of MHC class IIB genes of sympatric Neotropical cichlids

et al. 2017

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BackgroundThe Major Histocompatibility Complex (MHC) is a key component of the adaptive immune system of all vertebrates and consists of the most polymorphic genes known to date. Due to this complexity, however, MHC remains to be characterized in many species including any Neotropical cichlid fish. Neotropical crater lake cichlids are ideal models to study evolutionary processes as they display one of the most convincing examples of sympatric and repeated parallel radiation events within and among isolated crater lakes.ResultsHere, we characterized the genes of MHC class IIB chain of the Midas cichlid species complex (Amphilophus cf. citrinellus) including fish from five lakes in Nicaragua. We designed 19 new specific primers anchored in a stepwise fashion in order to detect all alleles present. We obtained 866 genomic DNA (gDNA) sequences from thirteen individuals and 756 additional sequences from complementary DNA (cDNA) of seven of those individuals. We identified 69 distinct alleles with up to 25 alleles per individual. We also found considerable intron length variation and mismatches of alleles detected in cDNA and gDNA suggesting that some loci have undergone pseudogenization. Lastly, we created a model of protein structure homology for each allele and identified their key structural components.ConclusionsOverall, the Midas cichlid has one of the most diverse repertoires of MHC class IIB genes known, which could serve as a powerful tool to elucidate the process of divergent radiations, colonization and speciation in sympatry.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-017-0474-x) contains supplementary material, which is available to authorized users.

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Divergence between genes but limited allelic polymorphism in two MHC class II A genes in Leach’s storm-petrels Oceanodroma leucorhoa

et al. 2019

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The major histocompatibility complex (MHC) is critical to host-pathogen interactions. Class II MHC is a heterodimer, with α and β subunits encoded by different genes. The peptide binding groove is formed by the first domain of both subunits (α 1 and β 1 ), but studies of class II variation or natural selection focus primarily on the β subunit and II B genes. We explored MHC II A in Leach's storm-petrel, a seabird with two expressed, polymorphic II B genes. We found two II A genes, Ocle-DAA and Ocle-DBA, in contrast to the single II A gene in chicken and duck. In exon 2 which encodes the α 1 domain, the storm-petrel II A genes differed strongly from each other but showed little within-gene polymorphism in 30 individuals: just one Ocle-DAA allele, and three Ocle-DBA alleles differing from each other by single non-synonymous substitutions. In a comparable sample, the two II B genes had nine markedly diverged alleles each. Differences between the α 1 domains of Ocle-DAA and Ocle-DBA showed signatures of positive selection, but mainly at non-peptide binding site (PBS) positions. In contrast, positive selection within and between the II B genes corresponded to putative PBS codons. Phylogenetic analysis of the conserved α 2 domain did not reveal deep or well supported lineages of II A genes in birds, in contrast to the pronounced differentiation of DQA, DPA, and DRA isotypes in mammals. This uncertain homology complicates efforts to compare levels of functional variation and modes of evolution of II A genes across taxa.

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Characterization of 40 full-length MHC class IIA functional alleles in miiuy croaker: Polymorphism and positive selection

Cited by 11 publications

References 41 publications

MHC class IIA polymorphisms and their association with resistance–susceptibility to Streptococcus agalactiae in Nile tilapia, Oreochromis niloticus

MHC class IIA polymorphisms and their association with resistance–susceptibility to Streptococcus agalactiae in Nile tilapia, Oreochromis niloticus

Molecular characterization of MHC class IIB genes of sympatric Neotropical cichlids

Divergence between genes but limited allelic polymorphism in two MHC class II A genes in Leach’s storm-petrels Oceanodroma leucorhoa

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