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

The major histocompatibility complex is a highly polymorphic gene superfamily in vertebrates that plays an important role in adaptive immune response. In the present study, we identified 40 full-length miiuy croaker MHC class IIA (Mimi-DAA) functional alleles from 26 miiuy croaker individuals and fo...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Developmental and comparative immunology 2016-02, Vol.55, p.138-143
Hauptverfasser: Xu, Tianjun, Liu, Jiang, Sun, Yueyan, Zhu, Zhihuang, Liu, Tianxing
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page 143
container_issue
container_start_page 138
container_title Developmental and comparative immunology
container_volume 55
creator Xu, Tianjun
Liu, Jiang
Sun, Yueyan
Zhu, Zhihuang
Liu, Tianxing
description The major histocompatibility complex is a highly polymorphic gene superfamily in vertebrates that plays an important role in adaptive immune response. In the present study, we identified 40 full-length miiuy croaker MHC class IIA (Mimi-DAA) functional alleles from 26 miiuy croaker individuals and found that the alleles encode 30 amino acid sequences. A high level of polymorphism in Mimi-DAA was detected in miiuy croaker. The rate of non-synonymous substitutions (dN) occurred at a significantly higher frequency than that of synonymous substitutions (dS) in the peptide-binding region (PBR) and non-PBR. This result suggests that balancing selection maintains polymorphisms at the Mimi-DAA locus. Phylogenetic analysis based on the full-length sequences showed that the Mimi-DAA alleles clustered into three groups. However, the phylogenetic tree constructed using the exon 2 sequences indicated that the Mimi-DAA alleles clustered into two groups. A total of 22 positively selected sites were identified on the Mimi-DAA alleles after testing for positive selection, and five sites were predicted to be associated with the binding of peptide antigen, suggesting that a few selected residues may play a significant role in immune function. •Forty full-length Mimi-DAA functional alleles were firstly identified.•High level of polymorphism in Mimi-DAA functional alleles was discovered.•Twenty-two positively selected sites were located on the Mimi-DAA alleles.•More DAA alleles detected in miiuy croaker than other teleost studied to date.
doi_str_mv 10.1016/j.dci.2015.10.019
format Article
fullrecord <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_1750437441</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><els_id>S0145305X1530063X</els_id><sourcerecordid>1750437441</sourcerecordid><originalsourceid>FETCH-LOGICAL-c353t-1d384377a18c7b7909338d81e3985dfe319901e1b30cb66eb11e4cd05679fae83</originalsourceid><addsrcrecordid>eNp9kM2OFCEURonROO3oA7gxLN1Ue-9QP6CrSWd0OhmjC03cEQpu2bRU0ULVJO3TS9ujS9kQ4HwfuYexlwhrBGzf7NfO-vUVYFPOa0D1iK1QdqoCkOoxWwHWTSWg-XbBnuW8h7IkwlN2cdU2SiLiih03O5OMnSn5X2b2ceJx4DXwYQmhCjR9n3f84-2G22By5tvtdXmZ7Ak0gZsQKFDmfuKj98uR2xTND0pv-ecYjmNMh53PIzeT44eY_ezvieeS-JN_zp4MJmR68bBfsq_vb75sbqu7Tx-2m-u7yopGzBU6IWvRdQal7fpOgRJCOokklGzcQAKVAiTsBdi-balHpNo6aNpODYakuGSvz72HFH8ulGc9-mwpBDNRXLLGroHyQV1jQfGMljlyTjToQ_KjSUeNoE_G9V4X4_pk_HRVjJfMq4f6pR_J_Uv8VVyAd2eAypD3npLO1tNkyflUTGgX_X_qfwMWxJF-</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1750437441</pqid></control><display><type>article</type><title>Characterization of 40 full-length MHC class IIA functional alleles in miiuy croaker: Polymorphism and positive selection</title><source>MEDLINE</source><source>Elsevier ScienceDirect Journals Complete</source><creator>Xu, Tianjun ; Liu, Jiang ; Sun, Yueyan ; Zhu, Zhihuang ; Liu, Tianxing</creator><creatorcontrib>Xu, Tianjun ; Liu, Jiang ; Sun, Yueyan ; Zhu, Zhihuang ; Liu, Tianxing</creatorcontrib><description>The major histocompatibility complex is a highly polymorphic gene superfamily in vertebrates that plays an important role in adaptive immune response. In the present study, we identified 40 full-length miiuy croaker MHC class IIA (Mimi-DAA) functional alleles from 26 miiuy croaker individuals and found that the alleles encode 30 amino acid sequences. A high level of polymorphism in Mimi-DAA was detected in miiuy croaker. The rate of non-synonymous substitutions (dN) occurred at a significantly higher frequency than that of synonymous substitutions (dS) in the peptide-binding region (PBR) and non-PBR. This result suggests that balancing selection maintains polymorphisms at the Mimi-DAA locus. Phylogenetic analysis based on the full-length sequences showed that the Mimi-DAA alleles clustered into three groups. However, the phylogenetic tree constructed using the exon 2 sequences indicated that the Mimi-DAA alleles clustered into two groups. A total of 22 positively selected sites were identified on the Mimi-DAA alleles after testing for positive selection, and five sites were predicted to be associated with the binding of peptide antigen, suggesting that a few selected residues may play a significant role in immune function. •Forty full-length Mimi-DAA functional alleles were firstly identified.•High level of polymorphism in Mimi-DAA functional alleles was discovered.•Twenty-two positively selected sites were located on the Mimi-DAA alleles.•More DAA alleles detected in miiuy croaker than other teleost studied to date.</description><identifier>ISSN: 0145-305X</identifier><identifier>EISSN: 1879-0089</identifier><identifier>DOI: 10.1016/j.dci.2015.10.019</identifier><identifier>PMID: 26598111</identifier><language>eng</language><publisher>United States: Elsevier Ltd</publisher><subject>Amino Acid Sequence ; Animals ; Antigens - immunology ; Antigens - metabolism ; Binding Sites - genetics ; Evolution, Molecular ; Fish Proteins - genetics ; Fish Proteins - metabolism ; Histocompatibility Antigens Class II - genetics ; Histocompatibility Antigens Class II - metabolism ; Major histocompatibility complex ; Miiuy croaker ; Models, Molecular ; Molecular Sequence Data ; Mutation - genetics ; Perciformes - immunology ; Phylogeny ; Polymorphism ; Polymorphism, Genetic ; Positive selection ; Protein Binding ; Sequence Alignment</subject><ispartof>Developmental and comparative immunology, 2016-02, Vol.55, p.138-143</ispartof><rights>2015 Elsevier Ltd</rights><rights>Copyright © 2015 Elsevier Ltd. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c353t-1d384377a18c7b7909338d81e3985dfe319901e1b30cb66eb11e4cd05679fae83</citedby><cites>FETCH-LOGICAL-c353t-1d384377a18c7b7909338d81e3985dfe319901e1b30cb66eb11e4cd05679fae83</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.dci.2015.10.019$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26598111$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Xu, Tianjun</creatorcontrib><creatorcontrib>Liu, Jiang</creatorcontrib><creatorcontrib>Sun, Yueyan</creatorcontrib><creatorcontrib>Zhu, Zhihuang</creatorcontrib><creatorcontrib>Liu, Tianxing</creatorcontrib><title>Characterization of 40 full-length MHC class IIA functional alleles in miiuy croaker: Polymorphism and positive selection</title><title>Developmental and comparative immunology</title><addtitle>Dev Comp Immunol</addtitle><description>The major histocompatibility complex is a highly polymorphic gene superfamily in vertebrates that plays an important role in adaptive immune response. In the present study, we identified 40 full-length miiuy croaker MHC class IIA (Mimi-DAA) functional alleles from 26 miiuy croaker individuals and found that the alleles encode 30 amino acid sequences. A high level of polymorphism in Mimi-DAA was detected in miiuy croaker. The rate of non-synonymous substitutions (dN) occurred at a significantly higher frequency than that of synonymous substitutions (dS) in the peptide-binding region (PBR) and non-PBR. This result suggests that balancing selection maintains polymorphisms at the Mimi-DAA locus. Phylogenetic analysis based on the full-length sequences showed that the Mimi-DAA alleles clustered into three groups. However, the phylogenetic tree constructed using the exon 2 sequences indicated that the Mimi-DAA alleles clustered into two groups. A total of 22 positively selected sites were identified on the Mimi-DAA alleles after testing for positive selection, and five sites were predicted to be associated with the binding of peptide antigen, suggesting that a few selected residues may play a significant role in immune function. •Forty full-length Mimi-DAA functional alleles were firstly identified.•High level of polymorphism in Mimi-DAA functional alleles was discovered.•Twenty-two positively selected sites were located on the Mimi-DAA alleles.•More DAA alleles detected in miiuy croaker than other teleost studied to date.</description><subject>Amino Acid Sequence</subject><subject>Animals</subject><subject>Antigens - immunology</subject><subject>Antigens - metabolism</subject><subject>Binding Sites - genetics</subject><subject>Evolution, Molecular</subject><subject>Fish Proteins - genetics</subject><subject>Fish Proteins - metabolism</subject><subject>Histocompatibility Antigens Class II - genetics</subject><subject>Histocompatibility Antigens Class II - metabolism</subject><subject>Major histocompatibility complex</subject><subject>Miiuy croaker</subject><subject>Models, Molecular</subject><subject>Molecular Sequence Data</subject><subject>Mutation - genetics</subject><subject>Perciformes - immunology</subject><subject>Phylogeny</subject><subject>Polymorphism</subject><subject>Polymorphism, Genetic</subject><subject>Positive selection</subject><subject>Protein Binding</subject><subject>Sequence Alignment</subject><issn>0145-305X</issn><issn>1879-0089</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kM2OFCEURonROO3oA7gxLN1Ue-9QP6CrSWd0OhmjC03cEQpu2bRU0ULVJO3TS9ujS9kQ4HwfuYexlwhrBGzf7NfO-vUVYFPOa0D1iK1QdqoCkOoxWwHWTSWg-XbBnuW8h7IkwlN2cdU2SiLiih03O5OMnSn5X2b2ceJx4DXwYQmhCjR9n3f84-2G22By5tvtdXmZ7Ak0gZsQKFDmfuKj98uR2xTND0pv-ecYjmNMh53PIzeT44eY_ezvieeS-JN_zp4MJmR68bBfsq_vb75sbqu7Tx-2m-u7yopGzBU6IWvRdQal7fpOgRJCOokklGzcQAKVAiTsBdi-balHpNo6aNpODYakuGSvz72HFH8ulGc9-mwpBDNRXLLGroHyQV1jQfGMljlyTjToQ_KjSUeNoE_G9V4X4_pk_HRVjJfMq4f6pR_J_Uv8VVyAd2eAypD3npLO1tNkyflUTGgX_X_qfwMWxJF-</recordid><startdate>201602</startdate><enddate>201602</enddate><creator>Xu, Tianjun</creator><creator>Liu, Jiang</creator><creator>Sun, Yueyan</creator><creator>Zhu, Zhihuang</creator><creator>Liu, Tianxing</creator><general>Elsevier Ltd</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>201602</creationdate><title>Characterization of 40 full-length MHC class IIA functional alleles in miiuy croaker: Polymorphism and positive selection</title><author>Xu, Tianjun ; Liu, Jiang ; Sun, Yueyan ; Zhu, Zhihuang ; Liu, Tianxing</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c353t-1d384377a18c7b7909338d81e3985dfe319901e1b30cb66eb11e4cd05679fae83</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Amino Acid Sequence</topic><topic>Animals</topic><topic>Antigens - immunology</topic><topic>Antigens - metabolism</topic><topic>Binding Sites - genetics</topic><topic>Evolution, Molecular</topic><topic>Fish Proteins - genetics</topic><topic>Fish Proteins - metabolism</topic><topic>Histocompatibility Antigens Class II - genetics</topic><topic>Histocompatibility Antigens Class II - metabolism</topic><topic>Major histocompatibility complex</topic><topic>Miiuy croaker</topic><topic>Models, Molecular</topic><topic>Molecular Sequence Data</topic><topic>Mutation - genetics</topic><topic>Perciformes - immunology</topic><topic>Phylogeny</topic><topic>Polymorphism</topic><topic>Polymorphism, Genetic</topic><topic>Positive selection</topic><topic>Protein Binding</topic><topic>Sequence Alignment</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Xu, Tianjun</creatorcontrib><creatorcontrib>Liu, Jiang</creatorcontrib><creatorcontrib>Sun, Yueyan</creatorcontrib><creatorcontrib>Zhu, Zhihuang</creatorcontrib><creatorcontrib>Liu, Tianxing</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Developmental and comparative immunology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Xu, Tianjun</au><au>Liu, Jiang</au><au>Sun, Yueyan</au><au>Zhu, Zhihuang</au><au>Liu, Tianxing</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Characterization of 40 full-length MHC class IIA functional alleles in miiuy croaker: Polymorphism and positive selection</atitle><jtitle>Developmental and comparative immunology</jtitle><addtitle>Dev Comp Immunol</addtitle><date>2016-02</date><risdate>2016</risdate><volume>55</volume><spage>138</spage><epage>143</epage><pages>138-143</pages><issn>0145-305X</issn><eissn>1879-0089</eissn><abstract>The major histocompatibility complex is a highly polymorphic gene superfamily in vertebrates that plays an important role in adaptive immune response. In the present study, we identified 40 full-length miiuy croaker MHC class IIA (Mimi-DAA) functional alleles from 26 miiuy croaker individuals and found that the alleles encode 30 amino acid sequences. A high level of polymorphism in Mimi-DAA was detected in miiuy croaker. The rate of non-synonymous substitutions (dN) occurred at a significantly higher frequency than that of synonymous substitutions (dS) in the peptide-binding region (PBR) and non-PBR. This result suggests that balancing selection maintains polymorphisms at the Mimi-DAA locus. Phylogenetic analysis based on the full-length sequences showed that the Mimi-DAA alleles clustered into three groups. However, the phylogenetic tree constructed using the exon 2 sequences indicated that the Mimi-DAA alleles clustered into two groups. A total of 22 positively selected sites were identified on the Mimi-DAA alleles after testing for positive selection, and five sites were predicted to be associated with the binding of peptide antigen, suggesting that a few selected residues may play a significant role in immune function. •Forty full-length Mimi-DAA functional alleles were firstly identified.•High level of polymorphism in Mimi-DAA functional alleles was discovered.•Twenty-two positively selected sites were located on the Mimi-DAA alleles.•More DAA alleles detected in miiuy croaker than other teleost studied to date.</abstract><cop>United States</cop><pub>Elsevier Ltd</pub><pmid>26598111</pmid><doi>10.1016/j.dci.2015.10.019</doi><tpages>6</tpages></addata></record>
fulltext fulltext
identifier ISSN: 0145-305X
ispartof Developmental and comparative immunology, 2016-02, Vol.55, p.138-143
issn 0145-305X
1879-0089
language eng
recordid cdi_proquest_miscellaneous_1750437441
source MEDLINE; Elsevier ScienceDirect Journals Complete
subjects Amino Acid Sequence
Animals
Antigens - immunology
Antigens - metabolism
Binding Sites - genetics
Evolution, Molecular
Fish Proteins - genetics
Fish Proteins - metabolism
Histocompatibility Antigens Class II - genetics
Histocompatibility Antigens Class II - metabolism
Major histocompatibility complex
Miiuy croaker
Models, Molecular
Molecular Sequence Data
Mutation - genetics
Perciformes - immunology
Phylogeny
Polymorphism
Polymorphism, Genetic
Positive selection
Protein Binding
Sequence Alignment
title Characterization of 40 full-length MHC class IIA functional alleles in miiuy croaker: Polymorphism and positive selection
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-24T13%3A52%3A37IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Characterization%20of%2040%20full-length%20MHC%20class%20IIA%20functional%20alleles%20in%20miiuy%20croaker:%20Polymorphism%20and%20positive%20selection&rft.jtitle=Developmental%20and%20comparative%20immunology&rft.au=Xu,%20Tianjun&rft.date=2016-02&rft.volume=55&rft.spage=138&rft.epage=143&rft.pages=138-143&rft.issn=0145-305X&rft.eissn=1879-0089&rft_id=info:doi/10.1016/j.dci.2015.10.019&rft_dat=%3Cproquest_cross%3E1750437441%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1750437441&rft_id=info:pmid/26598111&rft_els_id=S0145305X1530063X&rfr_iscdi=true