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Zhang T, Li Q, Li X, Kang L, Jiang Y, Sun Y. Characterization of the chicken T cell receptor γ repertoire by high-throughput sequencing. BMC Genomics 2021; 22:683. [PMID: 34548028 PMCID: PMC8456604 DOI: 10.1186/s12864-021-07975-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 09/01/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As one of "γδ-high" species, chicken is an excellent model for the study of γδ T cells in non-mammalian animals. However, a comprehensive characterization of the TCRγδ repertoire is still missing in chicken. The objective of this study was to characterize the expressed TCRγ repertoire in chicken thymus using high-throughput sequencing. METHODS In this study, we first obtained the detailed genomic organization of the TCRγ locus of chicken based on the latest assembly of the red jungle fowl genome sequences (GRCg6a) and then characterized the TCRγ repertoire in the thymus of four chickens by using 5' Rapid Amplification of cDNA Ends (5' RACE) along with high-throughput sequencing (HTS). RESULTS The chicken TCRγ locus contains a single Cγ gene, three functional Jγ segments and 44 Vγ segments that could be classified into six subgroups, each containing six, nineteen, nine, four, three and three members. Dot-plot analysis of the chicken TCRγ locus against itself showed that almost all the entire zone containing Vγ segments had arisen through tandem duplication events, and the main homology unit, containing 9 or 10 Vγ gene segments, has tandemly duplicated for four times. For the analysis of chicken TCRγ repertoire, more than 100,000 unique Vγ-region nucleotide sequences were obtained from the thymus of each chicken. After alignment to the germline Vγ and Jγ segments identified above, we found that the four chickens had similar repertoire profile of TCRγ. In brief, four Vγ segments (including Vγ3.7, Vγ2.13, Vγ1.6 and Vγ1.3) and six Vγ-Jγ pairs (including Vγ3.7-Jγ3, Vγ2.13-Jγ1, Vγ2.13-Jγ3, Vγ1.6-Jγ3, Vγ3.7-Jγ1 and Vγ1.6-Jγ1) were preferentially utilized by all four individuals, and vast majority of the unique CDR3γ sequences encoded 4 to 22 amino acids with mean 12.90 amino acids, which exhibits a wider length distribution and/or a longer mean length than CDR3γ of human, mice and other animal species. CONCLUSIONS In this study, we present the first in-depth characterization of the TCRγ repertoire in chicken thymus. We believe that these data will facilitate the studies of adaptive immunology in birds.
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Affiliation(s)
- Tongtong Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Shandong Province, 271018, Taian City, People's Republic of China
| | - Qian Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Shandong Province, 271018, Taian City, People's Republic of China
| | - Xiaoqing Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Shandong Province, 271018, Taian City, People's Republic of China
| | - Li Kang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Shandong Province, 271018, Taian City, People's Republic of China
| | - Yunliang Jiang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Shandong Province, 271018, Taian City, People's Republic of China.
| | - Yi Sun
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Shandong Province, 271018, Taian City, People's Republic of China.
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Oliveira TMD, Burlamaqui TCT, Sá ALAD, Breaux B, Luna FDO, Attademo FLN, Klautau AGCDM, Oliveira JM, Sena L, Criscitiello MF, Schneider MPC. TLR4 and TLR8 variability in Amazonian and West Indian manatee species from Brazil. Genet Mol Biol 2021; 44:e20190252. [PMID: 33847701 PMCID: PMC8042642 DOI: 10.1590/1678-4685-gmb-2019-0252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 01/29/2021] [Indexed: 11/22/2022] Open
Abstract
Amazonian (Trichechus inunguis) and West Indian (Trichechus manatus) manatees are aquatic mammals vulnerable to extinction found in the Amazon basin and the coastal western Atlantic. Toll-like receptors (TLR) play a key role in recognizing pathogen-associated molecular patterns using leucine-rich repeats (LRRs). We described the diversity of TLR4 and TLR8 genes in these two species of manatee. Amazonian manatee showed seven SNPs in TLR4 and the eight in TLR8, while West Indian manatee shared four and six of those SNPs, respectively. In our analysis, TLR4 showed one non-conservative amino acid replacement substitution in LRR7 and LRR8, on the other hand, TLR8 was less variable and showed only conserved amino acid substitutions. Selection analysis showed that only one TLR4 site was subjected to positive selection and none in TLR8. TLR4 in manatees did not show any evidence of convergent evolution compared to species of the cetacean lineage. Differences in TLR4 and TLR8 polymorphism may be related to distinct selection by pathogens, population reduction of West Indian manatees, or an expected consequence of population expansion in Amazonian manatees. Future studies combining pathogen association and TLR polymorphism may clarify possible roles of these genes and be used for conservation purposes of manatee species.
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Affiliation(s)
| | | | - André Luiz Alves de Sá
- Universidade Federal do Pará, Instituto de Ciências Biológicas, Belém, PA, Brazil.,Universidade Federal Rural da Amazônia, Instituto Socioambiental e dos Recursos Hídricos, Laboratório de Genética Aplicada, Belém, PA, Brazil
| | - Breanna Breaux
- Texas A&M University, College of Veterinary Medicine and Biomedical Sciences, Department of Veterinary Pathobiology, Comparative Immunogenetics Laboratory, College Station, TX, USA
| | - Fábia de Oliveira Luna
- Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), Centro Nacional de Pesquisa e Conservação de Mamíferos Aquáticos (CMA), Santos, SP, Brazil
| | - Fernanda Löffler Niemeyer Attademo
- Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), Centro Nacional de Pesquisa e Conservação de Mamíferos Aquáticos (CMA), Itamaracá, PE, Brazil.,Centro de Estudos e Monitoramento Ambiental (CEMAM), Areia Branca, RN, Brazil
| | - Alex Garcia Cavalleiro de Macedo Klautau
- Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), Centro Nacional de Pesquisa e Conservação da Biodiversidade Marinha do Norte (CEPNOR), Belém, PA, Brazil
| | - Jairo Moura Oliveira
- Universidade da Amazônia, Parque Zoológico da UNAMA (ZOOUNAMA), Santarém, PA, Brazil
| | - Leonardo Sena
- Universidade Federal do Pará, Instituto de Ciências Biológicas, Belém, PA, Brazil
| | - Michael F Criscitiello
- Texas A&M University, College of Veterinary Medicine and Biomedical Sciences, Department of Veterinary Pathobiology, Comparative Immunogenetics Laboratory, College Station, TX, USA.,Texas A&M University, Texas A&M Health Science Center, College of Medicine, Department of Microbial Pathogenesis and Immunology, College Station, TX, USA
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3
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Ott JA, Ohta Y, Flajnik MF, Criscitiello MF. Lost structural and functional inter-relationships between Ig and TCR loci in mammals revealed in sharks. Immunogenetics 2021; 73:17-33. [PMID: 33449123 PMCID: PMC7909615 DOI: 10.1007/s00251-020-01183-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/26/2020] [Indexed: 12/19/2022]
Abstract
Immunoglobulins and T cell receptors (TCR) have obvious structural similarities as well as similar immunogenetic diversification and selection mechanisms. Nevertheless, the two receptor systems and the loci that encode them are distinct in humans and classical murine models, and the gene segments comprising each repertoire are mutually exclusive. Additionally, while both B and T cells employ recombination-activating genes (RAG) for primary diversification, immunoglobulins are afforded a supplementary set of activation-induced cytidine deaminase (AID)-mediated diversification tools. As the oldest-emerging vertebrates sharing the same adaptive B and T cell receptor systems as humans, extant cartilaginous fishes allow a potential view of the ancestral immune system. In this review, we discuss breakthroughs we have made in studies of nurse shark (Ginglymostoma cirratum) T cell receptors demonstrating substantial integration of loci and diversification mechanisms in primordial B and T cell repertoires. We survey these findings in this shark model where they were first described, while noting corroborating examples in other vertebrate groups. We also consider other examples where the gnathostome common ancestry of the B and T cell receptor systems have allowed dovetailing of genomic elements and AID-based diversification approaches for the TCR. The cartilaginous fish seem to have retained this T/B cell plasticity to a greater extent than more derived vertebrate groups, but representatives in all vertebrate taxa except bony fish and placental mammals show such plasticity.
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Affiliation(s)
- Jeannine A Ott
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland Baltimore School of Medicine, Baltimore, MD, 21201, USA
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland Baltimore School of Medicine, Baltimore, MD, 21201, USA
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA.
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, College Station, TX, 77843, USA.
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4
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Ott JA, Harrison J, Flajnik MF, Criscitiello MF. Nurse shark T-cell receptors employ somatic hypermutation preferentially to alter alpha/delta variable segments associated with alpha constant region. Eur J Immunol 2020; 50:1307-1320. [PMID: 32346855 DOI: 10.1002/eji.201948495] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/02/2020] [Accepted: 04/24/2020] [Indexed: 12/25/2022]
Abstract
In addition to canonical TCR and BCR, cartilaginous fish assemble noncanonical TCR that employ various B-cell components. For example, shark T cells associate alpha (TCR-α) or delta (TCR-δ) constant (C) regions with Ig heavy chain (H) variable (V) segments or TCR-associated Ig-like V (TAILV) segments to form chimeric IgV-TCR, and combine TCRδC with both Ig-like and TCR-like V segments to form the doubly rearranging NAR-TCR. Activation-induced (cytidine) deaminase-catalyzed somatic hypermutation (SHM), typically used for B-cell affinity maturation, also is used by TCR-α during selection in the shark thymus presumably to salvage failing receptors. Here, we found that the use of SHM by nurse shark TCR varies depending on the particular V segment or C region used. First, SHM significantly alters alpha/delta V (TCRαδV) segments using TCR αC but not δC. Second, mutation to IgHV segments associated with TCR δC was reduced compared to mutation to TCR αδV associated with TCR αC. Mutation was present but limited in V segments of all other TCR chains including NAR-TCR. Unexpectedly, we found preferential rearrangement of the noncanonical IgHV-TCRδC over canonical TCR αδV-TCRδC receptors. The differential use of SHM may reveal how activation-induced (cytidine) deaminase targets V regions.
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Affiliation(s)
- Jeannine A Ott
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Jenna Harrison
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Martin F Flajnik
- Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore, Baltimore, MD, USA
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA.,Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, College Station, TX, USA
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5
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Dunst J, Glaros V, Englmaier L, Sandoz PA, Önfelt B, Kisielow J, Kreslavsky T. Recognition of synthetic polyanionic ligands underlies "spontaneous" reactivity of Vγ1 γδTCRs. J Leukoc Biol 2020; 107:1033-1044. [PMID: 31943366 PMCID: PMC7317387 DOI: 10.1002/jlb.2ma1219-392r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 12/05/2019] [Accepted: 12/11/2019] [Indexed: 01/02/2023] Open
Abstract
Although γδTCRs were discovered more than 30 yr ago, principles of antigen recognition by these receptors remain unclear and the nature of these antigens is largely elusive. Numerous studies reported that T cell hybridomas expressing several Vγ1-containing TCRs, including the Vγ1Vδ6 TCR of γδNKT cells, spontaneously secrete cytokines. This property was interpreted as recognition of a self-ligand expressed on the hybridoma cells themselves. Here, we revisited this finding using a recently developed reporter system and live single cell imaging. We confirmed strong spontaneous signaling by Vγ1Vδ6 and related TCRs, but not by TCRs from several other γδ or innate-like αβ T cells, and demonstrated that both γ and δ chains contributed to this reactivity. Unexpectedly, live single cell imaging showed that activation of this signaling did not require any interaction between cells. Further investigation revealed that the signaling is instead activated by interaction with negatively charged surfaces abundantly present under regular cell culture conditions and was abrogated when noncharged cell culture vessels were used. This mode of TCR signaling activation was not restricted to the reporter cell lines, as interaction with negatively charged surfaces also triggered TCR signaling in ex vivo Vγ1 γδ T cells. Taken together, these results explain long-standing observations on the spontaneous reactivity of Vγ1Vδ6 TCR and demonstrate an unexpected antigen presentation-independent mode of TCR activation by a spectrum of chemically unrelated polyanionic ligands.
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Affiliation(s)
- Josefine Dunst
- Department of Medicine, Division of Immunology and Allergy, Karolinska InstitutetKarolinska University HospitalStockholmSweden
- Center for Molecular MedicineKarolinska InstitutetStockholmSweden
| | - Vassilis Glaros
- Department of Medicine, Division of Immunology and Allergy, Karolinska InstitutetKarolinska University HospitalStockholmSweden
- Center for Molecular MedicineKarolinska InstitutetStockholmSweden
| | - Lukas Englmaier
- Department of Medicine, Division of Immunology and Allergy, Karolinska InstitutetKarolinska University HospitalStockholmSweden
- Center for Molecular MedicineKarolinska InstitutetStockholmSweden
| | - Patrick A. Sandoz
- Department of Applied PhysicsScience for Life LaboratoryKTH Royal Institute of TechnologyStockholmSweden
| | - Björn Önfelt
- Department of Applied PhysicsScience for Life LaboratoryKTH Royal Institute of TechnologyStockholmSweden
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstituteSolnaSweden
| | - Jan Kisielow
- Institute of Molecular Health SciencesETHZurichSwitzerland
| | - Taras Kreslavsky
- Department of Medicine, Division of Immunology and Allergy, Karolinska InstitutetKarolinska University HospitalStockholmSweden
- Center for Molecular MedicineKarolinska InstitutetStockholmSweden
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6
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Zhang T, Liu G, Wei Z, Wang Y, Kang L, Jiang Y, Sun Y. Genomic organization of the chicken TCRβ locus originated by duplication of a Vβ segment combined with a trypsinogen gene. Vet Immunol Immunopathol 2019; 219:109974. [PMID: 31765881 DOI: 10.1016/j.vetimm.2019.109974] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 10/21/2019] [Accepted: 11/07/2019] [Indexed: 01/09/2023]
Abstract
Based on the latest assembly of the red jungle fowl (Gallus gallus) genome sequence, we characterized the detailed genomic organization of the T cell receptor beta (TCRβ) locus of chicken. The chicken TCRβ locus spans approximately 210 kb, and is organized in a typical translocon organization as previously reported. Within this locus, a total of 16 germline Vβ gene segments were classified into three subgroups, containing 11, four, and one members, respectively. Phylogenetic analysis revealed that the chicken Vβ3.1 segment was homologous with the duck Vβ1 subgroup, and further clustered with Vβ segments from reptiles but not amphibians. We also identified nine protease serine 1 (PRSS1) and three protease serine 2 (PRSS2) genes, which were interspersed within the chicken TCRβ locus. Dot-plot analysis of the chicken TCRβ locus against itself revealed that the 5' part of the locus had arisen through a series of tandem duplication events. The homology units were composed of one Vβ1 segment followed by a PRSS1 gene, or one Vβ2 segment followed by a PRSS2 gene. This duplication pattern, in which the Vβ segments and trypsinogen genes form a duplication unit, was unique to TCRβ loci of chicken and duck, but not observed in TCRβ loci of other tetrapods studied thus far. By analyzing the cloned TCRβ cDNA sequences, we found that the usage pattern of Vβ segments was consistent with the results of previous studies. These studies showed that members of the Vβ1 subgroup are preferentially utilized in V-D-J recombination. Furthermore, we found that the Vβ3.1 segment participated into V-D-J recombination, but at a very low frequency. The length distribution of the chicken complementarity-determining region 3β (CDR3β) showed a tendency similar to that observed for the duck.
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Affiliation(s)
- Tongtong Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, Shandong Province 271018, PR China
| | - Gen Liu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, Shandong Province 271018, PR China
| | - Zhiguo Wei
- College of Animal Science and Technology, Henan University of Science and Technology, 263 Kaiyuan Road, Luoyang City, Henan Province 471023, PR China
| | - Yanchao Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, Shandong Province 271018, PR China
| | - Li Kang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, Shandong Province 271018, PR China
| | - Yunliang Jiang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, Shandong Province 271018, PR China.
| | - Yi Sun
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Taian City, Shandong Province 271018, PR China.
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Zhang Z, Mu Y, Shan L, Sun D, Guo W, Yu Z, Tian R, Xu S, Yang G. Divergent Evolution of TRC Genes in Mammalian Niche Adaptation. Front Immunol 2019; 10:871. [PMID: 31068942 PMCID: PMC6491686 DOI: 10.3389/fimmu.2019.00871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/04/2019] [Indexed: 12/01/2022] Open
Abstract
Mammals inhabit a wide variety of ecological niches, which in turn can be affected by various ecological factors, especially in relation to immunity. The canonical TRC repertoire (TRAC, TRBC, TRGC, and TRDC) codes C regions of T cell receptor chains that form the primary antigen receptors involved in the activation of cellular immunity. At present, little is known about the correlation between the evolution of mammalian TRC genes and ecological factors. In this study, four types canonical of TRC genes were identified from 37 mammalian species. Phylogenetic comparative methods (phyANOVA and PGLS) and selective pressure analyses among different groups of ecological factors (habitat, diet, and sociality) were carried out. The results showed that habitat was the major ecological factor shaping mammalian TRC repertoires. Specifically, trade-off between TRGC numbers and positive selection of TRAC and the balanced evolutionary rates between TRAC and TRDC genes were speculated as two main mechanisms in adaption to habitat and sociality. Overall, our study suggested divergent mechanisms for the evolution of TRCs, prompting mammalian immunity adaptions within diverse niches.
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Affiliation(s)
- Zepeng Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yuan Mu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Lei Shan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Di Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Weijian Guo
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhenpeng Yu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ran Tian
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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de Sá ALA, Breaux B, Burlamaqui TCT, Deiss TC, Sena L, Criscitiello MF, Schneider MPC. The Marine Mammal Class II Major Histocompatibility Complex Organization. Front Immunol 2019; 10:696. [PMID: 31019512 PMCID: PMC6459222 DOI: 10.3389/fimmu.2019.00696] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/13/2019] [Indexed: 12/17/2022] Open
Abstract
Sirenians share with cetaceans and pinnipeds several convergent traits selected for the aquatic lifestyle. Living in water poses new challenges not only for locomotion and feeding but also for combating new pathogens, which may render the immune system one of the best tools aquatic mammals have for dealing with aquatic microbial threats. So far, only cetaceans have had their class II Major Histocompatibility Complex (MHC) organization characterized, despite the importance of MHC genes for adaptive immune responses. This study aims to characterize the organization of the marine mammal class II MHC using publicly available genomes. We located class II sequences in the genomes of one sirenian, four pinnipeds and eight cetaceans using NCBI-BLAST and reannotated the sequences using local BLAST search with exon and intron libraries. Scaffolds containing class II sequences were compared using dotplot analysis and introns were used for phylogenetic analysis. The manatee class II region shares overall synteny with other mammals, however most DR loci were translocated from the canonical location, past the extended class II region. Detailed analysis of the genomes of closely related taxa revealed that this presumed translocation is shared with all other living afrotherians. Other presumptive chromosome rearrangements in Afrotheria are the deletion of DQ loci in Afrosoricida and deletion of DP in E. telfairi. Pinnipeds share the main features of dog MHC: lack of a functional pair of DPA/DPB genes and inverted DRB locus between DQ and DO subregions. All cetaceans share the Cetartiodactyla inversion separating class II genes into two subregions: class IIa, with DR and DQ genes, and class IIb, with non-classic genes and a DRB pseudogene. These results point to three distinct and unheralded class II MHC structures in marine mammals: one canonical organization but lacking DP genes in pinnipeds; one bearing an inversion separating IIa and IIb subregions lacking DP genes found in cetaceans; and one with a translocation separating the most diverse class II gene from the MHC found in afrotherians and presumptive functional DR, DQ, and DP genes. Future functional research will reveal how these aquatic mammals cope with pathogen pressures with these divergent MHC organizations.
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Affiliation(s)
- André Luiz Alves de Sá
- Laboratory of Applied Genetics, Socio-Environmental and Water Resources Institute, Federal Rural University of the Amazon, Belém, Brazil.,Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará, Belém, Brazil
| | - Breanna Breaux
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | | | - Thaddeus Charles Deiss
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Leonardo Sena
- Center of Biodiversity Advanced Studies, Biological Sciences Institute, Federal University of Pará, Belém, Brazil
| | - Michael Frederick Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Maria Paula Cruz Schneider
- Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará, Belém, Brazil
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