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Adeyemi OD, Tian Y, Khwatenge CN, Grayfer L, Sang Y. Molecular diversity and functional implication of amphibian interferon complex: Remarking immune adaptation in vertebrate evolution. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 140:104624. [PMID: 36586430 DOI: 10.1016/j.dci.2022.104624] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 12/07/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Cross-species comparison of vertebrate genomes has unraveled previously unknown complexities of interferon (IFN) systems in amphibian species. Recent genomic curation revealed that amphibian species have evolved expanded repertoires of four types of intron-containing IFN genes akin to those seen in jawed fish, intronless type I IFNs and intron-containing type III IFNs akin to those seen in amniotes, as well as uniquely intronless type III IFNs. This appears to be the case with at least ten analyzed amphibian species; with distinct species encoding diverse repertoires of these respective IFN gene subsets. Amphibians represent a key stage in vertebrate evolution, and in this context offer a unique perspective into the divergent and converged pathways leading to the emergence of distinct IFN families and groups. Recent studies have begun to unravel the roles of amphibian IFNs during these animals' immune responses in general and during their antiviral responses, in particular. However, the pleiotropic potentials of these highly expanded amphibian IFN repertoires warrant further studies. Based on recent reports and our omics analyses using Xenopus models, we posit that amphibian IFN complex may have evolved novel functions, as indicated by their extensive molecular diversity. Here, we provide an overview and an update of the present understanding of the amphibian IFN complex in the context of the evolution of vertebrate immune systems. A greater understanding of the amphibian IFN complex will grant new perspectives on the evolution of vertebrate immunity and may yield new measures by which to counteract the global amphibian declines.
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Affiliation(s)
- Oluwaseun D Adeyemi
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Boulevard, Nashville, TN, USA
| | - Yun Tian
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Boulevard, Nashville, TN, USA
| | - Collins N Khwatenge
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Boulevard, Nashville, TN, USA
| | - Leon Grayfer
- Department of Biological Sciences, George Washington University, Washington, DC, USA
| | - Yongming Sang
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Boulevard, Nashville, TN, USA.
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Kaganer AW, Ossiboff RJ, Keith NI, Schuler KL, Comizzoli P, Hare MP, Fleischer RC, Gratwicke B, Bunting EM. Immune priming prior to pathogen exposure sheds light on the relationship between host, microbiome and pathogen in disease. ROYAL SOCIETY OPEN SCIENCE 2023; 10:220810. [PMID: 36756057 PMCID: PMC9890126 DOI: 10.1098/rsos.220810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Dynamic interactions between host, pathogen and host-associated microbiome dictate infection outcomes. Pathogens including Batrachochytrium dendrobatidis (Bd) threaten global biodiversity, but conservation efforts are hindered by limited understanding of amphibian host, Bd and microbiome interactions. We conducted a vaccination and infection experiment using Eastern hellbender salamanders (Cryptobranchus alleganiensis alleganiensis) challenged with Bd to observe infection, skin microbial communities and gene expression of host skin, pathogen and microbiome throughout the experiment. Most animals survived high Bd loads regardless of their vaccination status and vaccination did not affect pathogen load, but host gene expression differed based on vaccination. Oral vaccination (exposure to killed Bd) stimulated immune gene upregulation while topically and sham-vaccinated animals did not significantly upregulate immune genes. In early infection, topically vaccinated animals upregulated immune genes but orally and sham-vaccinated animals downregulated immune genes. Bd increased pathogenicity-associated gene expression in late infection when Bd loads were highest. The microbiome was altered by Bd, but there was no correlation between anti-Bd microbe abundance or richness and pathogen burden. Our observations suggest that hellbenders initially generate a vigorous immune response to Bd, which is ineffective at controlling disease and is subsequently modulated. Interactions with antifungal skin microbiota did not influence disease progression.
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Affiliation(s)
- Alyssa W. Kaganer
- Department of Natural Resources and the Environment, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
| | - Robert J. Ossiboff
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Nicole I. Keith
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Biology Department, Hamilton College, Clinton, NY, 13323, USA
| | - Krysten L. Schuler
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Pierre Comizzoli
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Matthew P. Hare
- Department of Natural Resources and the Environment, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Robert C. Fleischer
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Brian Gratwicke
- Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, 22630, USA
| | - Elizabeth M. Bunting
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
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Wang X, Xie Y, Hu W, Wei Z, Wei X, Yuan H, Yao H, Dunxue C. Transcriptome characterization and SSR discovery in the giant spiny frog Quasipaa spinosa. Gene 2022; 842:146793. [PMID: 35952842 DOI: 10.1016/j.gene.2022.146793] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 07/31/2022] [Accepted: 08/05/2022] [Indexed: 11/04/2022]
Abstract
The giant spiny frog Quasipaa spinosa (Amphibia: Ranidae) is a large unique frog species found mainly in southern China with a low amount of fat and high protein, and it has become one of the most important aquaculture animal species in China. To better understand its genetic background and screen potential molecular markers for artificial breeding and species conservation, we constructed an expression profile of Q. spinosa with high-throughput RNA sequencing and acquired potential SSR markers. Approximately 81.7 Gb of data and 93,887 unigenes were generated. The transcriptome contains 2085 (80.7 %) complete BUSCOs, suggesting that our assembly methods were effective and accurate.These unigenes were functionally classified using 7 functional databases, yielding 17,482 Pfam-, 12,752 Sting-, 17,526 KEGG-, 24,341 Swiss-Prot-, 28,604 Nr-, 16,287 GO- and 12,752 COG-annotated unigenes. Among several amphibian species, Q. spinosa unigenes had the highest number of hits to Xenopus tropicalis (35.25 %), followed by Xenopus laevis (12.68 %). 1417 unigenes were assigned to the immune system. In addition, a total of 33,019 candidate SSR markers were identified from the constructed library. Further tests with 20 loci and 118 large-scale breeding specimens gathered from four culture farms in China showed that 15 (75 %) loci were polymorphic, with the number of alleles per locus varying from 3 to 9 (mean of 4.3). The PIC values for the SSR markers ranged from 0.19 to 0.82, with an average value of 0.43, indicating moderate polymorphism in Q. spinosa. The transcriptomic profile and SSR repertoire obtained in the present study will facilitate population genetic studies and the selective breeding of amphibian species.
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Affiliation(s)
- Xiaodong Wang
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China; Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha 410128, China
| | - Yongguang Xie
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Wei Hu
- School of Animal Science, Yangtze University, Jingzhou 434020, China
| | - Zhaoyu Wei
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Xiuying Wei
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Hong Yuan
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Hongyan Yao
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China
| | - Chen Dunxue
- College of Animal Science/Key Laboratory of Animal Genetics and Breeding and Reproduction of Plateau and Mountain Animals of Guizhou University, Guiyang, China.
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Rollins-Smith LA. Global Amphibian Declines, Disease, and the Ongoing Battle between Batrachochytrium Fungi and the Immune System. HERPETOLOGICA 2020. [DOI: 10.1655/0018-0831-76.2.178] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Louise A. Rollins-Smith
- Departments of Pathology, Microbiology and Immunology and Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
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Tian Y, Jennings J, Gong Y, Sang Y. Xenopus Interferon Complex: Inscribing the Amphibiotic Adaption and Species-Specific Pathogenic Pressure in Vertebrate Evolution? Cells 2019; 9:E67. [PMID: 31888074 PMCID: PMC7016992 DOI: 10.3390/cells9010067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 12/24/2022] Open
Abstract
Several recent studies have revealed previously unknown complexity of the amphibian interferon (IFN) system. Being unique in vertebrate animals, amphibians not only conserve and multiply the fish-like intron-containing IFN genes, but also rapidly evolve amniote-like intronless IFN genes in each tested species. We postulate that the amphibian IFN system confers an essential model to study vertebrate immune evolution in molecular and functional diversity to cope with unprecedented pathophysiological requirement during terrestrial adaption. Studies so far have ascribed a potential role of these IFNs in immune regulation against intracellular pathogens, particularly viruses; however, many knowledge gaps remain elusive. Based on recent reports about IFN's multifunctional properties in regulation of animal physiological and defense responses, we interpret that amphibian IFNs may evolve novel function pertinent to their superior molecular diversity. Such new function revealed by the emerging studies about antifungal and developmental regulation of amphibian IFNs will certainly promote our understanding of immune evolution in vertebrates to address current pathogenic threats causing amphibian decline.
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Affiliation(s)
| | | | | | - Yongming Sang
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN 37209, USA; (Y.T.); (J.J.); (Y.G.)
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Varga JFA, Bui-Marinos MP, Katzenback BA. Frog Skin Innate Immune Defences: Sensing and Surviving Pathogens. Front Immunol 2019; 9:3128. [PMID: 30692997 PMCID: PMC6339944 DOI: 10.3389/fimmu.2018.03128] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 12/18/2018] [Indexed: 01/26/2023] Open
Abstract
Amphibian skin is a mucosal surface in direct and continuous contact with a microbially diverse and laden aquatic and/or terrestrial environment. As such, frog skin is an important innate immune organ and first line of defence against pathogens in the environment. Critical to the innate immune functions of frog skin are the maintenance of physical, chemical, cellular, and microbiological barriers and the complex network of interactions that occur across all the barriers. Despite the global decline in amphibian populations, largely as a result of emerging infectious diseases, we understand little regarding the cellular and molecular mechanisms that underlie the innate immune function of amphibian skin and defence against pathogens. In this review, we discuss the structure, cell composition and cellular junctions that contribute to the skin physical barrier, the antimicrobial peptide arsenal that, in part, comprises the chemical barrier, the pattern recognition receptors involved in recognizing pathogens and initiating innate immune responses in the skin, and the contribution of commensal microbes on the skin to pathogen defence. We briefly discuss the influence of environmental abiotic factors (natural and anthropogenic) and pathogens on the immunocompetency of frog skin defences. Although some aspects of frog innate immunity, such as antimicrobial peptides are well-studied; other components and how they contribute to the skin innate immune barrier, are lacking. Elucidating the complex network of interactions occurring at the interface of the frog's external and internal environments will yield insight into the crucial role amphibian skin plays in host defence and the environmental factors leading to compromised barrier integrity, disease, and host mortality.
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Affiliation(s)
- Joseph F A Varga
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
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Identification of critical sex-biased genes in Andrias davidianus by de novo transcriptome. Mol Genet Genomics 2018; 294:287-299. [PMID: 30377773 DOI: 10.1007/s00438-018-1508-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 10/22/2018] [Indexed: 02/06/2023]
Abstract
The Chinese giant salamander Andrias davidianus is a protected amphibian with high nutritional and economic value. Understanding its sex determination mechanism is important for improving culture techniques and sex control in breeding. However, little information on the characterization of critical genes involved in sex is available. Herein, sequencing of ovary and test produced 40,783,222 and 46,128,902 raw reads, respectively, which were jointly assembled into 80,497 unigenes. Of these, 36,609 unigenes were annotated, of which 8907 were female-biased and 10,385 were male-biased. Several sex-related pathways were observed, including the Wnt signaling pathway. After elevated temperature and estrogen exposure, neomale and neofemale specimens were identified by a female-specific marker for the first time. RT-qPCR analysis showed the expression profile of ten selected sex-biased genes to be exhibited consistently in male and neomale and in female and neofemale, with the exception of the Amh and TfIIIa genes. Results suggested that these genes may play important roles in A. davidianus sex determination and gonad development. This provides a basis for further investigation of the molecular mechanisms of sex determination in amphibians.
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FEATURES OF ULTRAMICROSCOPIC STRUCTURES OF THE SPLEEN IN MARSH AND POOL FROGS. WORLD OF MEDICINE AND BIOLOGY 2018. [DOI: 10.26724/2079-8334-2018-2-64-194-198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Lau Q, Igawa T, Minei R, Kosch TA, Satta Y. Transcriptome analyses of immune tissues from three Japanese frogs (genus Rana ) reveals their utility in characterizing major histocompatibility complex class II. BMC Genomics 2017; 18:994. [PMID: 29281968 PMCID: PMC5745589 DOI: 10.1186/s12864-017-4404-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 12/19/2017] [Indexed: 01/05/2023] Open
Abstract
Background In Japan and East Asia, endemic frogs appear to be tolerant or not susceptible to chytridiomycosis, a deadly amphibian disease caused by the chytrid fungus Batrachochytridium dendrobatidis (Bd). Japanese frogs may have evolved mechanisms of immune resistance to pathogens such as Bd. This study characterizes immune genes expressed in various tissues of healthy Japanese Rana frogs. Results We generated transcriptome data sets of skin, spleen and blood from three adult Japanese Ranidae frogs (Japanese brown frog Rana japonica, the montane brown frog Rana ornativentris, and Tago’s brown frog Rana tagoi tagoi) as well as whole body of R. japonica and R. ornativentris tadpoles. From this, we identified tissue- and stage-specific differentially expressed genes; in particular, the spleen was most enriched for immune-related genes. A specific immune gene, major histocompatibility complex class IIB (MHC-IIB), was further characterized due to its role in pathogen recognition. We identified a total of 33 MHC-IIB variants from the three focal species (n = 7 individuals each), which displayed evolutionary signatures related to increased MHC variation, including balancing selection. Our supertyping analyses of MHC-IIB variants from Japanese frogs and previously studied frog species identified potential physiochemical properties of MHC-II that may be important for recognizing and binding chytrid-related antigens. Conclusions This is one of the first studies to generate transcriptomic resources for Japanese frogs, and contributes to further understanding the immunogenetic factors associated with resistance to infectious diseases in amphibians such as chytridiomycosis. Notably, MHC-IIB supertyping analyses identified unique functional properties of specific MHC-IIB alleles that may partially contribute to Bd resistance, and such properties provide a springboard for future experimental validation. Electronic supplementary material The online version of this article (10.1186/s12864-017-4404-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Quintin Lau
- Department of Evolutionary Studies of Biosystems, Sokendai, The Graduate University for Advanced Studies, Kamiyamaguchi 1560-35, Hayama, Kanagawa, 240-0193, Japan.
| | - Takeshi Igawa
- Amphibian Research Center, Hiroshima University, 1-3-1, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Ryuhei Minei
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura-cho 1266, Nagahama, Shiga, 526-0829, Japan
| | - Tiffany A Kosch
- One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, Sokendai, The Graduate University for Advanced Studies, Kamiyamaguchi 1560-35, Hayama, Kanagawa, 240-0193, Japan
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Garner TWJ, Schmidt BR, Martel A, Pasmans F, Muths E, Cunningham AA, Weldon C, Fisher MC, Bosch J. Mitigating amphibian chytridiomycoses in nature. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2016.0207. [PMID: 28080996 DOI: 10.1098/rstb.2016.0207] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2016] [Indexed: 12/11/2022] Open
Abstract
Amphibians across the planet face the threat of population decline and extirpation caused by the disease chytridiomycosis. Despite consensus that the fungal pathogens responsible for the disease are conservation issues, strategies to mitigate their impacts in the natural world are, at best, nascent. Reducing risk associated with the movement of amphibians, non-amphibian vectors and other sources of infection remains the first line of defence and a primary objective when mitigating the threat of disease in wildlife. Amphibian-associated chytridiomycete fungi and chytridiomycosis are already widespread, though, and we therefore focus on discussing options for mitigating the threats once disease emergence has occurred in wild amphibian populations. All strategies have shortcomings that need to be overcome before implementation, including stronger efforts towards understanding and addressing ethical and legal considerations. Even if these issues can be dealt with, all currently available approaches, or those under discussion, are unlikely to yield the desired conservation outcome of disease mitigation. The decision process for establishing mitigation strategies requires integrated thinking that assesses disease mitigation options critically and embeds them within more comprehensive strategies for the conservation of amphibian populations, communities and ecosystems.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.
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Affiliation(s)
- Trenton W J Garner
- Institute of Zoology, Zoological Society of London, Regents Park, NW1 4RY London, UK .,Unit for Environmental Research and Management, North-West University, Potchefstroom 2520, South Africa
| | - Benedikt R Schmidt
- Karch, Passage Maximilien-de-Meuron 6, 2000 Neuchâtel, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - An Martel
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Frank Pasmans
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Erin Muths
- U.S. Geological Survey, Fort Collins Science Fort Collins, 2150 Centre Avenue Building C, Fort Collins, CO 80526, USA
| | - Andrew A Cunningham
- Institute of Zoology, Zoological Society of London, Regents Park, NW1 4RY London, UK
| | - Che Weldon
- Unit for Environmental Research and Management, North-West University, Potchefstroom 2520, South Africa
| | - Matthew C Fisher
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Jaime Bosch
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006 Madrid, Spain
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Burns JA, Zhang H, Hill E, Kim E, Kerney R. Transcriptome analysis illuminates the nature of the intracellular interaction in a vertebrate-algal symbiosis. eLife 2017; 6:e22054. [PMID: 28462779 PMCID: PMC5413350 DOI: 10.7554/elife.22054] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 03/15/2017] [Indexed: 12/19/2022] Open
Abstract
During embryonic development, cells of the green alga Oophila amblystomatis enter cells of the salamander Ambystoma maculatum forming an endosymbiosis. Here, using de novo dual-RNA seq, we compared the host salamander cells that harbored intracellular algae to those without algae and the algae inside the animal cells to those in the egg capsule. This two-by-two-way analysis revealed that intracellular algae exhibit hallmarks of cellular stress and undergo a striking metabolic shift from oxidative metabolism to fermentation. Culturing experiments with the alga showed that host glutamine may be utilized by the algal endosymbiont as a primary nitrogen source. Transcriptional changes in salamander cells suggest an innate immune response to the alga, with potential attenuation of NF-κB, and metabolic alterations indicative of modulation of insulin sensitivity. In stark contrast to its algal endosymbiont, the salamander cells did not exhibit major stress responses, suggesting that the host cell experience is neutral or beneficial.
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Affiliation(s)
- John A Burns
- Division of Invertebrate Zoology, American Museum of Natural History, New York, United States
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, United States
| | - Huanjia Zhang
- Department of Biology, Gettysburg College, Gettysburg, United States
| | - Elizabeth Hill
- Department of Biology, Gettysburg College, Gettysburg, United States
| | - Eunsoo Kim
- Division of Invertebrate Zoology, American Museum of Natural History, New York, United States
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, United States
| | - Ryan Kerney
- Department of Biology, Gettysburg College, Gettysburg, United States
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Fijarczyk A, Dudek K, Babik W. Selective Landscapes in newt Immune Genes Inferred from Patterns of Nucleotide Variation. Genome Biol Evol 2016; 8:3417-3432. [PMID: 27702815 PMCID: PMC5203778 DOI: 10.1093/gbe/evw236] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Host–pathogen interactions may result in either directional selection or in pressure for the maintenance of polymorphism at the molecular level. Hence signatures of both positive and balancing selection are expected in immune genes. Because both overall selective pressure and specific targets may differ between species, large-scale population genomic studies are useful in detecting functionally important immune genes and comparing selective landscapes between taxa. Such studies are of particular interest in amphibians, a group threatened worldwide by emerging infectious diseases. Here, we present an analysis of polymorphism and divergence of 634 immune genes in two lineages of Lissotriton newts: L. montandoni and L. vulgaris graecus. Variation in newt immune genes has been shaped predominantly by widespread purifying selection and strong evolutionary constraint, implying long-term importance of these genes for functioning of the immune system. The two evolutionary lineages differ in the overall strength of purifying selection which can partially be explained by demographic history but may also signal differences in long-term pathogen pressure. The prevalent constraint notwithstanding, 23 putative targets of positive selection and 11 putative targets of balancing selection were identified. The latter were detected by composite tests involving the demographic model and further validated in independent population samples. Putative targets of balancing selection encode proteins which may interact closely with pathogens but include also regulators of immune response. The identified candidates will be useful for testing whether genes affected by balancing selection are more prone to interspecific introgression than other genes in the genome.
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Affiliation(s)
- Anna Fijarczyk
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Wieslaw Babik
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
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Liu LS, Zhao LY, Wang SH, Jiang JP. Research proceedings on amphibian model organisms. DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2016; 37:237-45. [PMID: 27469255 PMCID: PMC4980064 DOI: 10.13918/j.issn.2095-8137.2016.4.237] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 06/10/2016] [Indexed: 12/26/2022]
Abstract
Model organisms have long been important in biology and medicine due to their specific characteristics. Amphibians, especially Xenopus, play key roles in answering fundamental questions on developmental biology, regeneration, genetics, and toxicology due to their large and abundant eggs, as well as their versatile embryos, which can be readily manipulated and developed in vivo. Furthermore, amphibians have also proven to be of considerable benefit in human disease research due to their conserved cellular developmental and genomic organization. This review gives a brief introduction on the progress and limitations of these animal models in biology and human disease research, and discusses the potential and challenge of Microhyla fissipes as a new model organism.
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Affiliation(s)
- Lu-Sha Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Lan-Ying Zhao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China;University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shou-Hong Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China;University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian-Ping Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
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Limborg MT, Seeb LW, Seeb JE. Sorting duplicated loci disentangles complexities of polyploid genomes masked by genotyping by sequencing. Mol Ecol 2016; 25:2117-29. [PMID: 26939067 DOI: 10.1111/mec.13601] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 02/19/2016] [Accepted: 02/24/2016] [Indexed: 01/04/2023]
Abstract
Many plants and animals of polyploid origin are currently enjoying a genomics explosion enabled by modern sequencing and genotyping technologies. However, routine filtering of duplicated loci in most studies using genotyping by sequencing introduces an unacceptable, but often overlooked, bias when detecting selection. Retained duplicates from ancient whole-genome duplications (WGDs) may be found throughout genomes, whereas retained duplicates from recent WGDs are concentrated at distal ends of some chromosome arms. Additionally, segmental duplicates can be found at distal ends or nearly anywhere in a genome. Evidence shows that these duplications facilitate adaptation through one of two pathways: neo-functionalization or increased gene expression. Filtering duplicates removes distal ends of some chromosomes, and distal ends are especially known to harbour adaptively important genes. Thus, filtering of duplicated loci impoverishes the interpretation of genomic data as signals from contiguous duplicated genes are ignored. We review existing strategies to genotype and map duplicated loci; we focus in detail on an overlooked strategy of using gynogenetic haploids (1N) as a part of new genotyping by sequencing studies. We provide guidelines on how to use this haploid strategy for studies on polyploid-origin vertebrates including how it can be used to screen duplicated loci in natural populations. We conclude by discussing areas of research that will benefit from better inclusion of polyploid loci; we particularly stress the sometimes overlooked fact that basing genomic studies on dense maps provides value added in the form of locating and annotating outlier loci or colocating outliers into islands of divergence.
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Affiliation(s)
- Morten T Limborg
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195, USA.,National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark
| | - Lisa W Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195, USA
| | - James E Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195, USA
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15
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Huang L, Li J, Anboukaria H, Luo Z, Zhao M, Wu H. Comparative transcriptome analyses of seven anurans reveal functions and adaptations of amphibian skin. Sci Rep 2016; 6:24069. [PMID: 27040083 PMCID: PMC4819189 DOI: 10.1038/srep24069] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 03/18/2016] [Indexed: 01/06/2023] Open
Abstract
Animal skin, which is the tissue that directly contacts the external surroundings, has evolved diverse functions to adapt to various environments. Amphibians represent the transitional taxon from aquatic to terrestrial life. Exploring the molecular basis of their skin function and adaptation is important to understand the survival and evolutionary mechanisms of vertebrates. However, comprehensive studies on the molecular mechanisms of skin functions in amphibians are scarce. In this study, we sequenced the skin transcriptomes of seven anurans belonging to three families and compared the similarities and differences in expressed genes and proteins. Unigenes and pathways related to basic biological processes and special functions, such as defense, immunity, and respiration, were enriched in functional annotations. A total of 108 antimicrobial peptides were identified. The highly expressed genes were similar in species of the same family but were different among families. Additionally, the positively selected orthologous groups were involved in biosynthesis, metabolism, immunity, and defense processes. This study is the first to generate extensive transcriptome data for the skin of seven anurans and provides unigenes and pathway candidates for further studies on amphibian skin function and adaptation.
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Affiliation(s)
- Li Huang
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan 430079, China
| | - Jun Li
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan 430079, China
| | - Housseni Anboukaria
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan 430079, China
| | - Zhenhua Luo
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan 430079, China
| | - Mian Zhao
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan 430079, China
| | - Hua Wu
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, 152 Luoyulu, Hongshan District, Wuhan 430079, China
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16
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Rebollar EA, Antwis RE, Becker MH, Belden LK, Bletz MC, Brucker RM, Harrison XA, Hughey MC, Kueneman JG, Loudon AH, McKenzie V, Medina D, Minbiole KPC, Rollins-Smith LA, Walke JB, Weiss S, Woodhams DC, Harris RN. Using "Omics" and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious Diseases. Front Microbiol 2016; 7:68. [PMID: 26870025 PMCID: PMC4735675 DOI: 10.3389/fmicb.2016.00068] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 01/14/2016] [Indexed: 12/20/2022] Open
Abstract
Emerging infectious diseases in wildlife are responsible for massive population declines. In amphibians, chytridiomycosis caused by Batrachochytrium dendrobatidis, Bd, has severely affected many amphibian populations and species around the world. One promising management strategy is probiotic bioaugmentation of antifungal bacteria on amphibian skin. In vivo experimental trials using bioaugmentation strategies have had mixed results, and therefore a more informed strategy is needed to select successful probiotic candidates. Metagenomic, transcriptomic, and metabolomic methods, colloquially called "omics," are approaches that can better inform probiotic selection and optimize selection protocols. The integration of multiple omic data using bioinformatic and statistical tools and in silico models that link bacterial community structure with bacterial defensive function can allow the identification of species involved in pathogen inhibition. We recommend using 16S rRNA gene amplicon sequencing and methods such as indicator species analysis, the Kolmogorov-Smirnov Measure, and co-occurrence networks to identify bacteria that are associated with pathogen resistance in field surveys and experimental trials. In addition to 16S amplicon sequencing, we recommend approaches that give insight into symbiont function such as shotgun metagenomics, metatranscriptomics, or metabolomics to maximize the probability of finding effective probiotic candidates, which can then be isolated in culture and tested in persistence and clinical trials. An effective mitigation strategy to ameliorate chytridiomycosis and other emerging infectious diseases is necessary; the advancement of omic methods and the integration of multiple omic data provide a promising avenue toward conservation of imperiled species.
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Affiliation(s)
- Eria A. Rebollar
- Department of Biology, James Madison UniversityHarrisonburg, VA, USA
| | - Rachael E. Antwis
- Unit for Environmental Sciences and Management, North-West UniversityPotchefstroom, South Africa
- Institute of Zoology, Zoological Society of LondonLondon, UK
- School of Environment and Life Sciences, University of SalfordSalford, UK
| | - Matthew H. Becker
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological ParkWashington, DC, USA
| | - Lisa K. Belden
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | - Molly C. Bletz
- Zoological Institute, Technische Universität BraunschweigBraunschweig, Germany
| | | | | | - Myra C. Hughey
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | - Jordan G. Kueneman
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - Andrew H. Loudon
- Department of Zoology, Biodiversity Research Centre, University of British ColumbiaVancouver, BC, Canada
| | - Valerie McKenzie
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - Daniel Medina
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | | | - Louise A. Rollins-Smith
- Department of Pathology, Microbiology and Immunology and Department of Pediatrics, Vanderbilt University School of Medicine, Department of Biological Sciences, Vanderbilt UniversityNashville, TN, USA
| | - Jenifer B. Walke
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | - Sophie Weiss
- Department of Chemical and Biological Engineering, University of Colorado at BoulderBoulder, CO, USA
| | | | - Reid N. Harris
- Department of Biology, James Madison UniversityHarrisonburg, VA, USA
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17
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Pina-Martins F, Vieira BM, Seabra SG, Batista D, Paulo OS. 4Pipe4--A 454 data analysis pipeline for SNP detection in datasets with no reference sequence or strain information. BMC Bioinformatics 2016; 17:41. [PMID: 26787189 PMCID: PMC4719533 DOI: 10.1186/s12859-016-0892-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 01/15/2016] [Indexed: 11/10/2022] Open
Abstract
Background Next-generation sequencing datasets are becoming more frequent, and their use in population studies is becoming widespread. For non-model species, without a reference genome, it is possible from a panel of individuals to identify a set of SNPs that can be used for further population genotyping. However the lack of a reference genome to which the sequenced data could be compared makes the finding of SNPs more troublesome. Additionally when the data sources (strains) are not identified (e.g. in datasets of pooled individuals), the problem of finding reliable variation in these datasets can become much more difficult due to the lack of specialized software for this specific task. Results Here we describe 4Pipe4, a 454 data analysis pipeline particularly focused on SNP detection when no reference or strain information is available. It uses a command line interface to automatically call other programs, parse their outputs and summarize the results. The variation detection routine is built-in in the program itself. Despite being optimized for SNP mining in 454 EST data, it is flexible enough to automate the analysis of genomic data or even data from other NGS technologies. 4Pipe4 will output several HTML formatted reports with metrics on many of the most common assembly values, as well as on all the variation found. There is also a module available for finding putative SSRs in the analysed datasets. Conclusions This program can be especially useful for researchers that have 454 datasets of a panel of pooled individuals and want to discover and characterize SNPs for subsequent individual genotyping with customized genotyping arrays. In comparison with other SNP detection approaches, 4Pipe4 showed the best validation ratio, retrieving a smaller number of SNPs but with a considerably lower false positive rate than other methods. 4Pipe4’s source code is available at https://github.com/StuntsPT/4Pipe4.
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Affiliation(s)
- Francisco Pina-Martins
- Departamento de Biologia Animal, Faculdade de Ciências, Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal. .,Departamento de Biologia e CESAM, Univ. de Aveiro, Aveiro, Portugal.
| | - Bruno M Vieira
- Departamento de Biologia Animal, Faculdade de Ciências, Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.,Wurm Lab, School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Sofia G Seabra
- Departamento de Biologia Animal, Faculdade de Ciências, Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Dora Batista
- Departamento de Biologia Animal, Faculdade de Ciências, Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.,Centro de Investigação das Ferrugens do Cafeeiro (CIFC), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Quinta do Marquês, 2784-505, Oeiras, Portugal
| | - Octávio S Paulo
- Departamento de Biologia Animal, Faculdade de Ciências, Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
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18
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McCartney-Melstad E, Shaffer HB. Amphibian molecular ecology and how it has informed conservation. Mol Ecol 2015; 24:5084-109. [PMID: 26437125 DOI: 10.1111/mec.13391] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 09/15/2015] [Accepted: 09/16/2015] [Indexed: 02/02/2023]
Abstract
Molecular ecology has become one of the key tools in the modern conservationist's kit. Here we review three areas where molecular ecology has been applied to amphibian conservation: genes on landscapes, within-population processes, and genes that matter. We summarize relevant analytical methods, recent important studies from the amphibian literature, and conservation implications for each section. Finally, we include five in-depth examples of how molecular ecology has been successfully applied to specific amphibian systems.
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Affiliation(s)
- Evan McCartney-Melstad
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, 610 Charles E Young Drive South, Los Angeles, CA, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, 610 Charles E Young Drive South, Los Angeles, CA, USA
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19
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Birol I, Behsaz B, Hammond SA, Kucuk E, Veldhoen N, Helbing CC. De novo Transcriptome Assemblies of Rana (Lithobates) catesbeiana and Xenopus laevis Tadpole Livers for Comparative Genomics without Reference Genomes. PLoS One 2015; 10:e0130720. [PMID: 26121473 PMCID: PMC4488148 DOI: 10.1371/journal.pone.0130720] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 05/23/2015] [Indexed: 12/04/2022] Open
Abstract
In this work we studied the liver transcriptomes of two frog species, the American bullfrog (Rana (Lithobates) catesbeiana) and the African clawed frog (Xenopus laevis). We used high throughput RNA sequencing (RNA-seq) data to assemble and annotate these transcriptomes, and compared how their baseline expression profiles change when tadpoles of the two species are exposed to thyroid hormone. We generated more than 1.5 billion RNA-seq reads in total for the two species under two conditions as treatment/control pairs. We de novo assembled these reads using Trans-ABySS to reconstruct reference transcriptomes, obtaining over 350,000 and 130,000 putative transcripts for R. catesbeiana and X. laevis, respectively. Using available genomics resources for X. laevis, we annotated over 97% of our X. laevis transcriptome contigs, demonstrating the utility and efficacy of our methodology. Leveraging this validated analysis pipeline, we also annotated the assembled R. catesbeiana transcriptome. We used the expression profiles of the annotated genes of the two species to examine the similarities and differences between the tadpole liver transcriptomes. We also compared the gene ontology terms of expressed genes to measure how the animals react to a challenge by thyroid hormone. Our study reports three main conclusions. First, de novo assembly of RNA-seq data is a powerful method for annotating and establishing transcriptomes of non-model organisms. Second, the liver transcriptomes of the two frog species, R. catesbeiana and X. laevis, show many common features, and the distribution of their gene ontology profiles are statistically indistinguishable. Third, although they broadly respond the same way to the presence of thyroid hormone in their environment, their receptor/signal transduction pathways display marked differences.
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Affiliation(s)
- Inanc Birol
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
- * E-mail:
| | - Bahar Behsaz
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - S. Austin Hammond
- Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 1700, Stn CSC, Victoria, BC, V8W 2Y2, Canada
| | - Erdi Kucuk
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Nik Veldhoen
- Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 1700, Stn CSC, Victoria, BC, V8W 2Y2, Canada
| | - Caren C. Helbing
- Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 1700, Stn CSC, Victoria, BC, V8W 2Y2, Canada
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20
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Price SJ, Garner TWJ, Balloux F, Ruis C, Paszkiewicz KH, Moore K, Griffiths AGF. A de novo Assembly of the Common Frog (Rana temporaria) Transcriptome and Comparison of Transcription Following Exposure to Ranavirus and Batrachochytrium dendrobatidis. PLoS One 2015; 10:e0130500. [PMID: 26111016 PMCID: PMC4481470 DOI: 10.1371/journal.pone.0130500] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/19/2015] [Indexed: 12/22/2022] Open
Abstract
Amphibians are experiencing global declines and extinctions, with infectious diseases representing a major factor. In this study we examined the transcriptional response of metamorphic hosts (common frog, Rana temporaria) to the two most important amphibian pathogens: Batrachochytrium dendrobatidis (Bd) and Ranavirus. We found strong up-regulation of a gene involved in the adaptive immune response (AP4S1) at four days post-exposure to both pathogens. We detected a significant transcriptional response to Bd, covering the immune response (innate and adaptive immunity, complement activation, and general inflammatory responses), but relatively little transcriptional response to Ranavirus. This may reflect the higher mortality rates found in wild common frogs infected with Ranavirus as opposed to Bd. These data provide a valuable genomic resource for the amphibians, contribute insight into gene expression changes after pathogen exposure, and suggest potential candidate genes for future host-pathogen research.
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Affiliation(s)
- Stephen J. Price
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, United Kingdom
- Institute of Zoology, Zoological Society of London, London, United Kingdom
- * E-mail: (SJP); (AGFG)
| | | | - Francois Balloux
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, United Kingdom
| | - Chris Ruis
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, United Kingdom
| | - Konrad H. Paszkiewicz
- Wellcome Trust Biomedical Informatics Hub, Biosciences, Geoffrey Pope Building, University of Exeter, Streatham Campus, Exeter, United Kingdom
| | - Karen Moore
- Wellcome Trust Biomedical Informatics Hub, Biosciences, Geoffrey Pope Building, University of Exeter, Streatham Campus, Exeter, United Kingdom
| | - Amber G. F. Griffiths
- Environment and Sustainability Institute, University of Exeter, Penryn Campus, Penryn, Cornwall, United Kingdom
- * E-mail: (SJP); (AGFG)
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21
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Savage AE, Becker CG, Zamudio KR. Linking genetic and environmental factors in amphibian disease risk. Evol Appl 2015; 8:560-72. [PMID: 26136822 PMCID: PMC4479512 DOI: 10.1111/eva.12264] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/07/2015] [Indexed: 01/13/2023] Open
Abstract
A central question in evolutionary biology is how interactions between organisms and the environment shape genetic differentiation. The pathogen Batrachochytrium dendrobatidis (Bd) has caused variable population declines in the lowland leopard frog (Lithobates yavapaiensis); thus, disease has potentially shaped, or been shaped by, host genetic diversity. Environmental factors can also influence both amphibian immunity and Bd virulence, confounding our ability to assess the genetic effects on disease dynamics. Here, we used genetics, pathogen dynamics, and environmental data to characterize L. yavapaiensis populations, estimate migration, and determine relative contributions of genetic and environmental factors in predicting Bd dynamics. We found that the two uninfected populations belonged to a single genetic deme, whereas each infected population was genetically unique. We detected an outlier locus that deviated from neutral expectations and was significantly correlated with mortality within populations. Across populations, only environmental variables predicted infection intensity, whereas environment and genetics predicted infection prevalence, and genetic diversity alone predicted mortality. At one locality with geothermally elevated water temperatures, migration estimates revealed source-sink dynamics that have likely prevented local adaptation. We conclude that integrating genetic and environmental variation among populations provides a better understanding of Bd spatial epidemiology, generating more effective conservation management strategies for mitigating amphibian declines.
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Affiliation(s)
- Anna E Savage
- Department of Ecology and Evolutionary Biology, Cornell University Ithaca, NY, USA ; Department of Biology, University of Central Florida 4110 Libra Drive, Orlando, FL 32816, USA
| | - Carlos G Becker
- Department of Ecology and Evolutionary Biology, Cornell University Ithaca, NY, USA ; Department of Zoology, State University of Sao Paulo Av. 24A No. 1515, Rio Claro, SP 13506-900, Brazil
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University Ithaca, NY, USA
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22
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Kornobis E, Cabellos L, Aguilar F, Frías-López C, Rozas J, Marco J, Zardoya R. TRUFA: A User-Friendly Web Server for de novo RNA-seq Analysis Using Cluster Computing. Evol Bioinform Online 2015; 11:97-104. [PMID: 26056424 PMCID: PMC4444131 DOI: 10.4137/ebo.s23873] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/09/2015] [Accepted: 03/16/2015] [Indexed: 01/08/2023] Open
Abstract
Application of next-generation sequencing (NGS) methods for transcriptome analysis (RNA-seq) has become increasingly accessible in recent years and are of great interest to many biological disciplines including, eg, evolutionary biology, ecology, biomedicine, and computational biology. Although virtually any research group can now obtain RNA-seq data, only a few have the bioinformatics knowledge and computation facilities required for transcriptome analysis. Here, we present TRUFA (TRanscriptome User-Friendly Analysis), an open informatics platform offering a web-based interface that generates the outputs commonly used in de novo RNA-seq analysis and comparative transcriptomics. TRUFA provides a comprehensive service that allows performing dynamically raw read cleaning, transcript assembly, annotation, and expression quantification. Due to the computationally intensive nature of such analyses, TRUFA is highly parallelized and benefits from accessing high-performance computing resources. The complete TRUFA pipeline was validated using four previously published transcriptomic data sets. TRUFA’s results for the example datasets showed globally similar results when comparing with the original studies, and performed particularly better when analyzing the green tea dataset. The platform permits analyzing RNA-seq data in a fast, robust, and user-friendly manner. Accounts on TRUFA are provided freely upon request at https://trufa.ifca.es.
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Affiliation(s)
- Etienne Kornobis
- Departamento de biodiversidad y biología evolutiva, Museo Nacional de Ciencias Naturales MNCN (CSIC), Madrid, Spain
| | - Luis Cabellos
- Instituto de Física de Cantabria, IFCA (CSIC-UC), Edificio Juan Jordá, Santander, Spain
| | - Fernando Aguilar
- Instituto de Física de Cantabria, IFCA (CSIC-UC), Edificio Juan Jordá, Santander, Spain
| | - Cristina Frías-López
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Julio Rozas
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Jesús Marco
- Instituto de Física de Cantabria, IFCA (CSIC-UC), Edificio Juan Jordá, Santander, Spain
| | - Rafael Zardoya
- Departamento de biodiversidad y biología evolutiva, Museo Nacional de Ciencias Naturales MNCN (CSIC), Madrid, Spain
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23
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Xiao J, Zhong H, Liu Z, Yu F, Luo Y, Gan X, Zhou Y. Transcriptome analysis revealed positive selection of immune-related genes in tilapia. FISH & SHELLFISH IMMUNOLOGY 2015; 44:60-65. [PMID: 25659230 DOI: 10.1016/j.fsi.2015.01.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 01/17/2015] [Accepted: 01/25/2015] [Indexed: 06/04/2023]
Abstract
High-throughput sequencing of transcriptome promises a new approach for detecting evolutionary divergence among species. Up to now, the information about evolution of immune genes in cultured fish, especially in tilapias which would aid to understand the molecular basis of immune phenotypic differentiation is still lack. Thus, in the present study, we used high-throughput sequencing to obtain large amount of gene sequences in blue tilapia and characterized the diversity of orthologs among Nile tilapia, blue tilapia and zebrafish. A total of 52,424,506 raw reads, representing 31,404 unigenes were obtained from blue tilapia cDNA library of mixed tissues, including brain, pituitary, gill, heart, liver, spleen, kidney, intestine, muscle, testis and ovary. Based on Ks value, we calculated that the divergence time between Nile tilapia and blue tilapia is 2.93 million years ago. And the tilapias are both apart from zebrafish in 197 million years ago. Furthermore, the positive selected genes were identified by calculating of Ka/Ks ratio. Several immune-related genes were identified as positively selected genes, such as Notch2 and nfatc3b. Considering that these genes play crucial role in immune regulating function, the immune system genes met a great variation under environment selection in tilapias which suggests fast evolution in immune system of cultured tilapias.
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Affiliation(s)
- Jun Xiao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi 530021, China
| | - Huan Zhong
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi 530021, China
| | - Zhen Liu
- Department of Biotechnology and Environmental Science, Changsha University, Changsha 410003, China
| | - Fan Yu
- Key Laboratory for Genetic Breeding of Aquatic Animals, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214081, China
| | - Yongju Luo
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi 530021, China
| | - Xi Gan
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi 530021, China
| | - Yi Zhou
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi 530021, China; Department of Biotechnology and Environmental Science, Changsha University, Changsha 410003, China.
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24
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Shaffer HB, Gidiş M, McCartney-Melstad E, Neal KM, Oyamaguchi HM, Tellez M, Toffelmier EM. Conservation genetics and genomics of amphibians and reptiles. Annu Rev Anim Biosci 2015; 3:113-38. [PMID: 25580719 DOI: 10.1146/annurev-animal-022114-110920] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Amphibians and reptiles as a group are often secretive, reach their greatest diversity often in remote tropical regions, and contain some of the most endangered groups of organisms on earth. Particularly in the past decade, genetics and genomics have been instrumental in the conservation biology of these cryptic vertebrates, enabling work ranging from the identification of populations subject to trade and exploitation, to the identification of cryptic lineages harboring critical genetic variation, to the analysis of genes controlling key life history traits. In this review, we highlight some of the most important ways that genetic analyses have brought new insights to the conservation of amphibians and reptiles. Although genomics has only recently emerged as part of this conservation tool kit, several large-scale data sources, including full genomes, expressed sequence tags, and transcriptomes, are providing new opportunities to identify key genes, quantify landscape effects, and manage captive breeding stocks of at-risk species.
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Longo AV, Burrowes PA, Zamudio KR. Genomic Studies of Disease-Outcome in Host-Pathogen Dynamics. Integr Comp Biol 2014; 54:427-38. [DOI: 10.1093/icb/icu073] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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