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Day G, Robb K, Oxley A, Telonis-Scott M, Ujvari B. Organisation and evolution of the major histocompatibility complex class I genes in cetaceans. iScience 2024; 27:109590. [PMID: 38632986 PMCID: PMC11022044 DOI: 10.1016/j.isci.2024.109590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/30/2023] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
A quarter of marine mammals are at risk of extinction, with disease and poor habitat quality contributing to population decline. Investigation of the Major Histocompatibility Complex (MHC) provides insight into species' capacity to respond to immune and environmental challenges. The eighteen available cetacean chromosome level genomes were used to annotate MHC Class I loci, and to reconstruct the phylogenetic relationship of the described loci. The highest number of loci was observed in the striped dolphin (Stenella coeruleoalba), while the least was observed in the pygmy sperm whale (Kogia breviceps) and rough toothed dolphin (Steno bredanensis). Of the species studied, Mysticetes had the most pseudogenes. Evolutionarily, MHC Class I diverged before the speciation of cetaceans. Yet, locus one was genomically and phylogenetically similar in many species, persisting over evolutionary time. This characterisation of MHC Class I in cetaceans lays the groundwork for future population genetics and MHC expression studies.
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Affiliation(s)
- Grace Day
- School of Life and Environmental Sciences, Deakin University, Geelong 3216, VIC, Australia
- Marine Mammal Foundation, Melbourne 3194, VIC, Australia
| | - Kate Robb
- Marine Mammal Foundation, Melbourne 3194, VIC, Australia
| | - Andrew Oxley
- School of Life and Environmental Sciences, Deakin University, Geelong 3216, VIC, Australia
| | - Marina Telonis-Scott
- School of Life and Environmental Sciences, Deakin University, Melbourne 3125, VIC, Australia
| | - Beata Ujvari
- School of Life and Environmental Sciences, Deakin University, Geelong 3216, VIC, Australia
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2
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Sá ALAD, Baker PKB, Breaux B, Oliveira JM, Klautau AGCDM, Legatzki K, Luna FDO, Attademo FLN, Hunter ME, Criscitiello MF, Schneider MPC, Sena LDS. Novel insights on aquatic mammal MHC evolution: Evidence from manatee DQB diversity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 132:104398. [PMID: 35307479 DOI: 10.1016/j.dci.2022.104398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
The low diversity in marine mammal major histocompatibility complex (MHC) appears to support the hypothesis of reduced pathogen selective pressure in aquatic systems compared to terrestrial environments. However, the lack of characterization of the aquatic and evolutionarily distant Sirenia precludes drawing more generalized conclusions. Therefore, we aimed to characterize the MHC DQB diversity of two manatee species and compare it with those reported for marine mammals. Our results identified 12 and 6 alleles in T. inunguis and T. manatus, respectively. Alleles show high rates of nonsynonymous substitutions, suggesting loci are evolving under positive selection. Among aquatic mammals, Pinnipeda DQB had smaller numbers of alleles, higher synonymous substitution rate, and a dN/dS ratio closer to 1, suggesting it may be evolving under more relaxed selection compared to fully aquatic mammals. This contradicts one of the predictions of the hypothesis that aquatic environments impose reduced pathogen pressure to mammalian immune system. These results suggest that the unique evolutionary trajectories of mammalian MHC may impose challenges in drawing ecoevolutionary conclusions from comparisons across distant vertebrate lineages.
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Affiliation(s)
- André Luiz Alves de Sá
- Laboratory of Applied Genetics (LGA), Socio-Environmental and Water Resources Institute (ISARH), Federal Rural University of the Amazon (UFRA), Av. Presidente Tancredo Neves 2501, 66077-830, Belém, PA, Brazil; Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará (UFPA), R. Augusto Correa 01, 66075-110, Belém, PA, Brazil.
| | - Pamela Ketrya Barreiros Baker
- Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará (UFPA), R. Augusto Correa 01, 66075-110, Belém, PA, Brazil
| | - Breanna Breaux
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Jairo Moura Oliveira
- Zoological Park of Santarém - Universidade da Amazônia (ZOOUNAMA), R. Belo Horizonte, 68030-150, Santarém, PA, Brazil
| | - Alex Garcia Cavalleiro de Macedo Klautau
- Centro Nacional de Pesquisa e Conservação da Biodiversidade Marinha do Norte (CEPNOR), Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), Av. Presidente Tancredo Neves 2501, 66077-830, Belém, PA, Brazil
| | - Kristian Legatzki
- Centro Nacional de Pesquisa e Conservação da Biodiversidade Marinha do Norte (CEPNOR), Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), Av. Presidente Tancredo Neves 2501, 66077-830, Belém, PA, Brazil
| | - Fábia de Oliveira Luna
- National Center for Research and Conservation of Aquatic Mammals, Chico Mendes Institute for Biodiversity Conservation (CMA), ICMBio, Rua Alexandre Herculano 197, 11050-031, Santos, SP, Brazil
| | - Fernanda Löffler Niemeyer Attademo
- National Center for Research and Conservation of Aquatic Mammals, Chico Mendes Institute for Biodiversity Conservation (CMA), ICMBio, Rua Alexandre Herculano 197, 11050-031, Santos, SP, Brazil
| | - Margaret Elizabeth Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA.
| | - Michael Frederick Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA.
| | - Maria Paula Cruz Schneider
- Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará (UFPA), R. Augusto Correa 01, 66075-110, Belém, PA, Brazil.
| | - Leonardo Dos Santos Sena
- Center for Advanced Biodiversity Studies (CEABIO), Biological Sciences Institute, Federal University of Pará (UFPA), R. Augusto Correa 01, 66075-110, Belém, PA, Brazil.
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Ordoñez D, Bohórquez MD, Avendaño C, Patarroyo MA. Comparing Class II MHC DRB3 Diversity in Colombian Simmental and Simbrah Cattle Across Worldwide Bovine Populations. Front Genet 2022; 13:772885. [PMID: 35186024 PMCID: PMC8854852 DOI: 10.3389/fgene.2022.772885] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/17/2022] [Indexed: 11/22/2022] Open
Abstract
The major histocompatibility complex (MHC) exerts great influence on responses to infectious diseases and vaccination due to its fundamental role in the adaptive immune system. Knowledge about MHC polymorphism distribution among breeds can provide insights into cattle evolution and diversification as well as population-based immune response variability, thus guiding further studies. Colombian Simmental and Simbrah cattle’s BoLA-DRB3 genetic diversity was compared to that of taurine and zebuine breeds worldwide to estimate functional diversity. High allele richness was observed for Simmental and Simbrah cattle; nevertheless, high homozygosity was associated with individual low sequence variability in both the β1 domain and the peptide binding region (PBR), thereby implying reduced MHC-presented peptide repertoire size. There were strong signals of positive selection acting on BoLA-DRB3 in all populations, some of which were poorly structured and displayed common alleles accounting for their high genetic similarity. PBR sequence correlation analysis suggested that, except for a few populations exhibiting some divergence at PBR, global diversity regarding potential MHC-presented peptide repertoire could be similar for the cattle populations analyzed here, which points to the retention of functional diversity in spite of the selective pressures imposed by breeding.
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Affiliation(s)
- Diego Ordoñez
- Animal Science Faculty, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Bogotá, Colombia
- PhD Program in Tropical Health and Development, Universidad de Salamanca, Salamanca, Spain
| | - Michel David Bohórquez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- MSc Program in Microbiology, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Catalina Avendaño
- Animal Science Faculty, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Bogotá, Colombia
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Health Sciences Division, Main Campus, Universidad Santo Tomás, Bogotá, Colombia
- Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Bogotá, Colombia
- *Correspondence: Manuel Alfonso Patarroyo,
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Guo L, Zhang X, Luo D, Yu RQ, Xie Q, Wu Y. Population-level effects of polychlorinated biphenyl (PCB) exposure on highly vulnerable Indo-Pacific humpback dolphins from their largest habitat. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 286:117544. [PMID: 34119862 DOI: 10.1016/j.envpol.2021.117544] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 06/12/2023]
Abstract
While polychlorinated biphenyl (PCB)-related risks have been reported at the cellular, organ, and individual levels in some marine mammals, studies quantifying the PCB-associated population-level effects are limited. Here, we combined chemical analysis and individual-based model simulation to investigate the impact of PCBs on the Indo-Pacific humpback dolphin (sub)population from the Pearl River Estuary (PRE). An annual PCB accumulation rate of 0.29 ± 0.07 mg/kg lipid per year was estimated based on the measured age-specific male data as males continue to accumulate PCBs throughout their lifetime, without depurating contaminant loads. Using the Taiwan Strait dolphin population with low PCBs as a baseline, we compare our model simulations in PRE population to estimate relative population impacts of PCBs and other stressors. When using the current vital rates of the PRE dolphins which have been affected by PCBs and other stressors (e.g., underwater noise, prey limitation, etc.), our simulations revealed a substantial decline (8.1%) in the annual population growth rate (λ) of PRE metapopulation compared to baseline over the next 100 years. At the estimated PCB accumulation rate, the PCB-mediated effects on calf survival and immunity would cause a slight decline (0.9%) in λ relative to baseline. Our findings suggest a relatively limited impact of PCBs on the long-term survival of PRE dolphins among all stressors. However, it should be noted that even under model simulations where dietary PCBs were eliminated, humpback dolphins would still need a long time to reduce their PCB burdens to a relatively "safe" level through biological cycling. Considering that the baseline vital rates might also have been affected by PCBs and other stressors, our results are considered relative rather than absolute. This study provides a starting point for quantifying population-level consequences of contaminant exposure on humpback dolphins, although more efforts are needed to perfect this type of analysis.
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Affiliation(s)
- Lang Guo
- School of Marine Sciences, Zhuhai Key Laboratory of Marine Bioresources and Environment, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Sun Yat-Sen University, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, China
| | - Xiyang Zhang
- School of Marine Sciences, Zhuhai Key Laboratory of Marine Bioresources and Environment, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Sun Yat-Sen University, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, China
| | - Dingyu Luo
- School of Marine Sciences, Zhuhai Key Laboratory of Marine Bioresources and Environment, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Sun Yat-Sen University, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, China
| | - Ri-Qing Yu
- Department of Biology, Center for Environment, Biodiversity and Conservation, The University of Texas at Tyler, Tyler, TX, USA
| | - Qiang Xie
- School of Marine Sciences, Zhuhai Key Laboratory of Marine Bioresources and Environment, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Sun Yat-Sen University, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, China
| | - Yuping Wu
- School of Marine Sciences, Zhuhai Key Laboratory of Marine Bioresources and Environment, Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Sun Yat-Sen University, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, China.
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5
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Bohórquez MD, Ordoñez D, Suárez CF, Vicente B, Vieira C, López-Abán J, Muro A, Ordóñez I, Patarroyo MA. Major Histocompatibility Complex Class II (DRB3) Genetic Diversity in Spanish Morucha and Colombian Normande Cattle Compared to Taurine and Zebu Populations. Front Genet 2020; 10:1293. [PMID: 31998362 PMCID: PMC6965167 DOI: 10.3389/fgene.2019.01293] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/25/2019] [Indexed: 11/13/2022] Open
Abstract
Bovine leukocyte antigens (BoLA) have been used as disease markers and immunological traits in cattle due to their primary role in pathogen recognition by the immune system. A higher MHC allele diversity in a population will allow presenting a broader peptide repertoire. However, loss of overall diversity due to domestication process can decrease a population's peptide repertoire. Within the context of zebu and taurine cattle populations, BoLA-DRB3 genetic diversity in Spanish Morucha and Colombian Normande cattle was analyzed and an approach to estimate functional diversity was performed. Sequence-based typing was used for identifying 29, 23, 27, and 28 alleles in Spanish Morucha, Nariño-, Boyacá-, and Cundinamarca-Normande cattle, respectively. These breeds had remarkably low heterozygosity levels and the Hardy-Weinberg principle revealed significant heterozygote deficiency. FST and DA genetic distance showed that Colombian Normande populations had greater variability than other phenotypically homogeneous breeds, such as Holstein. It was also found that Spanish Morucha cattle were strongly differentiated from other cattle breeds. Spanish Morucha had greater divergence in the peptide-binding region regarding other cattle breeds. However, peptide-binding region covariation indicated that the potential peptide repertoire seemed equivalent among cattle breeds. Despite the genetic divergence observed, the extent of the potential peptide repertoire in the cattle populations studied appears to be similar and thus their pathogen recognition potential should be equivalent, suggesting that functional diversity might persist in the face of bottlenecks imposed by domestication and breeding.
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Affiliation(s)
- Michel David Bohórquez
- Microbiology Postgraduate Programme, Universidad Nacional de Colombia, Bogotá, Colombia.,Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Diego Ordoñez
- PhD Programme in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá, Colombia.,Faculty of Agricultural Sciences, Universidad de Ciencias Aplicadas y Ambientales (UDCA), Bogotá, Colombia
| | - Carlos Fernando Suárez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia.,Basic Sciences Department, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Belén Vicente
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Carmen Vieira
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Julio López-Abán
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Antonio Muro
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Iván Ordóñez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia.,Basic Sciences Department, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
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Whole Genome Sequencing of Chinese White Dolphin ( Sousa chinensis) for High-Throughput Screening of Antihypertensive Peptides. Mar Drugs 2019; 17:md17090504. [PMID: 31466310 PMCID: PMC6780146 DOI: 10.3390/md17090504] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/16/2019] [Accepted: 08/26/2019] [Indexed: 01/17/2023] Open
Abstract
Chinese white dolphin (Sousa chinensis), also known as the Indo-Pacific humpback dolphin, has been classified as “Vulnerable” on the IUCN Red List of Threatened Species. It is a special cetacean species that lives in tropical and subtropical nearshore waters, with significant differences from other cetaceans. Here, we sequenced and assembled a draft genome of the Chinese white dolphin with a total length of 2.3 Gb and annotation of 18,387 protein-coding genes. Genes from certain expanded families are potentially involved in DNA replication and repairing, suggesting that they may be related to adaptation of this marine mammal to nearshore environments. We also discovered that its historical population had undergone a remarkable bottleneck incident before the Mindel glaciation. In addition, a comparative genomic survey on antihypertensive peptides (AHTPs) among five representative mammals with various residential habitats (such as remarkable differences in exogenous ion concentrations and sea depth) revealed that these small bioactive peptides were highly conserved among these examined mammals, and they had the most abundant hits in collagen subunit proteins, especially for two putative AHTP peptides Gly-Leu-Pro (GLP) and Leu-Gly-Pro (LGP). Our genome assembly will be a valuable resource for further genetic researches on adaptive ecology and conservation biology of cetaceans, and for in-depth investigations into bioactive peptides in aquatic and terrestrial mammals for development of peptide-based drugs to treat various human cardiovascular diseases.
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Ming Y, Jian J, Yu X, Wang J, Liu W. The genome resources for conservation of Indo-Pacific humpback dolphin, Sousa chinensis. Sci Data 2019; 6:68. [PMID: 31118413 PMCID: PMC6531461 DOI: 10.1038/s41597-019-0078-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/16/2019] [Indexed: 11/24/2022] Open
Abstract
The Indo-Pacific humpback dolphin (Sousa chinensis), is a threatened marine mammal and belongs to the First Order of the National Key Protected Wild Aquatic Animals List in China. However, limited genomic information is available for studies of its population genetics and biological conservation. Here, we have assembled a genomic sequence of this species using a whole genome shotgun (WGS) sequencing strategy after a pilot low coverage genome survey. The total assembled genome size was 2.34 Gb: with a contig N50 of 67 kb and a scaffold N50 of 9 Mb (107.6-fold sequencing coverage). The S. chinensis genome contained 24,640 predicted protein-coding genes and had approximately 37% repeated sequences. The completeness of the genome assembly was evaluated by benchmarking universal single copy orthologous genes (BUSCOs): 94.3% of a total 4,104 expected mammalian genes were identified as complete, and 2.3% were identified as fragmented. This newly produced high-quality assembly and annotation of the genome will greatly promote the future studies of the genetic diversity, conservation and evolution. Design Type(s) | sequence assembly objective • sequence annotation objective | Measurement Type(s) | whole genome sequencing assay | Technology Type(s) | DNA sequencing | Factor Type(s) | | Sample Characteristic(s) | Sousa chinensis • skin of body |
Machine-accessible metadata file describing the reported data (ISA-Tab format)
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Affiliation(s)
- Yao Ming
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Jianbo Jian
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Xueying Yu
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou, Guangxi, 535011, P.R. China
| | - Jingzhen Wang
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou, Guangxi, 535011, P.R. China.
| | - Wenhua Liu
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. 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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Dooley CT, Ferrer T, Pagán H, O’Corry-Crowe GM. Bridging immunogenetics and immunoproteomics: Model positional scanning library analysis for Major Histocompatibility Complex class II DQ in Tursiops truncatus. PLoS One 2018; 13:e0201299. [PMID: 30070993 PMCID: PMC6072028 DOI: 10.1371/journal.pone.0201299] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 07/12/2018] [Indexed: 02/02/2023] Open
Abstract
The Major Histocompatibility Complex (MHC) is a critical element in mounting an effective immune response in vertebrates against invading pathogens. Studies of MHC in wildlife populations have typically focused on assessing diversity within the peptide binding regions (PBR) of the MHC class II (MHC II) family, especially the DQ receptor genes. Such metrics of diversity, however, are of limited use to health risk assessment since functional analyses (where changes in the PBR are correlated to recognition/pathologies of known pathogen proteins), are difficult to conduct in wildlife species. Here we describe a means to predict the binding preferences of MHC proteins: We have developed a model positional scanning library analysis (MPSLA) by harnessing the power of mixture based combinatorial libraries to probe the peptide landscapes of distinct MHC II DQ proteins. The algorithm provided by NNAlign was employed to predict the binding affinities of sets of peptides generated for DQ proteins. These binding affinities were then used to retroactively construct a model Positional Scanning Library screen. To test the utility of the approach, a model screen was compared to physical combinatorial screens for human MHC II DP. Model library screens were generated for DQ proteins derived from sequence data from bottlenose dolphins from the Indian River Lagoon (IRL) and the Atlantic coast of Florida, and compared to screens of DQ proteins from Genbank for dolphin and three other cetaceans. To explore the peptide binding landscape for DQ proteins from the IRL, combinations of the amino acids identified as active were compiled into peptide sequence lists that were used to mine databases for representation in known proteins. The frequency of which peptide sequences predicted to bind the MHC protein are found in proteins from pathogens associated with marine mammals was found to be significant (p values <0.0001). Through this analysis, genetic variation in MHC (classes I and II) can now be associated with the binding repertoires of the expressed MHC proteins and subsequently used to identify target pathogens. This approach may be eventually applied to evaluate individual population and species risk for outbreaks of emerging diseases.
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Affiliation(s)
- Colette T. Dooley
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida, United States of America
| | - Tatiana Ferrer
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
| | - Heidi Pagán
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
| | - Gregory M. O’Corry-Crowe
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
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10
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Li L, Rong X, Li G, Wang Y, Chen B, Ren W, Yang G, Xu S. Genomic organization and adaptive evolution of IGHC genes in marine mammals. Mol Immunol 2018; 99:75-81. [PMID: 29723770 PMCID: PMC7112648 DOI: 10.1016/j.molimm.2018.04.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/19/2018] [Accepted: 04/19/2018] [Indexed: 01/08/2023]
Abstract
The genomic organization of IGHC genes in marine mammal is similar to that of terrestrial relatives. The number of the immunoglobulin heavy chain constant region genes vary among different mammals. Different levels of selective pressures were detected between marine and terrestrial mammalian lineages.
Immunoglobulins are important elements of the adaptive immune system that bind to an immense variety of microbial antigens to neutralize infectivity and specify effector functions. In the present study, the immunoglobulin heavy chain constant region (IGHC) genes from marine mammals were identified and compared with those of their terrestrial relatives to explore their genomic organization and evolutionary characteristics. The genomic organization of marine mammal IGHC genes was shown to be conservative with other eutherian mammals. Stronger signals of positive selection on IGHC were revealed in terrestrial mammals than that in marine mammals with the branch-site model, displaying different selective pressure, which might suggest their divergent adaptations to contrasted environments.
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Affiliation(s)
- Lili Li
- Jiangsu Key Lab for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, 210023, China.
| | - Xinghua Rong
- Jiangsu Key Lab for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, 210023, China.
| | - Guiting Li
- Jiangsu Key Lab for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, 210023, China.
| | - Yingying Wang
- Jiangsu Key Lab for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, 210023, China.
| | - Bingyao Chen
- Jiangsu Key Lab for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, 210023, China.
| | - Wenhua Ren
- Jiangsu Key Lab for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, 210023, China.
| | - Guang Yang
- Jiangsu Key Lab for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, 210023, China.
| | - Shixia Xu
- Jiangsu Key Lab for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, 210023, China.
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11
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Santonastaso T, Lighten J, van Oosterhout C, Jones KL, Foufopoulos J, Anthony NM. The effects of historical fragmentation on major histocompatibility complex class II β and microsatellite variation in the Aegean island reptile, Podarcis erhardii. Ecol Evol 2017; 7:4568-4581. [PMID: 28690787 PMCID: PMC5496512 DOI: 10.1002/ece3.3022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 03/16/2017] [Accepted: 03/27/2017] [Indexed: 01/29/2023] Open
Abstract
The major histocompatibility complex (MHC) plays a key role in disease resistance and is the most polymorphic gene region in vertebrates. Although habitat fragmentation is predicted to lead to a loss in MHC variation through drift, the impact of other evolutionary forces may counter this effect. Here we assess the impact of selection, drift, migration, and recombination on MHC class II and microsatellite variability in 14 island populations of the Aegean wall lizard Podarcis erhardii. Lizards were sampled from islands within the Cyclades (Greece) formed by rising sea levels as the last glacial maximum approximately 20,000 before present. Bathymetric data were used to determine the area and age of each island, allowing us to infer the corresponding magnitude and timing of genetic bottlenecks associated with island formation. Both MHC and microsatellite variation were positively associated with island area, supporting the hypothesis that drift governs neutral and adaptive variation in this system. However, MHC but not microsatellite variability declined significantly with island age. This discrepancy is likely due to the fact that microsatellites attain mutation‐drift equilibrium more rapidly than MHC. Although we detected signals of balancing selection, recombination and migration, the effects of these evolutionary processes appeared negligible relative to drift. This study demonstrates how land bridge islands can provide novel insights into the impact of historical fragmentation on genetic diversity as well as help disentangle the effects of different evolutionary forces on neutral and adaptive diversity.
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Affiliation(s)
- Trent Santonastaso
- Department of Biological Sciences University of New Orleans New Orleans LA USA
| | - Jackie Lighten
- School of Environmental Sciences University of East Anglia Norwich Research Park Norwich UK
| | - Cock van Oosterhout
- School of Environmental Sciences University of East Anglia Norwich Research Park Norwich UK
| | - Kenneth L Jones
- Department of Biochemistry and Molecular Genetics University of Colorado Denver School of Medicine Denver CO USA
| | - Johannes Foufopoulos
- School of the Environment and Sustainability University of Michigan Ann Arbor MI USA
| | - Nicola M Anthony
- Department of Biological Sciences University of New Orleans New Orleans LA USA
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