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Hu M, Fan D, Hao J, Zhang F, Xu W, Zhu C, Wang K, Song X, Li L. A chromosome-level genome of the striated frogfish (Antennarius striatus). Sci Data 2024; 11:654. [PMID: 38906880 PMCID: PMC11192929 DOI: 10.1038/s41597-024-03514-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/12/2024] [Indexed: 06/23/2024] Open
Abstract
The striated frogfish (Antennarius striatus), a member of the sub-order Antennarioidei within the order Lophiiformes, possesses remarkable adaptations. These include the ability to modulate body coloration for camouflage, utilize bioluminescent esca for predation, and employ elbow-like pectoral fins for terrestrial locomotion, making it a valuable model for studying bioluminescence, adaptive camouflage, fin-to-limb transition, and walking-like behaviors. To better study and contribute to the conservation of the striated frogfish, we obtained the micro-CT image of the pectoral fin bones and generated a high-quality, chromosome-level genome assembly using multiple sequencing technologies. The assembly spans 548.56 Mb with a contig N50 of 21.05 Mb, and 99.35% of the genome is anchored on 24 chromosomes, making it the most complete genome available within Lophiiformes. The genome annotation revealed 28.43% repetitive sequences and 23,945 protein-coding genes. This chromosome-level genome provides valuable genetic resources for frogfish conservation and offers insights into the genetic mechanisms underlying its unique phenotypic evolution. Furthermore, it establishes a foundation for future research on limb development and adaptive camouflage in this species.
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Affiliation(s)
- Mingliang Hu
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Deqian Fan
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Jiaqi Hao
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Fenghua Zhang
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Wenjie Xu
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Chenglong Zhu
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Kun Wang
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710129, China.
| | - Xiaojing Song
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, China.
| | - Lisen Li
- Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection, School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710129, China.
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2
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Brownstein CD, Zapfe KL, Lott S, Harrington R, Ghezelayagh A, Dornburg A, Near TJ. Synergistic innovations enabled the radiation of anglerfishes in the deep open ocean. Curr Biol 2024; 34:2541-2550.e4. [PMID: 38788708 DOI: 10.1016/j.cub.2024.04.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/10/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024]
Abstract
Major ecological transitions are thought to fuel diversification, but whether they are contingent on the evolution of certain traits called key innovations1 is unclear. Key innovations are routinely invoked to explain how lineages rapidly exploit new ecological opportunities.1,2,3 However, investigations of key innovations often focus on single traits rather than considering trait combinations that collectively produce effects of interest.4 Here, we investigate the evolution of synergistic trait interactions in anglerfishes, which include one of the most species-rich vertebrate clades in the bathypelagic, or "midnight," zone of the deep sea: Ceratioidea.5 Ceratioids are the only vertebrates that possess sexual parasitism, wherein males temporarily attach or permanently fuse to females to mate.6,7 We show that the rapid transition of ancestrally benthic anglerfishes into pelagic habitats occurred during a period of major global warming 50-35 million years ago.8,9 This transition coincided with the origins of sexual parasitism, which is thought to increase the probability of successful reproduction once a mate is found in the midnight zone, Earth's largest habitat.5,6,7 Our reconstruction of the evolutionary history of anglerfishes and the loss of immune genes support that permanently fusing clades have convergently degenerated their adaptive immunity. We find that degenerate adaptive immune genes and sexual body size dimorphism, both variably present in anglerfishes outside the ceratioid radiation, likely promoted their transition into the bathypelagic zone. These results show how traits from separate physiological, morphological, and reproductive systems can interact synergistically to drive major transitions and subsequent diversification in novel environments.
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Affiliation(s)
- Chase D Brownstein
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06511, USA.
| | - Katerina L Zapfe
- Department of Bioinformatics and Genomics, University of North Carolina Charlotte, 9331 Robert D. Snyder Rd., Charlotte, NC 28223, USA
| | - Spencer Lott
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06511, USA
| | - Richard Harrington
- Department of Natural Resources, Marine Resources Division, 217 Ft. Johnson Road, Charleston, SC 29412-9110, USA
| | - Ava Ghezelayagh
- Department of Geophysical Sciences, University of Chicago, 5734 S. Ellis Avenue, Chicago, IL 60637, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina Charlotte, 9331 Robert D. Snyder Rd., Charlotte, NC 28223, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06511, USA; Peabody Museum, Yale University, 21 Sachem Street, New Haven, CT 06511, USA
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3
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Wainwright PC. Deep sea evolution: Glowing lures, parasitic males and rapid speciation in anglerfishes. Curr Biol 2024; 34:R549-R551. [PMID: 38834031 DOI: 10.1016/j.cub.2024.04.077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Anglerfish are creatures of the deep ocean, featuring glowing lures, huge, toothy mouths and parasitic males physically attached to females. A new study finds that genomic degradation of the immune system facilitated the origin of parasitic males as anglerfishes invaded the deep zone where they experienced an adaptive radiation.
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Affiliation(s)
- Peter C Wainwright
- Department of Evolution and Ecology, University of California, Davis, Davis, CA 95616, USA.
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4
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Parker J, Marten SM, Ó Corcora TC, Rajkov J, Dubin A, Roth O. The effects of primary and secondary bacterial exposure on the seahorse (Hippocampus erectus) immune response. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 153:105136. [PMID: 38185263 DOI: 10.1016/j.dci.2024.105136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/09/2024]
Abstract
Evolutionary adaptations in the Syngnathidae teleost family (seahorses, pipefish and seadragons) culminated in an array of spectacular morphologies, key immune gene losses, and the enigmatic male pregnancy. In seahorses, genome modifications associated with immunoglobulins, complement, and major histocompatibility complex (MHC II) pathway components raise questions concerning their immunological efficiency and the evolution of compensatory measures that may act in their place. In this investigation heat-killed bacteria (Vibrio aestuarianus and Tenacibaculum maritimum) were used in a two-phased experiment to assess the immune response dynamics of Hippocampus erectus. Gill transcriptomes from double and single-exposed individuals were analysed in order to determine the differentially expressed genes contributing to immune system responses towards immune priming. Double-exposed individuals exhibited a greater adaptive immune response when compared with single-exposed individuals, while single-exposed individuals, particularly with V. aestuarianus replicates, associated more with the innate branch of the immune system. T. maritimum double-exposed replicates exhibited the strongest immune reaction, likely due to their immunological naivety towards the bacterium, while there are also potential signs of innate trained immunity. MHC II upregulated expression was identified in selected V. aestuarianus-exposed seahorses, in the absence of other pathway constituents suggesting a possible alternative or non-classical MHC II immune function in seahorses. Gene Ontology (GO) enrichment analysis highlighted prominent angiogenesis activity following secondary exposure, which could be linked to an adaptive immune process in seahorses. This investigation highlights the prominent role of T-cell mediated adaptive immune responses in seahorses when exposed to sequential foreign bacteria exposures. If classical MHC II pathway function has been lost, innate trained immunity in syngnathids could be a potential compensatory mechanism.
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Affiliation(s)
- Jamie Parker
- Marine Evolutionary Biology, Christian-Albrechts-University, D-24118, Kiel, Germany.
| | - Silke-Mareike Marten
- Marine Evolutionary Biology, Christian-Albrechts-University, D-24118, Kiel, Germany
| | - Tadhg C Ó Corcora
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, D-24105, Kiel, Germany
| | - Jelena Rajkov
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, D-24105, Kiel, Germany
| | - Arseny Dubin
- Marine Evolutionary Biology, Christian-Albrechts-University, D-24118, Kiel, Germany
| | - Olivia Roth
- Marine Evolutionary Biology, Christian-Albrechts-University, D-24118, Kiel, Germany
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5
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Franke A, Beemelmanns A, Miest JJ. Are fish immunocompetent enough to face climate change? Biol Lett 2024; 20:20230346. [PMID: 38378140 PMCID: PMC10878809 DOI: 10.1098/rsbl.2023.0346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 01/26/2024] [Indexed: 02/22/2024] Open
Abstract
Ongoing climate change has already been associated with increased disease outbreaks in wild and farmed fish. Here, we evaluate the current knowledge of climate change-related ecoimmunology in teleosts with a focus on temperature, hypoxia, salinity and acidification before exploring interactive effects of multiple stressors. Our literature review reveals that acute and chronic changes in temperature and dissolved oxygen can compromise fish immunity which can lead to increased disease susceptibility. Moreover, temperature and hypoxia have already been shown to enhance the infectivity of certain pathogens/parasites and to accelerate disease progression. Too few studies exist that have focussed on acidification, but direct immune effects seem to be limited while salinity studies have led to contrasting results. Likewise, multi-stressor experiments essential for unravelling the interactions of simultaneously changing environmental factors are still scarce. This ultimately impedes our ability to estimate to what extent climate change will hamper fish immunity. Our review about epigenetic regulation mechanisms highlights the acclimation potential of the fish immune response to changing environments. However, due to the limited number of epigenetic studies, overarching conclusions cannot be drawn. Finally, we provide an outlook on how to better estimate the effects of realistic climate change scenarios in future immune studies in fish.
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Affiliation(s)
- Andrea Franke
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), 26129 Oldenburg, Germany
- Alfred-Wegener-Institute, Helmholtz-Centre for Polar and Marine Research (AWI), 27570 Bremerhaven, Germany
| | - Anne Beemelmanns
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V0A6 Québec, Canada
| | - Joanna J. Miest
- School of Psychology and Life Sciences, Canterbury, Kent CT1 1QU, UK
- School of Science, University of Greenwich, Chatham Maritime, Kent ME4 4TB, UK
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6
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Swann JB, Grammer C, Schorpp M, Boehm T. A survey of the adaptive immune genes of the polka-dot batfish Ogcocephalus cubifrons. BMC Immunol 2023; 24:20. [PMID: 37480016 PMCID: PMC10362645 DOI: 10.1186/s12865-023-00557-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 07/12/2023] [Indexed: 07/23/2023] Open
Abstract
BACKGROUND The anglerfish, belonging to the teleost order Lophiiformes, are a diverse and species-rich group of fish that are known to exhibit a number of unique morphological, reproductive and immunological adaptations. Work to date has identified the loss of specific adaptive immune components in two of the five Lophiiformes sub-orders (Lophioidei and Ceratioidei), while no anomalies have been identified to date in two other sub-orders, Antennaroidei and Chaunacoidei. The immunogenome of the fifth sub-order, Ogcocephaloidei has not yet been investigated, and we have therefore used whole genome shotgun sequencing, combined with RNA-seq, to survey the adaptive immune capabilities of the polka-dot batfish, O. cubifrons, as a representative of this as yet unexplored sub-order. RESULTS We find that the O. cubifrons genome encodes the core genes needed to mount adaptive T and B cell responses. These genes include those necessary for rearranging and editing antigen receptors, the antigen receptors themselves; as well as the co-receptors, signalling molecules, and antigen presenting molecules (both class I and class II) needed for B cell and T cell development and activation. CONCLUSIONS From an immune perspective, the polka-dot batfish has a canonical complement of adaptive immune genes, and does not exhibit any of the adaptive immune changes previously identified in monkfish and oceanic anglerfish.
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Affiliation(s)
- Jeremy B Swann
- Department of Developmental Immunology, Max Planck-Institute of Immunobiology and Epigenetics, Stübeweg 51, D-79108, Freiburg, Germany.
| | - Christiane Grammer
- Department of Developmental Immunology, Max Planck-Institute of Immunobiology and Epigenetics, Stübeweg 51, D-79108, Freiburg, Germany
| | - Michael Schorpp
- Department of Developmental Immunology, Max Planck-Institute of Immunobiology and Epigenetics, Stübeweg 51, D-79108, Freiburg, Germany
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck-Institute of Immunobiology and Epigenetics, Stübeweg 51, D-79108, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
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7
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Bjørnestad SA, Solbakken MH, Jakobsen KS, Jentoft S, Bakke O, Progida C. Atlantic cod ( Gadus morhua) MHC I localizes to endolysosomal compartments independently of cytosolic sorting signals. Front Cell Dev Biol 2023; 11:1050323. [PMID: 36760361 PMCID: PMC9905690 DOI: 10.3389/fcell.2023.1050323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/11/2023] [Indexed: 01/26/2023] Open
Abstract
Major histocompatibility complex (MHC) class I and II are crucial for the adaptive immune system because they are involved in peptide presentation to T cells. Until recently, it was believed that MHC genes and their associated immune components had been conserved since their evolutionary emergence in jawed fish. However, sequencing of the Atlantic cod (Gadus morhua) genome revealed a loss of MHC class II genes, and an extreme expansion of MHC class I genes. These findings lead to the hypothesis that a loss of the MHC class II pathway coincided with a more versatile use of MHC class I, but so far there is no direct experimental evidence in support of this. To gain a deeper understanding of the function of the expanded MHC class I, we selected five MHC class I gene variants representing five of the six clades identified in previous studies and investigated their intracellular localization in human and Atlantic cod larval cells. Intriguingly, we uncovered that all selected MHC class I variants localize to endolysosomal compartments in Atlantic cod cells. Additionally, by introducing point mutations or deletions in the cytosolic tail, we found that hypothetical sorting signals in the MHC class I cytosolic tail do not influence MHC class I trafficking. Moreover, we demonstrated that in Atlantic cod, tapasin and MHC class I colocalize on endolysosomes suggesting that peptide-loading assistance and stabilization of MHC class I occurs outside the endoplasmic reticulum. Altogether, our results demonstrate that MHC class I from Atlantic cod is sorted to the endolysosomal system, which may indicate that it interacts with exogenous peptides for potential cross presentation.
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Affiliation(s)
- Synne Arstad Bjørnestad
- Section of Physiology and Cell Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Monica Hongrø Solbakken
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kjetill S. Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Oddmund Bakke
- Section of Physiology and Cell Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Cinzia Progida
- Section of Physiology and Cell Biology, Department of Biosciences, University of Oslo, Oslo, Norway,*Correspondence: Cinzia Progida,
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8
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Liu Y, Qu M, Jiang H, Schneider R, Qin G, Luo W, Yu H, Zhang B, Wang X, Zhang Y, Zhang H, Zhang Z, Wu Y, Zhang Y, Yin J, Zhang S, Venkatesh B, Roth O, Meyer A, Lin Q. Immunogenetic losses co-occurred with seahorse male pregnancy and mutation in tlx1 accompanied functional asplenia. Nat Commun 2022; 13:7610. [PMID: 36494371 PMCID: PMC9734139 DOI: 10.1038/s41467-022-35338-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022] Open
Abstract
In the highly derived syngnathid fishes (pipefishes, seadragons & seahorses), the evolution of sex-role reversed brooding behavior culminated in the seahorse lineage's male pregnancy, whose males feature a specialized brood pouch into which females deposit eggs during mating. Then, eggs are intimately engulfed by a placenta-like tissue that facilitates gas and nutrient exchange. As fathers immunologically tolerate allogenic embryos, it was suggested that male pregnancy co-evolved with specific immunological adaptations. Indeed, here we show that a specific amino-acid replacement in the tlx1 transcription factor is associated with seahorses' asplenia (loss of spleen, an organ central in the immune system), as confirmed by a CRISPR-Cas9 experiment using zebrafish. Comparative genomics across the syngnathid phylogeny revealed that the complexity of the immune system gene repertoire decreases as parental care intensity increases. The synchronous evolution of immunogenetic alterations and male pregnancy supports the notion that male pregnancy co-evolved with the immunological tolerance of the embryo.
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Affiliation(s)
- Yali Liu
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 PR China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100101 Beijing, China
| | - Meng Qu
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 PR China
| | - Han Jiang
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100101 Beijing, China
| | - Ralf Schneider
- grid.9764.c0000 0001 2153 9986Marine Evolutionary Ecology, Zoological Institute, Kiel University, 24118 Kiel, Germany
| | - Geng Qin
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 PR China
| | - Wei Luo
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
| | - Haiyan Yu
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
| | - Bo Zhang
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
| | - Xin Wang
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 PR China
| | - Yanhong Zhang
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 PR China
| | - Huixian Zhang
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 PR China
| | - Zhixin Zhang
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.412785.d0000 0001 0695 6482Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Minato, Tokyo, Japan
| | - Yongli Wu
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China
| | - Yingyi Zhang
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100101 Beijing, China
| | - Jianping Yin
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 PR China
| | - Si Zhang
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 PR China
| | - Byrappa Venkatesh
- grid.418812.60000 0004 0620 9243Institute of Molecular and Cell Biology, A*STAR, 138673 Singapore, Singapore
| | - Olivia Roth
- grid.9764.c0000 0001 2153 9986Marine Evolutionary Ecology, Zoological Institute, Kiel University, 24118 Kiel, Germany
| | - Axel Meyer
- grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Qiang Lin
- grid.9227.e0000000119573309CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301 Guangzhou, China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 PR China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100101 Beijing, China
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Ai K, Li K, Jiao X, Zhang Y, Li J, Zhang Q, Wei X, Yang J. IL-2-mTORC1 signaling coordinates the STAT1/T-bet axis to ensure Th1 cell differentiation and anti-bacterial immune response in fish. PLoS Pathog 2022; 18:e1010913. [PMID: 36282845 PMCID: PMC9595569 DOI: 10.1371/journal.ppat.1010913] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 10/03/2022] [Indexed: 11/04/2022] Open
Abstract
Utilization of specialized Th1 cells to resist intracellular pathogenic infection represents an important innovation of adaptive immunity. Although transcriptional evidence indicates the potential presence of Th1-like cells in some fish species, the existence of CD3+CD4+IFN-γ+ T cells, their detailed functions, and the mechanism determining their differentiation in these early vertebrates remain unclear. In the present study, we identified a population of CD3+CD4-1+IFN-γ+ (Th1) cells in Nile tilapia upon T-cell activation in vitro or Edwardsiella piscicida infection in vivo. By depleting CD4-1+ T cells or blocking IFN-γ, Th1 cells and their produced IFN-γ were found to be essential for tilapia to activate macrophages and resist the E. piscicida infection. Mechanistically, activated T cells of tilapia produce IL-2, which enhances the STAT5 and mTORC1 signaling that in turn trigger the STAT1/T-bet axis-controlled IFN-γ transcription and Th1 cell development. Additionally, mTORC1 regulates the differentiation of these cells by promoting the proliferation of CD3+CD4-1+ T cells. Moreover, IFN-γ binds to its receptors IFNγR1 and IFNγR2 and further initiates a STAT1/T-bet axis-mediated positive feedback loop to stabilize the Th1 cell polarization in tilapia. These findings demonstrate that, prior to the emergence of tetrapods, the bony fish Nile tilapia had already evolved Th1 cells to fight intracellular bacterial infection, and support the notion that IL-2-mTORC1 signaling coordinates the STAT1/T-bet axis to determine Th1 cell fate, which is an ancient mechanism that has been programmed early during vertebrate evolution. Our study is expected to provide novel perspectives into the evolution of adaptive immunity.
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Affiliation(s)
- Kete Ai
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai, China
| | - Kang Li
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai, China
| | - Xinying Jiao
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai, China
| | - Yu Zhang
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai, China
| | - Jiaqi Li
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai, China
| | - Qian Zhang
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai, China
| | - Xiumei Wei
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai, China
| | - Jialong Yang
- State Key Laboratory of Estuarine and Coastal Research, School of Life Sciences, East China Normal University, Shanghai, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- * E-mail:
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10
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Yang S, Mkingule I, Liu L, Chen W, Yuan X, Ma Z, Liang L, Qian S, Huang M, Fei H. Protective efficacy evaluation of immunogenic protein AHA_3793 of Aeromonas hydrophila as vaccine candidate for largemouth bass Micropterus salmoides. JOURNAL OF OCEANOLOGY AND LIMNOLOGY 2022; 41:392-400. [PMID: 36287822 PMCID: PMC9584254 DOI: 10.1007/s00343-022-1326-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/13/2022] [Indexed: 06/16/2023]
Abstract
Aeromonas hydrophila is a Gram-negative pathogen that can infect various fish, including largemouth bass (Micropterus salmoides), which have caused huge economic losses. In present study, largemouth bass anti-A. hydrophila antibodies were produced, then a highly immunogenic outer membrane proteins, AHA_3793, was identified by combined western blotting and mass spectrometry analysis. Moreover, AHA_3793 was expressed, and its immunogenicity was further verified by western blotting. Subsequently, the protective efficacy of AHA_3793 were evaluated in largemouth bass. The results showed that rAHA_3793 could produce a relative percentage survival (RPS) of 61.76% for largemouth bass against A. hydrophila challenge. ELISA analysis showed the specific serum antibodies of largemouth bass against rAHA_3793 and A. hydrophila in vaccinated group in weeks 4 and 5 after immunization were significantly higher than those in control group, which suggested that rAHA_3793 induced production of specific serum antibodies against rAHA_3793 and A. hydrophila. The qRT-PCR analysis showed that expressions of CD4-2 and MHC IIα were also significantly up-regulated after immunization. These results collectively demonstrated that rAHA_3793 could induce a strong humoral immune response of largemouth bass, and then produce high immune protection effects against A. hydrophila infection.
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Affiliation(s)
- Shun Yang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 China
| | - Idefonce Mkingule
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 China
| | - Long Liu
- Zhejiang Development & Planning Institute, Hangzhou, 310012 China
| | - Wenqi Chen
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 China
| | - Xiangyu Yuan
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 China
| | - Zixuan Ma
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 China
| | - Liang Liang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 China
| | - Shichao Qian
- Huzhou Baijiayu Biotech Co., Ltd., Huzhou, 313000 China
| | - Mengmeng Huang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 China
| | - Hui Fei
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 China
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11
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Jakt LM, Dubin A, Johansen SD. Intron size minimisation in teleosts. BMC Genomics 2022; 23:628. [PMID: 36050638 PMCID: PMC9438311 DOI: 10.1186/s12864-022-08760-w] [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: 03/09/2021] [Accepted: 07/13/2022] [Indexed: 11/17/2022] Open
Abstract
Background Spliceosomal introns are parts of primary transcripts that are removed by RNA splicing. Although introns apparently do not contribute to the function of the mature transcript, in vertebrates they comprise the majority of the transcribed region increasing the metabolic cost of transcription. The persistence of long introns across evolutionary time suggests functional roles that can offset this metabolic cost. The teleosts comprise one of the largest vertebrate clades. They have unusually compact and variable genome sizes and provide a suitable system for analysing intron evolution. Results We have analysed intron lengths in 172 vertebrate genomes and show that teleost intron lengths are relatively short, highly variable and bimodally distributed. Introns that were long in teleosts were also found to be long in mammals and were more likely to be found in regulatory genes and to contain conserved sequences. Our results argue that intron length has decreased in parallel in a non-random manner throughout teleost evolution and represent a deviation from the ancestral state. Conclusion Our observations indicate an accelerated rate of intron size evolution in the teleosts and that teleost introns can be divided into two classes by their length. Teleost intron sizes have evolved primarily as a side-effect of genome size evolution and small genomes are dominated by short introns (<256 base pairs). However, a non-random subset of introns has resisted this process across the teleosts and these are more likely have functional roles in all vertebrate clades. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-022-08760-w).
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Affiliation(s)
- Lars Martin Jakt
- Faculty for bioscience and aquaculture, Nord University, Universitetsalléen 11, Bodoe, 8026, Norway.
| | - Arseny Dubin
- Faculty for bioscience and aquaculture, Nord University, Universitetsalléen 11, Bodoe, 8026, Norway.,Currently at: Parental Investment and Immune Dynamics, GEOMAR Helmholtz Centre for Ocean Research, Düsternbrookerweg 20, Kiel, D-24105, Germany
| | - Steinar Daae Johansen
- Faculty for bioscience and aquaculture, Nord University, Universitetsalléen 11, Bodoe, 8026, Norway
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12
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Haugland GT, Rønneseth A, Gundersen L, Lunde HS, Nordland K, Wergeland HI. Neutrophils in Atlantic salmon (Salmo salar L.) are MHC class II+ and secret IL-12p40 upon bacterial exposure. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Guslund NC, Krabberød AK, Nørstebø SF, Solbakken MH, Jakobsen KS, Johansen FE, Qiao SW. Lymphocyte subsets in Atlantic cod (Gadus morhua) interrogated by single-cell sequencing. Commun Biol 2022; 5:689. [PMID: 35821077 PMCID: PMC9276791 DOI: 10.1038/s42003-022-03645-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/27/2022] [Indexed: 11/30/2022] Open
Abstract
Atlantic Cod (Gadus morhua) has lost the major histocompatibility complex class II presentation pathway. We recently identified CD8-positive T cells, B cells, and plasma cells in cod, but further characterisation of lymphocyte subsets is needed to elucidate immune adaptations triggered by the absence of CD4-positive T lymphocytes. Here, we use single-cell RNA sequencing to examine the lymphocyte heterogeneity in Atlantic cod spleen. We describe five T cell subsets and eight B cell subsets and propose a B cell trajectory of differentiation. Notably, we identify a subpopulation of T cells that are CD8-negative. Most of the CD8-negative T lymphocytes highly express the homologue of monocyte chemotactic protein 1b, and another subset of CD8-negative T lymphocytes express the homologue of the scavenger receptor m130. Uncovering the multiple lymphocyte cell sub-clusters reveals the different immune states present within the B and T cell populations, building a foundation for further work. Single-cell sequencing of naïve and vaccinated Atlantic Cod uncovers multiple B and T lymphocyte subsets including a subset of T lymphocytes expressing neither CD4 or CD8 and reveals different immune states present within B and T cell populations.
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Affiliation(s)
- Naomi Croft Guslund
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences and the Department of Immunology, University of Oslo, Oslo, Norway.
| | - Anders K Krabberød
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences and the Department of Immunology, University of Oslo, Oslo, Norway.,Section for Genetics and Evolutionary Biology, Department of Biosciences and the Department of Immunology, University of Oslo, Oslo, Norway
| | - Simen F Nørstebø
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Monica Hongrø Solbakken
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences and the Department of Immunology, University of Oslo, Oslo, Norway
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences and the Department of Immunology, University of Oslo, Oslo, Norway
| | - Finn-Eirik Johansen
- Section for Physiology and Cell Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Shuo-Wang Qiao
- Department of Immunology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
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14
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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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15
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Parker J, Roth O. Comparative assessment of immunological tolerance in fish with natural immunodeficiency. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 132:104393. [PMID: 35276317 DOI: 10.1016/j.dci.2022.104393] [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: 12/13/2021] [Revised: 02/24/2022] [Accepted: 03/05/2022] [Indexed: 06/14/2023]
Abstract
Natural occurrences of immunodeficiency by definition should lead to compromised immune function. The major histocompatibility complexes (MHC) are key components of the vertebrate adaptive immune system, charged with mediating allorecognition and antigen presentation functions. To this end, the genomic loss of the MHC II pathway in Syngnathus pipefishes raises questions regarding their immunological vigilance and allorecognition capabilities. Utilising allograft and autograft fin-transplants, we compared the allorecognition immune responses of two pipefish species, with (Nerophis ophidion) and without (Syngnathus typhle) a functional MHC II. Transcriptome-wide assessments explored the immunological tolerance and potential compensatory measures occupying the role of the absent MHC II. Visual observations suggested a more acute rejection response in N. ophidion allografts compared with S. typhle allografts. Differentially expressed genes involved in innate immunity, angiogenesis and tissue recovery were identified among transplantees. The intriguing upregulation of the cytotoxic T-cell implicated gzma in S. typhle allografts, suggests a prominent MHC I related response, which may compensate for the MHC II and CD4 loss. MHC I related downregulation in N. ophidion autografts hints at an immunological tolerance related reaction. These findings may indicate alternative measures evolved to cope with the MHC II genomic loss enabling the maintenance of appropriate tolerance levels. This study provides intriguing insights into the immune and tissue recovery mechanisms associated with syngnathid transplantation, and can be a useful reference for future studies focusing on transplantation transcriptomics in non-model systems.
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Affiliation(s)
- Jamie Parker
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, D-24105, Kiel, Germany; Marine Evolutionary Biology, Christian-Albrechts-University, D-24118, Kiel, Germany.
| | - Olivia Roth
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, D-24105, Kiel, Germany; Marine Evolutionary Biology, Christian-Albrechts-University, D-24118, Kiel, Germany
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16
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Wong ATC, Lam DK, Poon ESK, Chan DTC, Sin SYW. Intra-specific copy number variation of MHC class II genes in the Siamese fighting fish. Immunogenetics 2022; 74:327-346. [PMID: 35229174 DOI: 10.1007/s00251-022-01255-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 02/04/2022] [Indexed: 11/28/2022]
Abstract
Duplicates of genes for major histocompatibility complex (MHC) molecules can be subjected to selection independently and vary markedly in their evolutionary rates, sequence polymorphism, and functional roles. Therefore, without a thorough understanding of their copy number variation (CNV) in the genome, the MHC-dependent fitness consequences within a species could be misinterpreted. Studying the intra-specific CNV of this highly polymorphic gene, however, has long been hindered by the difficulties in assigning alleles to loci and the lack of high-quality genomic data. Here, using the high-quality genome of the Siamese fighting fish (Betta splendens), a model for mate choice studies, and the whole-genome sequencing (WGS) data of 17 Betta species, we achieved locus-specific amplification of their three classical MHC class II genes - DAB1, DAB2, and DAB3. By performing quantitative PCR and depth-of-coverage analysis using the WGS data, we revealed intra-specific CNV at the DAB3 locus. We identified individuals that had two allelic copies (i.e., heterozygous or homozygous) or one allele (i.e., hemizygous) and individuals without this gene. The CNV was due to the deletion of a 20-kb-long genomic region harboring both the DAA3 and DAB3 genes. We further showed that the three DAB genes were under different modes of selection, which also applies to their corresponding DAA genes that share similar pattern of polymorphism. Our study demonstrates a combined approach to study CNV within a species, which is crucial for the understanding of multigene family evolution and the fitness consequences of CNV.
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Affiliation(s)
- Anson Tsz Chun Wong
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Derek Kong Lam
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Emily Shui Kei Poon
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - David Tsz Chung Chan
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Simon Yung Wa Sin
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China.
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17
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Parker J, Guslund NC, Jentoft S, Roth O. Characterization of Pipefish Immune Cell Populations Through Single-Cell Transcriptomics. Front Immunol 2022; 13:820152. [PMID: 35154138 PMCID: PMC8828949 DOI: 10.3389/fimmu.2022.820152] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/10/2022] [Indexed: 01/16/2023] Open
Abstract
Teleost adaptive immune systems have evolved with more flexibility than previously assumed. A particularly enigmatic system to address immune system modifications in the evolutionary past is represented by the Syngnathids, the family of pipefishes, seahorses and seadragons. These small fishes with their unique male pregnancy have lost the spleen as an important immune organ as well as a functional major histocompatibility class II (MHC II) pathway. How these evolutionary changes have impacted immune cell population dynamics have up to this point remained unexplored. Here, we present the first immune cell repertoire characterization of a syngnathid fish (Syngnathus typhle) using single-cell transcriptomics. Gene expression profiles of individual cells extracted from blood and head-kidney clustered in twelve putative cell populations with eight belonging to those with immune function. Upregulated cell marker genes identified in humans and teleosts were used to define cell clusters. While the suggested loss of CD4+ T-cells accompanied the loss of the MHC II pathway was supported, the upregulation of specific subtype markers within the T-cell cluster indicates subpopulations of regulatory T-cells (il2rb) and cytotoxic T-cells (gzma). Utilizing single-cell RNA sequencing this report is the first to characterize immune cell populations in syngnathids and provides a valuable foundation for future cellular classification and experimental work within the lineage.
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Affiliation(s)
- Jamie Parker
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Marine Evolutionary Biology, Christian-Albrechts-University, Kiel, Germany
| | - Naomi Croft Guslund
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway.,Department of Immunology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Olivia Roth
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Marine Evolutionary Biology, Christian-Albrechts-University, Kiel, Germany
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18
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Buckley KM, Dooley H. Immunological Diversity Is a Cornerstone of Organismal Defense and Allorecognition across Metazoa. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:203-211. [PMID: 35017209 DOI: 10.4049/jimmunol.2100754] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/16/2021] [Indexed: 01/09/2023]
Abstract
The ongoing arms race between hosts and microbes has fueled the evolution of novel strategies for diversifying the molecules involved in immune responses. Characterization of immune systems from an ever-broadening phylogenetic range of organisms reveals that there are many mechanisms by which this diversity can be generated and maintained. Diversification strategies operate at the level of populations, genomes, genes, and even individual transcripts. Lineage-specific innovations have been cataloged within the immune systems of both invertebrates and vertebrates. Furthermore, somatic diversification of immune receptor genes has now been described in jawless vertebrates and some invertebrate species. In addition to pathogen detection, immunological diversity plays important roles in several distinct allorecognition systems. In this Brief Review, we highlight some of the evolutionary innovations employed by a variety of metazoan species to generate the molecular diversity required to detect a vast array of molecules in the context of both immune response and self/nonself-recognition.
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Affiliation(s)
| | - Helen Dooley
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Institute of Marine & Environmental Technology, Baltimore, MD
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19
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Isakov N. Histocompatibility and Reproduction: Lessons from the Anglerfish. LIFE (BASEL, SWITZERLAND) 2022; 12:life12010113. [PMID: 35054506 PMCID: PMC8780861 DOI: 10.3390/life12010113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/06/2022] [Accepted: 01/08/2022] [Indexed: 11/16/2022]
Abstract
Reproduction in certain deep-sea anglerfishes involves the permanent attachment of dwarf males to much larger females and fusion of their tissues leading to the establishment of a shared circulatory system. This unusual phenomenon of sexual parasitism enables anglerfishes to maximize reproductive success in the vast and deep oceans, where females and males otherwise rarely meet. An even more surprising phenomenon relates to the observation that joining of genetically disparate male and female anglerfishes does not evoke a strong anti-graft immune rejection response, which occurs in vertebrates following allogeneic parabiosis. Recent studies demonstrated that the evolutionary processes that led to the unique mating strategy of anglerfishes coevolved with genetic changes that resulted in loss of functional genes encoding critical components of the adaptive immune system. These genetic alterations enabled anglerfishes to tolerate the histoincompatible tissue antigens of their mate and prevent the occurrence of reciprocal graft rejection responses. While the exact mechanisms by which anglerfishes defend themselves against pathogens have not yet been deciphered, it is speculated that during evolution, anglerfishes adopted new immune strategies that compensate for the loss of B and T lymphocyte functions and enable them to resist infection by pathogens.
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Affiliation(s)
- Noah Isakov
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben Gurion University of the Negev, P.O. Box 653, Beer Sheva 84105, Israel
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20
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Recurrent expansions of B30.2-associated immune receptor families in fish. Immunogenetics 2021; 74:129-147. [PMID: 34850255 DOI: 10.1007/s00251-021-01235-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 11/16/2021] [Indexed: 12/12/2022]
Abstract
B30.2 domains, also known as PRY/SPRY, are key components of specific subsets of two large families of proteins involved in innate immunity: the tripartite motif proteins (TRIMs) and the Nod-like receptors (NLRs). TRIM proteins are important, often inducible factors of antiviral innate immunity, targeting multiple steps of viral cycles through a variety of mechanisms. NLRs prime and regulate systemic innate defenses, especially against bacteria, and control inflammation. Large TRIM and NLR subsets characterized by the presence of a B30.2 domain have been reported from a few fish species including zebrafish and seem to be strongly prone to gene duplication/expansion. Here, we performed a large-scale survey of these receptors across about 150 fish genomes, focusing on ray-finned fishes. We assessed the number and genomic distribution of domains and domain combinations associated with TRIMs, NLRs, and other genes containing B30.2 domains and looked for gene expansion patterns across fish groups. We then used a model to test the impact of taxonomy, genome size, and environmental variables on the copy numbers of these genes. Our findings reveal novel domain structures, clade-specific gains and losses. They also assist with the timing of the gene expansions, reveal patterns associated with the MHC, and lay the groundwork for further studies delving deeper into the forces that drive the copy number variation of immune genes on a species level.
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21
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Aguirre‐Sarabia I, Díaz‐Arce N, Pereda‐Agirre I, Mendibil I, Urtizberea A, Gerritsen HD, Burns F, Holmes I, Landa J, Coscia I, Quincoces I, Santurtún M, Zanzi A, Martinsohn JT, Rodríguez‐Ezpeleta N. Evidence of stock connectivity, hybridization, and misidentification in white anglerfish supports the need of a genetics-informed fisheries management framework. Evol Appl 2021; 14:2221-2230. [PMID: 34603494 PMCID: PMC8477593 DOI: 10.1111/eva.13278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/29/2021] [Accepted: 07/02/2021] [Indexed: 11/27/2022] Open
Abstract
Understanding population connectivity within a species as well as potential interactions with its close relatives is crucial to define management units and to derive efficient management actions. However, although genetics can reveal mismatches between biological and management units and other relevant but hidden information such as species misidentification or hybridization, the uptake of genetic methods by the fisheries management process is far from having been consolidated. Here, we have assessed the power of genetics to better understand the population connectivity of white (Lophius piscatorius) and its interaction with its sister species, the black anglerfish (Lophius budegassa). Our analyses, based on thousands of genome-wide single nucleotide polymorphisms, show three findings that are crucial for white anglerfish management. We found (i) that white anglerfish is likely composed of a single panmictic population throughout the Northeast Atlantic, challenging the three-stock based management, (ii) that a fraction of specimens classified as white anglerfish using morphological characteristics are genetically identified as black anglerfish (L. budegassa), and iii) that the two Lophius species naturally hybridize leading to a population of hybrids of up to 20% in certain areas. Our results set the basics for a genetics-informed white anglerfish assessment framework that accounts for stock connectivity, revises and establishes new diagnostic characters for Lophius species identification, and evaluates the effect of hybrids in the current and future assessments of the white anglerfish. Furthermore, our study contributes to provide additional evidence of the potentially negative consequences of ignoring genetic data for assessing fisheries resources.
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Affiliation(s)
- Imanol Aguirre‐Sarabia
- Marine ResearchAZTI Basque Research and Technology Alliance (BRTA)SukarrietaBizkaiaSpain
| | - Natalia Díaz‐Arce
- Marine ResearchAZTI Basque Research and Technology Alliance (BRTA)SukarrietaBizkaiaSpain
| | - Iker Pereda‐Agirre
- Marine ResearchAZTI Basque Research and Technology Alliance (BRTA)SukarrietaBizkaiaSpain
| | - Iñaki Mendibil
- Marine ResearchAZTI Basque Research and Technology Alliance (BRTA)SukarrietaBizkaiaSpain
| | - Agurtzane Urtizberea
- Marine ResearchAZTI Basque Research and Technology Alliance (BRTA)SukarrietaBizkaiaSpain
| | | | - Finlay Burns
- Marine LaboratoryMarine Scotland ScienceAberdeenshireUK
| | - Ian Holmes
- Lowestoft LaboratoryCentre for Environment, Fisheries and Aquaculture ScienceLowestoftSuffolkUK
| | - Jorge Landa
- Centro Oceanográfico de SantanderInstituto Español de Oceanografía (IEO)SantanderSpain
| | - Ilaria Coscia
- School of Science, Engineering and EnvironmentUniversity of SalfordSalfordUK
| | - Iñaki Quincoces
- Marine ResearchAZTI Basque Research and Technology Alliance (BRTA)SukarrietaBizkaiaSpain
| | - Marina Santurtún
- Marine ResearchAZTI Basque Research and Technology Alliance (BRTA)SukarrietaBizkaiaSpain
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22
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Oral Immunization of Larvae and Juvenile of Lumpfish ( Cyclopterus lumpus) against Vibrio anguillarum Does Not Influence Systemic Immunity. Vaccines (Basel) 2021; 9:vaccines9080819. [PMID: 34451944 PMCID: PMC8402551 DOI: 10.3390/vaccines9080819] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 12/31/2022] Open
Abstract
Vibrio anguillarum, a marine bacterial pathogen that causes vibriosis, is a recurrent pathogen of lumpfish (Cyclopterus lumpus). Lumpfish is utilized as a cleaner fish in the Atlantic salmon (Salmo salar) aquaculture in the North Atlantic region because of its ability to visualize and prey on the ectoparasite sea lice (Lepeophtheirus salmonis) on the skin of Atlantic salmon, and its performance in cold environments. Lumpfish immunity is critical for optimal performance and sea lice removal. Oral vaccine delivery at a young age is the desired method for fish immunization because is easy to use, reduces fish stress during immunization, and can be applied on a large scale while the fish are at a young age. However, the efficacy of orally delivered inactivated vaccines is controversial. In this study, we evaluated the effectiveness of a V. anguillarum bacterin orally delivered to cultured lumpfish and contrasted it to an intraperitoneal (i.p.) boost delivery. We bio-encapsulated V. anguillarum bacterin in Artemia salina live-feed and orally immunized lumpfish larvae. Vaccine intake and immune response were evaluated by microscopy and quantitative polymerase chain reaction (qPCR) analysis, respectively. qPCR analyses showed that the oral immunization of lumpfish larvae resulted in a subtle stimulation of canonical immune transcripts such as il8b, il10, igha, ighmc, ighb, ccl19, ccl20, cd8a, cd74, ifng, and lgp2. Nine months after oral immunization, one group was orally boosted, and a second group was both orally and i.p. boosted. Two months after boost immunization, lumpfish were challenged with V. anguillarum (7.8 × 105 CFU dose−1). Orally boosted fish showed a relative percentage of survival (RPS) of 2%. In contrast, the oral and i.p. boosted group showed a RPS of 75.5% (p < 0.0001). V. anguillarum bacterin that had been orally delivered was not effective in lumpfish, which is in contrast to the i.p. delivered bacterin that protected the lumpfish against vibriosis. This suggests that orally administered V. anguillarum bacterin did not reach the deep lymphoid tissues, either in the larvae or juvenile fish, therefore oral immunization was not effective. Oral vaccines that are capable of crossing the epithelium and reach deep lymphoid tissues are required to confer an effective protection to lumpfish against V. anguillarum
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23
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Gouania willdenowi is a teleost fish without immunoglobulin genes. Mol Immunol 2021; 132:102-107. [PMID: 33578305 DOI: 10.1016/j.molimm.2021.01.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 02/04/2023]
Abstract
Immunoglobulin (Ig) genes encode antibodies in jawed vertebrates. They are essential elements of the adaptive immune response. Ig exists in soluble form or as part of the B cell membrane antigen receptor (BCR). Studies of Ig genes in fish genomes reveal the absence of Ig genes in Gouania willdenowi by deletion of the entire Ig locus from the canonical chromosomal region. The genes coding for integral BCR proteins, CD79a and CD79b, are also absent. Genes exist for T α/β lymphocyte receptors but not for the T γ/δ receptors. The results of the genomic analysis are independently corroborated with RNA-Seq transcriptomes from other Gobiesocidae species. From the transcriptome studies, Ig is also absent from these other Gobiesocidae species, Acyrtus sp. and Tomicodon sp. Present evidence suggests that Ig is missing from all species of the Gobiesocidae family.
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24
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Mirete-Bachiller S, Olivieri DN, Gambón-Deza F. Immunoglobulin T genes in Actinopterygii. FISH & SHELLFISH IMMUNOLOGY 2021; 108:86-93. [PMID: 33279606 DOI: 10.1016/j.fsi.2020.11.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/21/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
In teleost fishes, there are three immunoglobulin isotypes named immunoglobulin M (IgM), D (IgD), and T (IgT). IgT was the last to be described in teleost fishes, and it is specific to them. From recent fish genomes, we identified and studied the immunoglobulin heavy chain genes in Actinopterygii. For this analysis, a custom bioinformatics and machine learning pipeline, we call CHfinder, was developed that identifies the exons coding for the CH domains of fish immunoglobulins. Some IgT in teleost and holostean fish found from this systematic study have not been previously described. Phylogenetic analysis of the deduced amino acid sequences of the IgT CH1 exons reveals they are similar to the CH1 of IgM. This analysis also shows that the other three domains (CH2, CH3, and CH4) were not the result of recent IgM duplication processes in Actinopterygii, demonstrating that it is an immunoglobulin of earlier origin. The bioinformatics program, CHfinder, is publicly available at https://github.com/compimmuno/CHfinder.
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Affiliation(s)
| | - David N Olivieri
- Centro de Intelixencia Artificial, Ourense, Spain; ESE Informatica, Universidade de Vigo, Spain.
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25
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Grimholt U, Lukacs M. Fate of MHCII in salmonids following 4WGD. Immunogenetics 2020; 73:79-91. [PMID: 33225379 PMCID: PMC7862078 DOI: 10.1007/s00251-020-01190-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/11/2020] [Indexed: 12/27/2022]
Abstract
Major histocompatibility complex (MHC) genes are key players in the adaptive immunity providing a defense against invading pathogens. Although the basic structures are similar when comparing mammalian and teleost MHC class II (MHCII) molecules, there are also clear-cut differences. Based on structural requirements, the teleosts non-classical MHCII molecules do not comply with a function similar to the human HLA-DM and HLA-DO, i.e., assisting in peptide loading and editing of classical MHCII molecules. We have previously studied the evolution of teleost class II genes identifying various lineages and tracing their phylogenetic occurrence back to ancient ray-finned fishes. We found no syntenic MHCII regions shared between cyprinids, salmonids, and neoteleosts, suggesting regional instabilities. Salmonids have experienced a unique whole genome duplication 94 million years ago, providing them with the opportunity to experiment with gene duplicates. Many salmonid genomes have recently become available, and here we set out to investigate how MHCII has evolved in salmonids using Northern pike as a diploid sister phyla, that split from the salmonid lineage prior to the fourth whole genome duplication (4WGD) event. We identified 120 MHCII genes in pike and salmonids, ranging from 11 to 20 genes per species analyzed where DB-group genes had the most expansions. Comparing the MHC of Northern pike with that of Atlantic salmon and other salmonids species provides a tale of gene loss, translocations, and genome rearrangements.
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Affiliation(s)
- Unni Grimholt
- Norwegian Veterinary Institute, P.O. Box 8146 Dep, 0033, Oslo, Norway.
| | - Morten Lukacs
- Norwegian Veterinary Institute, P.O. Box 8146 Dep, 0033, Oslo, Norway
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26
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Swann JB, Holland SJ, Petersen M, Pietsch TW, Boehm T. The immunogenetics of sexual parasitism. Science 2020; 369:1608-1615. [PMID: 32732279 DOI: 10.1126/science.aaz9445] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 07/17/2020] [Indexed: 01/29/2023]
Abstract
Sexual parasitism has evolved as a distinctive mode of reproduction among deep-sea anglerfishes. The permanent attachment of males to host females observed in these species represents a form of anatomical joining, which is otherwise unknown in nature. Pronounced modifications to immune facilities are associated with this reproductive trait. The genomes of species with temporarily attaching males lack functional aicda genes that underpin affinity maturation of antibodies. Permanent attachment is associated with additional alterations, culminating in the loss of functional rag genes in some species, abolishing somatic diversification of antigen receptor genes, the hallmark of canonical adaptive immunity. In anglerfishes, coevolution of innate and adaptive immunity has been disentangled, implying that an alternative form of immunity supported the emergence of this evolutionarily successful group of vertebrates.
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Affiliation(s)
- Jeremy B Swann
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany.
| | - Stephen J Holland
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany
| | - Malte Petersen
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany
| | - Theodore W Pietsch
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98105-5020, USA
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany.
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27
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Dubin A, Jørgensen TE, Jakt LM, Johansen SD. The mitochondrial transcriptome of the anglerfish Lophius piscatorius. BMC Res Notes 2019; 12:800. [PMID: 31823814 PMCID: PMC6905026 DOI: 10.1186/s13104-019-4835-6] [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: 08/04/2019] [Accepted: 11/29/2019] [Indexed: 01/22/2023] Open
Abstract
Objective Analyze key features of the anglerfish Lophius piscatorius mitochondrial transcriptome based on high-throughput total RNA sequencing. Results We determined the complete mitochondrial DNA and corresponding transcriptome sequences of L. piscatorius. Key features include highly abundant mitochondrial ribosomal RNAs (10–100 times that of mRNAs), and that cytochrome oxidase mRNAs appeared > 5 times more abundant than both NADH dehydrogenase and ATPase mRNAs. Unusual for a vertebrate mitochondrial mRNA, the polyadenylated COI mRNA was found to harbor a 75 nucleotide 3′ untranslated region. The mitochondrial genome expressed several non-canonical genes, including the long noncoding RNAs lncCR-H, lncCR-L and lncCOI. Whereas lncCR-H and lncCR-L mapped to opposite strands in a non-overlapping organization within the control region, lncCOI appeared novel among vertebrates. We found lncCOI to be a highly abundant mitochondrial RNA in antisense to the COI mRNA. Finally, we present the coding potential of a humanin-like peptide within the large subunit ribosomal RNA.
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Affiliation(s)
- Arseny Dubin
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Tor Erik Jørgensen
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Lars Martin Jakt
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Steinar Daae Johansen
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway.
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28
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Dubin A, Jørgensen TE, Moum T, Johansen SD, Jakt LM. Complete loss of the MHC II pathway in an anglerfish, Lophius piscatorius. Biol Lett 2019; 15:20190594. [PMID: 31594494 PMCID: PMC6832177 DOI: 10.1098/rsbl.2019.0594] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Genome studies in fish provide evidence for the adaptability of the vertebrate immune system, revealing alternative immune strategies. The reported absence of the major compatibility complex (MHC) class II pathway components in certain species of pipefish (genus Syngnathus) and cod-like fishes (order Gadiformes) is of particular interest. The MHC II pathway is responsible for immunization and defence against extracellular threats through the presentation of exogenous peptides to T helper cells. Here, we demonstrate the absence of all genes encoding MHC II components (CD4, CD74 A/B, and both classical and non-classical MHC II α/β) in the genome of an anglerfish, Lophius piscatorius, indicating loss of the MHC II pathway. By contrast, it has previously been reported that another anglerfish, Antennarius striatus, retains all MHC II genes, placing the loss of MHC II in the Lophius clade to their most recent common ancestor. In the three taxa where MHC II loss has occurred, the gene loss has been restricted to four or five core MHC II components, suggesting that, in teleosts, only these genes have functions that are restricted to the MHC II pathway.
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Affiliation(s)
- Arseny Dubin
- Genomics group, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Tor Erik Jørgensen
- Genomics group, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Truls Moum
- Genomics group, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Steinar Daae Johansen
- Genomics group, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Lars Martin Jakt
- Genomics group, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
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