Annotation and characterization of immunoglobulin loci and CDR3 polymorphism in water buffalo (Bubalus bubalis)
IntroductionImmunoglobulin (Ig) refers to the nomenclature for all antibody proteins produced by B lymphocytes. The genetic locus encoding Ig is critical for vertebrate humoral immune responses and diverse antibody repertoires. Despite the critical role of buffaloes as livestock and their significan...
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Frontiers Media S.A.
2025-01-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2024.1503788/full |
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| author | Yunlan Deng Fengli Wu Fengli Wu Qianqian Li Lidie Yao Chengzhi Yang Long Ma Xinsheng Yao Jun Li |
| author_facet | Yunlan Deng Fengli Wu Fengli Wu Qianqian Li Lidie Yao Chengzhi Yang Long Ma Xinsheng Yao Jun Li |
| author_sort | Yunlan Deng |
| collection | DOAJ |
| description | IntroductionImmunoglobulin (Ig) refers to the nomenclature for all antibody proteins produced by B lymphocytes. The genetic locus encoding Ig is critical for vertebrate humoral immune responses and diverse antibody repertoires. Despite the critical role of buffaloes as livestock and their significance in disease transmission, the Ig loci of this species have not been thoroughly annotated. This study aimed to systematically characterize the Ig loci in buffaloes and their unique features, providing a foundation for understanding buffalo immune function.MethodsThe genomic assembly of Murrah buffalo (NDDB_SH_1) was analyzed to annotate Ig loci. Annotation criteria included functional motifs, RSS sequences, and structural features of V, D, J, and C genes. The CDR3 repertoires were constructed using genomic DNA extracted from spleen samples of five healthy buffaloes. High-throughput sequencing of multiplex PCR products enabled repertoire analysis, and MiXCR software was used for alignment and CDR3 extraction. Repertoire diversity, gene usage, and clonal frequencies were analyzed using the Immunarch R package.ResultsThe IgH locus spans approximately 667 kb on chromosome 20, containing two D-J-C clusters, 54 VH genes, 10 DH genes, 8 JH genes, and 9 CH genes. The Igκ locus, located on chromosome 12, encompasses 24 Vκ genes, 5 Jκ genes, and 1 Cκ gene, while the Igλ locus on chromosome 17 includes 71 Vλ genes, 3 Jλ genes, and 3 Cλ genes. We also conducted a detailed examination of the buffalo IgH CDR3 repertoire, revealing the presence of ultra-long CDR3 sequences, a biased usage of certain V genes, and a high-frequency usage of IgHJ1-4 genes. Furthermore, we identified a set of shared clonotypes across the samples, highlighting commonalities in the buffalo antibody repertoire.ConclusionThese findings contribute to the understanding of buffalo immune function and provide insights into the evolution and diversity of ruminant immunoglobulin genes. |
| format | Article |
| id | doaj-art-31f7420608d44fa9a628a82bde4353f7 |
| institution | Kabale University |
| issn | 1664-3224 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Immunology |
| spelling | doaj-art-31f7420608d44fa9a628a82bde4353f72025-01-20T05:23:50ZengFrontiers Media S.A.Frontiers in Immunology1664-32242025-01-011510.3389/fimmu.2024.15037881503788Annotation and characterization of immunoglobulin loci and CDR3 polymorphism in water buffalo (Bubalus bubalis)Yunlan Deng0Fengli Wu1Fengli Wu2Qianqian Li3Lidie Yao4Chengzhi Yang5Long Ma6Xinsheng Yao7Jun Li8Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, ChinaDepartment of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, ChinaDepartment of Laboratory, The Affiliated Yongchuan Hospital of Chongqing Medical University, Chongqing, ChinaDepartment of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, ChinaDepartment of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, ChinaDepartment of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, ChinaDepartment of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, ChinaDepartment of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, ChinaDepartment of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, ChinaIntroductionImmunoglobulin (Ig) refers to the nomenclature for all antibody proteins produced by B lymphocytes. The genetic locus encoding Ig is critical for vertebrate humoral immune responses and diverse antibody repertoires. Despite the critical role of buffaloes as livestock and their significance in disease transmission, the Ig loci of this species have not been thoroughly annotated. This study aimed to systematically characterize the Ig loci in buffaloes and their unique features, providing a foundation for understanding buffalo immune function.MethodsThe genomic assembly of Murrah buffalo (NDDB_SH_1) was analyzed to annotate Ig loci. Annotation criteria included functional motifs, RSS sequences, and structural features of V, D, J, and C genes. The CDR3 repertoires were constructed using genomic DNA extracted from spleen samples of five healthy buffaloes. High-throughput sequencing of multiplex PCR products enabled repertoire analysis, and MiXCR software was used for alignment and CDR3 extraction. Repertoire diversity, gene usage, and clonal frequencies were analyzed using the Immunarch R package.ResultsThe IgH locus spans approximately 667 kb on chromosome 20, containing two D-J-C clusters, 54 VH genes, 10 DH genes, 8 JH genes, and 9 CH genes. The Igκ locus, located on chromosome 12, encompasses 24 Vκ genes, 5 Jκ genes, and 1 Cκ gene, while the Igλ locus on chromosome 17 includes 71 Vλ genes, 3 Jλ genes, and 3 Cλ genes. We also conducted a detailed examination of the buffalo IgH CDR3 repertoire, revealing the presence of ultra-long CDR3 sequences, a biased usage of certain V genes, and a high-frequency usage of IgHJ1-4 genes. Furthermore, we identified a set of shared clonotypes across the samples, highlighting commonalities in the buffalo antibody repertoire.ConclusionThese findings contribute to the understanding of buffalo immune function and provide insights into the evolution and diversity of ruminant immunoglobulin genes.https://www.frontiersin.org/articles/10.3389/fimmu.2024.1503788/fullbuffaloimmunoglobulinCDR3 repertoireultra-long CDR3 sequencesV(D)J recombination |
| spellingShingle | Yunlan Deng Fengli Wu Fengli Wu Qianqian Li Lidie Yao Chengzhi Yang Long Ma Xinsheng Yao Jun Li Annotation and characterization of immunoglobulin loci and CDR3 polymorphism in water buffalo (Bubalus bubalis) Frontiers in Immunology buffalo immunoglobulin CDR3 repertoire ultra-long CDR3 sequences V(D)J recombination |
| title | Annotation and characterization of immunoglobulin loci and CDR3 polymorphism in water buffalo (Bubalus bubalis) |
| title_full | Annotation and characterization of immunoglobulin loci and CDR3 polymorphism in water buffalo (Bubalus bubalis) |
| title_fullStr | Annotation and characterization of immunoglobulin loci and CDR3 polymorphism in water buffalo (Bubalus bubalis) |
| title_full_unstemmed | Annotation and characterization of immunoglobulin loci and CDR3 polymorphism in water buffalo (Bubalus bubalis) |
| title_short | Annotation and characterization of immunoglobulin loci and CDR3 polymorphism in water buffalo (Bubalus bubalis) |
| title_sort | annotation and characterization of immunoglobulin loci and cdr3 polymorphism in water buffalo bubalus bubalis |
| topic | buffalo immunoglobulin CDR3 repertoire ultra-long CDR3 sequences V(D)J recombination |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2024.1503788/full |
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