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Cornman RS. A genomic hotspot of diversifying selection and structural change in the hoary bat ( Lasiurus cinereus). PeerJ 2024; 12:e17482. [PMID: 38832043 PMCID: PMC11146322 DOI: 10.7717/peerj.17482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 05/07/2024] [Indexed: 06/05/2024] Open
Abstract
Background Previous work found that numerous genes positively selected within the hoary bat (Lasiurus cinereus) lineage are physically clustered in regions of conserved synteny. Here I further validate and expand on those finding utilizing an updated L. cinereus genome assembly and additional bat species as well as other tetrapod outgroups. Methods A chromosome-level assembly was generated by chromatin-contact mapping and made available by DNAZoo (www.dnazoo.org). The genomic organization of orthologous genes was extracted from annotation data for multiple additional bat species as well as other tetrapod clades for which chromosome-level assemblies were available from the National Center for Biotechnology Information (NCBI). Tests of branch-specific positive selection were performed for L. cinereus using PAML as well as with the HyPhy package for comparison. Results Twelve genes exhibiting significant diversifying selection in the L. cinereus lineage were clustered within a 12-Mb genomic window; one of these (Trpc4) also exhibited diversifying selection in bats generally. Ten of the 12 genes are landmarks of two distinct blocks of ancient synteny that are not linked in other tetrapod clades. Bats are further distinguished by frequent structural rearrangements within these synteny blocks, which are rarely observed in other Tetrapoda. Patterns of gene order and orientation among bat taxa are incompatible with phylogeny as presently understood, implying parallel evolution or subsequent reversals. Inferences of positive selection were found to be robust to alternative phylogenetic topologies as well as a strong shift in background nucleotide composition in some taxa. Discussion This study confirms and further localizes a genomic hotspot of protein-coding divergence in the hoary bat, one that also exhibits an increased tempo of structural change in bats compared with other mammals. Most genes in the two synteny blocks have elevated expression in brain tissue in humans and model organisms, and genetic studies implicate the selected genes in cranial and neurological development, among other functions.
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Affiliation(s)
- Robert S. Cornman
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, United States
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2
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Demian WL, Cormier O, Mossman K. Immunological features of bats: resistance and tolerance to emerging viruses. Trends Immunol 2024; 45:198-210. [PMID: 38453576 DOI: 10.1016/j.it.2024.01.008] [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: 12/14/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 03/09/2024]
Abstract
Bats are among the most diverse mammalian species, representing over 20% of mammalian diversity. The past two decades have witnessed a disproportionate spillover of viruses from bats to humans compared with other mammalian hosts, attributed to the viral richness within bats, their phylogenetic likeness to humans, and increased human contact with wildlife. Unique evolutionary adaptations in bat genomes, particularly in antiviral protection and immune tolerance genes, enable bats to serve as reservoirs for pandemic-inducing viruses. Here, we discuss current limitations and advances made in understanding the role of bats as drivers of pandemic zoonoses. We also discuss novel technologies that have revealed spatial, dynamic, and physiological factors driving virus and host coevolution.
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Affiliation(s)
- Wael L Demian
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada; McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Olga Cormier
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada; McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Karen Mossman
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada; McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
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3
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Schoen A, Hölzer M, Müller MA, Wallerang KB, Drosten C, Marz M, Lamp B, Weber F. Functional comparisons of the virus sensor RIG-I from humans, the microbat Myotis daubentonii, and the megabat Rousettus aegyptiacus, and their response to SARS-CoV-2 infection. J Virol 2023; 97:e0020523. [PMID: 37728614 PMCID: PMC10653997 DOI: 10.1128/jvi.00205-23] [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: 02/07/2023] [Accepted: 07/09/2023] [Indexed: 09/21/2023] Open
Abstract
IMPORTANCE A common hypothesis holds that bats (order Chiroptera) are outstanding reservoirs for zoonotic viruses because of a special antiviral interferon (IFN) system. However, functional studies about key components of the bat IFN system are rare. RIG-I is a cellular sensor for viral RNA signatures that activates the antiviral signaling chain to induce IFN. We cloned and functionally characterized RIG-I genes from two species of the suborders Yangochiroptera and Yinpterochiroptera. The bat RIG-Is were conserved in their sequence and domain organization, and similar to human RIG-I in (i) mediating virus- and IFN-activated gene expression, (ii) antiviral signaling, (iii) temperature dependence, and (iv) recognition of RNA ligands. Moreover, RIG-I of Rousettus aegyptiacus (suborder Yinpterochiroptera) and of humans were found to recognize SARS-CoV-2 infection. Thus, members of both bat suborders encode RIG-Is that are comparable to their human counterpart. The ability of bats to harbor zoonotic viruses therefore seems due to other features.
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Affiliation(s)
- Andreas Schoen
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Giessen, Germany
| | - Martin Hölzer
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
- European Virus Bioinformatics Center, Jena, Germany
| | - Marcel A. Müller
- German Centre for Infection Research (DZIF), Partner Sites Giessen and Charité, Berlin, Germany
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Kai B. Wallerang
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Giessen, Germany
| | - Christian Drosten
- European Virus Bioinformatics Center, Jena, Germany
- German Centre for Infection Research (DZIF), Partner Sites Giessen and Charité, Berlin, Germany
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
- European Virus Bioinformatics Center, Jena, Germany
| | - Benjamin Lamp
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Giessen, Germany
| | - Friedemann Weber
- Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Giessen, Germany
- European Virus Bioinformatics Center, Jena, Germany
- German Centre for Infection Research (DZIF), Partner Sites Giessen and Charité, Berlin, Germany
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4
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Scheben A, Mendivil Ramos O, Kramer M, Goodwin S, Oppenheim S, Becker DJ, Schatz MC, Simmons NB, Siepel A, McCombie WR. Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats. Genome Biol Evol 2023; 15:evad148. [PMID: 37728212 PMCID: PMC10510315 DOI: 10.1093/gbe/evad148] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2023] [Indexed: 09/21/2023] Open
Abstract
Bats are exceptional among mammals for their powered flight, extended lifespans, and robust immune systems and therefore have been of particular interest in comparative genomics. Using the Oxford Nanopore Technologies long-read platform, we sequenced the genomes of two bat species with key phylogenetic positions, the Jamaican fruit bat (Artibeus jamaicensis) and the Mesoamerican mustached bat (Pteronotus mesoamericanus), and carried out a comprehensive comparative genomic analysis with a diverse collection of bats and other mammals. The high-quality, long-read genome assemblies revealed a contraction of interferon (IFN)-α at the immunity-related type I IFN locus in bats, resulting in a shift in relative IFN-ω and IFN-α copy numbers. Contradicting previous hypotheses of constitutive expression of IFN-α being a feature of the bat immune system, three bat species lost all IFN-α genes. This shift to IFN-ω could contribute to the increased viral tolerance that has made bats a common reservoir for viruses that can be transmitted to humans. Antiviral genes stimulated by type I IFNs also showed evidence of rapid evolution, including a lineage-specific duplication of IFN-induced transmembrane genes and positive selection in IFIT2. In addition, 33 tumor suppressors and 6 DNA-repair genes showed signs of positive selection, perhaps contributing to increased longevity and reduced cancer rates in bats. The robust immune systems of bats rely on both bat-wide and lineage-specific evolution in the immune gene repertoire, suggesting diverse immune strategies. Our study provides new genomic resources for bats and sheds new light on the extraordinary molecular evolution in this critically important group of mammals.
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Affiliation(s)
- Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | | | - Melissa Kramer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Sara Oppenheim
- American Museum of Natural History, Institute for Comparative Genomics, New York, New York, USA
| | - Daniel J Becker
- School of Biological Sciences, University of Oklahoma, Norman, Oklahoma, USA
| | - Michael C Schatz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
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5
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Zhang X, Wolinska J, Blair D, Hu W, Yin M. Responses to predation pressure involve similar sets of genes in two divergent species of Daphnia. J Anim Ecol 2023; 92:1743-1758. [PMID: 37337454 DOI: 10.1111/1365-2656.13969] [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: 07/12/2022] [Accepted: 06/02/2023] [Indexed: 06/21/2023]
Abstract
Species that are not closely related can express similar inducible traits, but molecular mechanisms underlying the observed responses are often unknown, nor is it known if these mechanisms are shared between such species. Here, we compared transcriptional profiles of two Daphnia species (D. mitsukuri and D. sinensis) from different subgenera, at both juvenile and adult developmental stages. Both species were exposed to the same predation threat (fish kairomones), and both showed similar induced morphological changes (reduced body length). At the early developmental stage, response to predation risk resulted in similar changes in expression levels of 23 orthologues in both species. These orthologues, involved in 107 GO categories, changed in the same direction in both species (over- or underexpressed), in comparison to non-exposed controls. Several of these orthologues were associated with DNA replication, structural constituents of cuticle or innate immune response. In both species, the differentially expressed (DE) genes on average had higher ω (dN /dS ) values than non-DE genes, suggesting that these genes had experienced greater positive selection or lower purifying selection than non-DE genes. Overall, our results suggest that similar suites of genes, responding in similar ways to predation pressure, have been retained in Daphnia for many millions of years.
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Affiliation(s)
- Xiuping Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Justyna Wolinska
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - David Blair
- College of Marine and Environmental Sciences, James Cook University, Townsville, Queensland, Australia
| | - Wei Hu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
- Department of Microbiology and Bioengineering, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Mingbo Yin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Shanghai, China
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6
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Zhang D, Irving AT. Antiviral effects of interferon-stimulated genes in bats. Front Cell Infect Microbiol 2023; 13:1224532. [PMID: 37661999 PMCID: PMC10472940 DOI: 10.3389/fcimb.2023.1224532] [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: 05/17/2023] [Accepted: 07/10/2023] [Indexed: 09/05/2023] Open
Abstract
The interferon pathway is the first line of defense in viral infection in all mammals, and its induction stimulates broad expression of interferon-stimulated genes (ISGs). In mice and also humans, the antiviral function of ISGs has been extensively studied. As an important viral reservoir in nature, bats can coexist with a variety of pathogenic viruses without overt signs of disease, yet only limited data are available for the role of ISGs in bats. There are multiple species of bats and work has begun deciphering the differences and similarities between ISG function of human/mouse and different bat species. This review summarizes the current knowledge of conserved and bat-specific-ISGs and their known antiviral effector functions.
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Affiliation(s)
- Dan Zhang
- Zhejiang University-University of Edinburgh Institute, Haining, China
| | - Aaron T. Irving
- Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Centre for Infection, Immunity & Cancer, Zhejiang University-University of Edinburgh Institute, Haining, China
- BIMET - Biomedical and Health Translational Research Centre of Zhejiang Province, China
- College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, United Kingdom
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7
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Schneor L, Kaltenbach S, Friedman S, Tussia-Cohen D, Nissan Y, Shuler G, Fraimovitch E, Kolodziejczyk AA, Weinberg M, Donati G, Teeling EC, Yovel Y, Hagai T. Comparison of antiviral responses in two bat species reveals conserved and divergent innate immune pathways. iScience 2023; 26:107435. [PMID: 37575178 PMCID: PMC10415932 DOI: 10.1016/j.isci.2023.107435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/28/2023] [Accepted: 07/14/2023] [Indexed: 08/15/2023] Open
Abstract
Bats host a range of disease-causing viruses without displaying clinical symptoms. The mechanisms behind this are a continuous source of interest. Here, we studied the antiviral response in the Egyptian fruit bat and Kuhl's pipistrelle, representing two subordinal clades. We profiled the antiviral response in fibroblasts using RNA sequencing and compared bat with primate and rodent responses. Both bats upregulate similar genes; however, a subset of these genes is transcriptionally divergent between them. These divergent genes also evolve rapidly in sequence, have specific promoter architectures, and are associated with programs underlying tolerance and resistance. Finally, we characterized antiviral genes that expanded in bats, with duplicates diverging in sequence and expression. Our study reveals a largely conserved antiviral program across bats and points to a set of genes that rapidly evolve through multiple mechanisms. These can contribute to bat adaptation to viral infection and provide directions to understanding the mechanisms behind it.
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Affiliation(s)
- Lilach Schneor
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Stefan Kaltenbach
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Sivan Friedman
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dafna Tussia-Cohen
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yomiran Nissan
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Gal Shuler
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Evgeny Fraimovitch
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | | | - Maya Weinberg
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Giacomo Donati
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center, University of Turin, Torino, Italy
| | - Emma C. Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Yossi Yovel
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tzachi Hagai
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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8
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He H, Yang H, Foo R, Chan W, Zhu F, Liu Y, Zhou X, Ma L, Wang LF, Zhai W. Population genomic analysis reveals distinct demographics and recent adaptation in the black flying fox (Pteropus alecto). J Genet Genomics 2023; 50:554-562. [PMID: 37182682 DOI: 10.1016/j.jgg.2023.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/16/2023]
Abstract
As the only mammalian group capable of powered flight, bats have many unique biological traits. Previous comparative genomic studies in bats have focused on long-term evolution. However, the micro-evolutionary processes driving recent evolution are largely under-explored. Using resequencing data from 50 black flying foxes (Pteropus alecto), one of the model species for bats, we find that black flying fox has much higher genetic diversity and lower levels of linkage disequilibrium than most of the mammalian species. Demographic inference reveals strong population fluctuations (>100 fold) coinciding with multiple historical events including the last glacial change and Toba super eruption, suggesting that the black flying fox is a very resilient species with strong recovery abilities. While long-term adaptation in the black flying fox is enriched in metabolic genes, recent adaptation in the black flying fox has a unique landscape where recently selected genes are not strongly enriched in any functional category. The demographic history and mode of adaptation suggest that black flying fox might be a well-adapted species with strong evolutionary resilience. Taken together, this study unravels a vibrant landscape of recent evolution for the black flying fox and sheds light on several unique evolutionary processes for bats comparing to other mammalian groups.
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Affiliation(s)
- Haopeng He
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hechuan Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Randy Foo
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; Singhealth Duke-NUS Global Health Institute, Singapore 169857, Singapore
| | - Wharton Chan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; Singhealth Duke-NUS Global Health Institute, Singapore 169857, Singapore
| | - Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; Singhealth Duke-NUS Global Health Institute, Singapore 169857, Singapore
| | - Yunsong Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liang Ma
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; Singhealth Duke-NUS Global Health Institute, Singapore 169857, Singapore.
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
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9
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Ahn M, Chen VCW, Rozario P, Ng WL, Kong PS, Sia WR, Kang AEZ, Su Q, Nguyen LH, Zhu F, Chan WOY, Tan CW, Cheong WS, Hey YY, Foo R, Guo F, Lim YT, Li X, Chia WN, Sobota RM, Fu NY, Irving AT, Wang LF. Bat ASC2 suppresses inflammasomes and ameliorates inflammatory diseases. Cell 2023; 186:2144-2159.e22. [PMID: 37172565 DOI: 10.1016/j.cell.2023.03.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/12/2022] [Accepted: 03/31/2023] [Indexed: 05/15/2023]
Abstract
Bats are special in their ability to live long and host many emerging viruses. Our previous studies showed that bats have altered inflammasomes, which are central players in aging and infection. However, the role of inflammasome signaling in combating inflammatory diseases remains poorly understood. Here, we report bat ASC2 as a potent negative regulator of inflammasomes. Bat ASC2 is highly expressed at both the mRNA and protein levels and is highly potent in inhibiting human and mouse inflammasomes. Transgenic expression of bat ASC2 in mice reduced the severity of peritonitis induced by gout crystals and ASC particles. Bat ASC2 also dampened inflammation induced by multiple viruses and reduced mortality of influenza A virus infection. Importantly, it also suppressed SARS-CoV-2-immune-complex-induced inflammasome activation. Four key residues were identified for the gain of function of bat ASC2. Our results demonstrate that bat ASC2 is an important negative regulator of inflammasomes with therapeutic potential in inflammatory diseases.
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Affiliation(s)
- Matae Ahn
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; SingHealth Duke-NUS Medicine Academic Clinical Program, Singapore 168753, Singapore; SingHealth PGY1 Residency Program, Singapore 169608, Singapore; Department of Internal Medicine, Singapore General Hospital, Singapore 169608, Singapore.
| | - Vivian Chih-Wei Chen
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Pritisha Rozario
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Wei Lun Ng
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Pui San Kong
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Wan Rong Sia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Adrian Eng Zheng Kang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Qi Su
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Lan Huong Nguyen
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Wharton O Y Chan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Wan Shoo Cheong
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Ying Ying Hey
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Randy Foo
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Fusheng Guo
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Yan Ting Lim
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138673, Singapore; SingMass - National Mass Spectrometry Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138673, Singapore
| | - Xin Li
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138673, Singapore; SingMass - National Mass Spectrometry Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138673, Singapore
| | - Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Radoslaw M Sobota
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138673, Singapore; SingMass - National Mass Spectrometry Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138673, Singapore
| | - Nai Yang Fu
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Aaron T Irving
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining 314400, China; Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; SingHealth Duke-NUS Global Health Institute, Singapore 169857, Singapore.
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10
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Clark AD, Hu H, Benson RBJ, O’Connor JK. Reconstructing the dietary habits and trophic positions of the Longipterygidae (Aves: Enantiornithes) using neontological and comparative morphological methods. PeerJ 2023; 11:e15139. [PMID: 37009163 PMCID: PMC10062354 DOI: 10.7717/peerj.15139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
The Longipterygidae are a unique clade among the enantiornithines in that they exhibit elongate rostra (≥60% total skull length) with dentition restricted to the distal tip of the rostrum, and pedal morphologies suited for an arboreal lifestyle (as in other enantiornithines). This suite of features has made interpretations of this group’s diet and ecology difficult to determine due to the lack of analogous taxa that exhibit similar morphologies together. Many extant bird groups exhibit rostral elongation, which is associated with several disparate ecologies and diets (e.g., aerial insectivory, piscivory, terrestrial carnivory). Thus, the presence of rostral elongation in the Longipterygidae only somewhat refines trophic predictions of this clade. Anatomical morphologies do not function singularly but as part of a whole and thus, any dietary or ecological hypothesis regarding this clade must also consider other features such as their unique dentition. The only extant group of dentulous volant tetrapods are the chiropterans, in which tooth morphology and enamel thickness vary depending upon food preference. Drawing inferences from both avian bill proportions and variations in the dental morphology of extinct and extant taxa, we provide quantitative data to support the hypothesis that the Longipterygidae were animalivorous, with greater support for insectivory.
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Affiliation(s)
- Alexander D. Clark
- Cincinnati Museum Center, Geier Collections & Research Center, Cincinnati, Ohio, United States
| | - Han Hu
- Department of Earth Sciences, University of Oxford, Oxford, United Kingdom
| | - Roger BJ Benson
- American Museum of Natural History, New York City, New York, United States
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Kundu S, Kamalakannan M, Mukherjee T, Banerjee D, Kim HW. Genetic Characterization and Insular Habitat Enveloping of Endangered Leaf-Nosed Bat, Hipposideros nicobarulae (Mammalia: Chiroptera) in India: Phylogenetic Inference and Conservation Implication. Genes (Basel) 2023; 14:genes14030765. [PMID: 36981035 PMCID: PMC10048616 DOI: 10.3390/genes14030765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
The Nicobar leaf-nosed Bat (Hipposideros nicobarulae) was described in the early 20th century; however, its systematic classification has been debated for over 100 years. This endangered and endemic species has achieved species status through morphological data in the last 10 years. However, the genetic information and phylogenetic relationships of H. nicobarulae remain neglected. The generated mitochondrial cytochrome b gene (mtCytb) sequences (438 bp) of H. nicobarulae contains 53.42-53.65% AT composition and 1.82% variable sites. The studied species, H. nicobarulae maintains an 8.1% to 22.6% genetic distance from other Hipposideros species. The genetic divergence estimated in this study is congruent with the concept of gene speciation in bats. The Bayesian and Maximum-Likelihood phylogenies clearly discriminated all Hipposideros species and showed a sister relationship between H. nicobarulae and H. cf. antricola. Current mtCytb-based investigations of H. nicobarulae have confirmed the species status at the molecular level. Further, the MaxEnt-based species distribution modelling illustrates the most suitable habitat of H. nicobarulae (294 km2), of which the majority (171 km2) is located on Great Nicobar Island. The present study suggests rigorous sampling across the range, taxonomic coverage, the generation of multiple molecular markers (mitochondrial and nuclear), as well as more ecological information, which will help in understanding population genetic structure, habitat suitability, and the implementation of appropriate conservation action plans for H. nicobarulae and other Hipposideros species.
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Affiliation(s)
- Shantanu Kundu
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
| | | | - Tanoy Mukherjee
- Agricultural and Ecological Research Unit, Indian Statistical Institute, Kolkata 700108, India
| | - Dhriti Banerjee
- Western Ghat Regional Centre, Zoological Survey of India, Kozhikode 673006, India
- Zoological Survey of India, M Block, New Alipore, Kolkata 700053, India
| | - Hyun-Woo Kim
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
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12
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Caña-Bozada V, Robinson MW, Hernández-Mena DI, Morales-Serna FN. Exploring Evolutionary Relationships within Neodermata Using Putative Orthologous Groups of Proteins, with Emphasis on Peptidases. Trop Med Infect Dis 2023; 8:tropicalmed8010059. [PMID: 36668966 PMCID: PMC9860727 DOI: 10.3390/tropicalmed8010059] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/14/2023] Open
Abstract
The phylogenetic relationships within Neodermata were examined based on putative orthologous groups of proteins (OGPs) from 11 species of Monogenea, Trematoda, and Cestoda. The dataset included OGPs from BUSCO and OMA. Additionally, peptidases were identified and evaluated as phylogenetic markers. Phylogenies were inferred using the maximum likelihood method. A network analysis and a hierarchical grouping analysis of the principal components (HCPC) of orthologous groups of peptidases were performed. The phylogenetic analyses showed the monopisthocotylean monogeneans as the sister-group of cestodes, and the polyopisthocotylean monogeneans as the sister-group of trematodes. However, the sister-group relationship between Monopisthocotylea and Cestoda was not statistically well supported. The network analysis and HCPC also showed a cluster formed by polyopisthocotyleans and trematodes. The present study supports the non-monophyly of Monogenea. An analysis of mutation rates indicated that secreted peptidases and inhibitors, and those with multiple copies, are under positive selection pressure, which could explain the expansion of some families such as C01, C19, I02, and S01. Whilst not definitive, our study presents another point of view in the discussion of the evolution of Neodermata, and we hope that our data drive further discussion and debate on this intriguing topic.
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Affiliation(s)
- Víctor Caña-Bozada
- Centro de Investigación en Alimentación y Desarrollo, Mazatlán 82112, Mexico
| | - Mark W. Robinson
- School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK
| | - David I. Hernández-Mena
- Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional, Unidad Mérida, Mérida 97310, Mexico
| | - Francisco N. Morales-Serna
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mazatlán 82040, Mexico
- Correspondence:
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13
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Clark AD, Hone DWE. Evolutionary pressures of aerial insectivory reflected in anurognathid pterosaurs. J Anat 2022; 242:917-926. [PMID: 36584353 PMCID: PMC10093155 DOI: 10.1111/joa.13814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022] Open
Abstract
Across the evolution of powered flight, the ecological niche of aerial insectivore has been occupied by members of the three volant vertebrate clades-Aves and Chiroptera, and the first known volant vertebrates, pterosaurs. However, morphological and quantitative evidence to support pterosaurs exhibiting this ecology remains scant. Anurognathids are an unusual group of pterosaurs in which the skull exhibits the unique morphology of being mediolaterally expanded, so much so that their skulls may be wider than rostrocaudally long. Here, we conduct quantitative comparative cranial measurements and dental morphology in anurognathids against extant avian and chiropteran taxa, respectively, with ecologies and behaviors that are similar to predicted putative behaviors of anurognathids. Comparative analyses of both skull and dental morphology suggest anurognathid specimens in similar morphospaces as insectivorous crepuscular and nocturnal extant volant taxa. Our results support that this unique group of pterosaurs likely occupied a niche of mid-flight insectivorous capture in low-light conditions.
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Affiliation(s)
- Alexander D Clark
- Cincinnati Museum Center, Geier Collections & Research Center, Cincinnati, Ohio, USA
| | - David W E Hone
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
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14
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Jacquet S, Culbertson M, Zhang C, El Filali A, De La Myre Mory C, Pons JB, Filippi-Codaccioni O, Lauterbur ME, Ngoubangoye B, Duhayer J, Verez C, Park C, Dahoui C, Carey CM, Brennan G, Enard D, Cimarelli A, Rothenburg S, Elde NC, Pontier D, Etienne L. Adaptive duplication and genetic diversification of protein kinase R contribute to the specificity of bat-virus interactions. SCIENCE ADVANCES 2022; 8:eadd7540. [PMID: 36417524 PMCID: PMC9683710 DOI: 10.1126/sciadv.add7540] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/05/2022] [Indexed: 05/29/2023]
Abstract
Several bat species act as asymptomatic reservoirs for many viruses that are highly pathogenic in other mammals. Here, we have characterized the functional diversification of the protein kinase R (PKR), a major antiviral innate defense system. Our data indicate that PKR has evolved under positive selection and has undergone repeated genomic duplications in bats in contrast to all studied mammals that have a single copy of the gene. Functional testing of the relationship between PKR and poxvirus antagonists revealed how an evolutionary conflict with ancient pathogenic poxviruses has shaped a specific bat host-virus interface. We determined that duplicated PKRs of the Myotis species have undergone genetic diversification, allowing them to collectively escape from and enhance the control of DNA and RNA viruses. These findings suggest that viral-driven adaptations in PKR contribute to modern virus-bat interactions and may account for bat-specific immunity.
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Affiliation(s)
- Stéphanie Jacquet
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, UCBL1, CNRS, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Michelle Culbertson
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Chi Zhang
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
| | - Adil El Filali
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, UCBL1, CNRS, Lyon, France
| | - Clément De La Myre Mory
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Jean-Baptiste Pons
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, UCBL1, CNRS, Lyon, France
| | | | - M. Elise Lauterbur
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Barthélémy Ngoubangoye
- International Centre of Medical Research of Franceville, Primatology Centre, Franceville, Gabon
| | - Jeanne Duhayer
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, UCBL1, CNRS, Lyon, France
| | - Clément Verez
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Chorong Park
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Clara Dahoui
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Clayton M. Carey
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Greg Brennan
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
| | - David Enard
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Andrea Cimarelli
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - Stefan Rothenburg
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA 95616, USA
| | - Nels C. Elde
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA
| | - Dominique Pontier
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR 5558, UCBL1, CNRS, Lyon, France
| | - Lucie Etienne
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
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15
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Unique Evolution of Antiviral Tetherin in Bats. J Virol 2022; 96:e0115222. [PMID: 36173189 PMCID: PMC9599465 DOI: 10.1128/jvi.01152-22] [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] [Indexed: 11/29/2022] Open
Abstract
Bats are recognized as important reservoirs of viruses deadly to other mammals, including humans. These infections are typically nonpathogenic in bats, raising questions about host response differences that might exist between bats and other mammals. Tetherin is a restriction factor which inhibits the release of a diverse range of viruses from host cells, including retroviruses, coronaviruses, filoviruses, and paramyxoviruses, some of which are deadly to humans and transmitted by bats. Here, we characterize the tetherin genes from 27 bat species, revealing that they have evolved under strong selective pressure, and that fruit bats and vesper bats express unique structural variants of the tetherin protein. Tetherin was widely and variably expressed across fruit bat tissue types and upregulated in spleen tissue when stimulated with Toll-like receptor agonists. The expression of two computationally predicted splice isoforms of fruit bat tetherin was verified. We identified an additional third unique splice isoform which includes a C-terminal region that is not homologous to known mammalian tetherin variants but was functionally capable of restricting the release of filoviral virus-like particles. We also report that vesper bats possess and express at least five tetherin genes, including structural variants, more than any other mammal reported to date. These findings support the hypothesis of differential antiviral gene evolution in bats relative to other mammals. IMPORTANCE Bats are an important host of various viruses which are deadly to humans and other mammals but do not cause outward signs of illness in bats. Furthering our understanding of the unique features of the immune system of bats will shed light on how they tolerate viral infections, potentially informing novel antiviral strategies in humans and other animals. This study examines the antiviral protein tetherin, which prevents viral particles from escaping their host cell. Analysis of tetherin from 27 bat species reveals that it is under strong evolutionary pressure, and we show that multiple bat species have evolved to possess more tetherin genes than other mammals, some of which encode structurally unique tetherins capable of activity against different viral particles. These data suggest that bat tetherin plays a potentially broad and important role in the management of viral infections in bats.
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16
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Donnik IM, Chvala IA, Kish LK, Ermakov AM. Coronavirus Infections in Animals: Risks of Direct and Reverse Zoonoses. HERALD OF THE RUSSIAN ACADEMY OF SCIENCES 2022; 92:491-496. [PMID: 36091853 PMCID: PMC9447960 DOI: 10.1134/s1019331622040116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/10/2022] [Accepted: 02/25/2022] [Indexed: 06/15/2023]
Abstract
The publications on animal coronavirus infections that have the greatest emerging potential, as well as official data from the World Organization for Animal Health (OIE) on cases of animal infection with COVID-19, are analyzed. Like most infectious diseases common to humans, coronavirus infections were first discovered in animals. Due to the increased rate of replication and recombination activity compared to other viruses, mutations occur more often in the genome of coronaviruses, which contribute to the acquisition of new qualities in order to consolidate in the host organism. Examples of cross-species transmission are not only SARS-CoV, MERS-CoV, and SARS-CoV-2, which are dangerous to humans, but also coronaviruses of agricultural and domestic animals, between which there is a genetic relationship. There are several known cases of zoo, wild, domestic, and farm animals displaying symptoms characteristic of COVID-19 and identification of the genome of the SARS-CoV-2 virus in them. The issue of cross-species transmission of coronavirus infections, in particular the reverse zoonosis of SARS-CoV-2 from animals to humans, is widely discussed. According to the conclusions of many researchers, including OIE experts, there is no direct evidence base for infection of humans with COVID-19 from animals. However, people with suspected COVID-19 and with a confirmed diagnosis are still advised to isolate not only from people but also from animals. A number of methods for specific prevention, diagnosis, and immunization against a wide range of coronavirus infections are being developed at the All-Russia Research Institute for Animal Protection.
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Affiliation(s)
| | - I. A. Chvala
- Federal Center for Animal Health, All-Russia Research Institute for Animal Protection (ARRIAH), Vladimir, Russia
| | - L. K. Kish
- Russian State Center for Animal Feed and Drug Standardization and Quality (VGNKI), Moscow, Russia
| | - A. M. Ermakov
- Don State Technical University (DSTU), Rostov-on-Don, Russia
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17
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Chirohepevirus from Bats: Insights into Hepatitis E Virus Diversity and Evolution. Viruses 2022; 14:v14050905. [PMID: 35632647 PMCID: PMC9146828 DOI: 10.3390/v14050905] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/22/2022] [Accepted: 04/25/2022] [Indexed: 02/06/2023] Open
Abstract
Homologs of the human hepatitis E virus (HEV) have been identified in more than a dozen animal species. Some of them have been evidenced to cross species barriers and infect humans. Zoonotic HEV infections cause chronic liver diseases as well as a broad range of extrahepatic manifestations, which increasingly become significant clinical problems. Bats comprise approximately one-fifth of all named mammal species and are unique in their distinct immune response to viral infection. Most importantly, they are natural reservoirs of several highly pathogenic viruses, which have induced severe human diseases. Since the first discovery of HEV-related viruses in bats in 2012, multiple genetically divergent HEV variants have been reported in a total of 12 bat species over the last decade, which markedly expanded the host range of the HEV family and shed light on the evolutionary origin of human HEV. Meanwhile, bat-borne HEV also raised critical public health concerns about its zoonotic potential. Bat HEV strains resemble genomic features but exhibit considerable heterogeneity. Due to the close evolutionary relationships, bat HEV altogether has been recently assigned to an independent genus, Chirohepevirus. This review focuses on the current state of bat HEV and provides novel insights into HEV genetic diversity and molecular evolution.
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18
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Immunity and lifespan: answering long-standing questions with comparative genomics. Trends Genet 2022; 38:650-661. [DOI: 10.1016/j.tig.2022.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/14/2022] [Accepted: 02/28/2022] [Indexed: 10/18/2022]
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19
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McDougal MB, Boys IN, De La Cruz-Rivera P, Schoggins JW. Evolution of the interferon response: lessons from ISGs of diverse mammals. Curr Opin Virol 2022; 53:101202. [DOI: 10.1016/j.coviro.2022.101202] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 02/07/2023]
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20
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Abstract
Upon infection, DNA viruses can be sensed by pattern recognition receptors (PRRs), leading to the activation of type I and III interferons to block infection. Therefore, viruses must inhibit these signaling pathways, avoid being detected, or both. Papillomavirus virions are trafficked from early endosomes to the Golgi apparatus and wait for the onset of mitosis to complete nuclear entry. This unique subcellular trafficking strategy avoids detection by cytoplasmic PRRs, a property that may contribute to the establishment of infection. However, as the capsid uncoats within acidic endosomal compartments, the viral DNA may be exposed to detection by Toll-like receptor 9 (TLR9). In this study, we characterized two new papillomaviruses from bats and used molecular archeology to demonstrate that their genomes altered their nucleotide compositions to avoid detection by TLR9, providing evidence that TLR9 acts as a PRR during papillomavirus infection. Furthermore, we showed that TLR9, like other components of the innate immune system, is under evolutionary selection in bats, providing the first direct evidence for coevolution between papillomaviruses and their hosts. Finally, we demonstrated that the cancer-associated human papillomaviruses show a reduction in CpG dinucleotides within a TLR9 recognition complex.
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21
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Cornman RS, Cryan PM. Positively selected genes in the hoary bat ( Lasiurus cinereus) lineage: prominence of thymus expression, immune and metabolic function, and regions of ancient synteny. PeerJ 2022; 10:e13130. [PMID: 35317076 PMCID: PMC8934532 DOI: 10.7717/peerj.13130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 02/25/2022] [Indexed: 01/12/2023] Open
Abstract
Background Bats of the genus Lasiurus occur throughout the Americas and have diversified into at least 20 species among three subgenera. The hoary bat (Lasiurus cinereus) is highly migratory and ranges farther across North America than any other wild mammal. Despite the ecological importance of this species as a major insect predator, and the particular susceptibility of lasiurine bats to wind turbine strikes, our understanding of hoary bat ecology, physiology, and behavior remains poor. Methods To better understand adaptive evolution in this lineage, we used whole-genome sequencing to identify protein-coding sequence and explore signatures of positive selection. Gene models were predicted with Maker and compared to seven well-annotated and phylogenetically representative species. Evolutionary rate analysis was performed with PAML. Results Of 9,447 single-copy orthologous groups that met evaluation criteria, 150 genes had a significant excess of nonsynonymous substitutions along the L. cinereus branch (P < 0.001 after manual review of alignments). Selected genes as a group had biased expression, most strongly in thymus tissue. We identified 23 selected genes with reported immune functions as well as a divergent paralog of Steep1 within suborder Yangochiroptera. Seventeen genes had roles in lipid and glucose metabolic pathways, partially overlapping with 15 mitochondrion-associated genes; these adaptations may reflect the metabolic challenges of hibernation, long-distance migration, and seasonal variation in prey abundance. The genomic distribution of positively selected genes differed significantly from background expectation by discrete Kolmogorov-Smirnov test (P < 0.001). Remarkably, the top three physical clusters all coincided with islands of conserved synteny predating Mammalia, the largest of which shares synteny with the human cat-eye critical region (CECR) on 22q11. This observation coupled with the expansion of a novel Tbx1-like gene family may indicate evolutionary innovation during pharyngeal arch development: both the CECR and Tbx1 cause dosage-dependent congenital abnormalities in thymus, heart, and head, and craniodysmorphy is associated with human orthologs of other positively selected genes as well.
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22
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Quer J, Colomer-Castell S, Campos C, Andrés C, Piñana M, Cortese MF, González-Sánchez A, Garcia-Cehic D, Ibáñez M, Pumarola T, Rodríguez-Frías F, Antón A, Tabernero D. Next-Generation Sequencing for Confronting Virus Pandemics. Viruses 2022; 14:v14030600. [PMID: 35337007 PMCID: PMC8950049 DOI: 10.3390/v14030600] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/01/2022] [Accepted: 03/10/2022] [Indexed: 02/06/2023] Open
Abstract
Virus pandemics have happened, are happening and will happen again. In recent decades, the rate of zoonotic viral spillover into humans has accelerated, mirroring the expansion of our global footprint and travel network, including the expansion of viral vectors and the destruction of natural spaces, bringing humans closer to wild animals. Once viral cross-species transmission to humans occurs, transmission cannot be stopped by cement walls but by developing barriers based on knowledge that can prevent or reduce the effects of any pandemic. Controlling a local transmission affecting few individuals is more efficient that confronting a community outbreak in which infections cannot be traced. Genetic detection, identification, and characterization of infectious agents using next-generation sequencing (NGS) has been proven to be a powerful tool allowing for the development of fast PCR-based molecular assays, the rapid development of vaccines based on mRNA and DNA, the identification of outbreaks, transmission dynamics and spill-over events, the detection of new variants and treatment of vaccine resistance mutations, the development of direct-acting antiviral drugs, the discovery of relevant minority variants to improve knowledge of the viral life cycle, strengths and weaknesses, the potential for becoming dominant to take appropriate preventive measures, and the discovery of new routes of viral transmission.
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Affiliation(s)
- Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), UAB Campus, Plaça Cívica, 08193 Bellaterra, Spain
- Correspondence: (J.Q.); (A.A.)
| | - Sergi Colomer-Castell
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
| | - Carolina Campos
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
| | - Cristina Andrés
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
| | - Maria Piñana
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
| | - Maria Francesca Cortese
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
- Clinical Biochemistry Research Group, Biochemistry Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Alejandra González-Sánchez
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
| | - Damir Garcia-Cehic
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
| | - Marta Ibáñez
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
| | - Tomàs Pumarola
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
- Microbiology Department, Universitat Autònoma de Barcelona (UAB), UAB Campus, Plaça Cívica, 08193 Bellaterra, Spain
| | - Francisco Rodríguez-Frías
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), UAB Campus, Plaça Cívica, 08193 Bellaterra, Spain
- Clinical Biochemistry Research Group, Biochemistry Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Andrés Antón
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
- Microbiology Department, Universitat Autònoma de Barcelona (UAB), UAB Campus, Plaça Cívica, 08193 Bellaterra, Spain
- Correspondence: (J.Q.); (A.A.)
| | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
- Microbiology Departments, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
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23
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Chiropteran (Chiroptera; Mammalia) taxonomy in light of modern methods and approaches. RUSSIAN JOURNAL OF THERIOLOGY 2021. [DOI: 10.15298/rusjtheriol.20.2.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Zhou H, Ma L, Liu L, Yao X. TR Locus Annotation and Characteristics of Rhinolophus ferrumequinum. Front Immunol 2021; 12:741408. [PMID: 34659234 PMCID: PMC8514952 DOI: 10.3389/fimmu.2021.741408] [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: 07/14/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
T-cell antigen receptors (TRs) in vertebrates can be divided into αβ or γδ, encoded by TRA/D, TRG, or TRB loci. TRs play a central role in mammal cellular immunity, which occurs by rearrangement of V, D, J, and C genes in the loci. The bat is the only mammal with flying ability and is considered the main host of zoonotic viruses, an important public health concern. However, at present, little is known about the composition of bat TR genes. Based on the whole genome sequence of the greater horseshoe bat (Rhinolophus ferrumequinum) and referring to the TR/IG annotation rules formulated by the international ImMunoGeneTics information system (IMGT), we present a complete annotation of TRA/D, TRG, and TRB loci of R. ferrumequinum. A total of 128 V segments, three D segments, 85 J segments, and 6 C segments were annotated and compared with other known mammalian data. The characteristics of the TR locus and germline genes of R. ferrumequinum are analyzed.
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Affiliation(s)
- Hao Zhou
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Long Ma
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Longyu Liu
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Xinsheng Yao
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
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25
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Christie MJ, Irving AT, Forster SC, Marsland BJ, Hansbro PM, Hertzog PJ, Nold-Petry CA, Nold MF. Of bats and men: Immunomodulatory treatment options for COVID-19 guided by the immunopathology of SARS-CoV-2 infection. Sci Immunol 2021; 6:eabd0205. [PMID: 34533977 DOI: 10.1126/sciimmunol.abd0205] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Michael J Christie
- Department of Paediatrics, Monash University, Melbourne, Victoria 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne, Victoria 3168, Australia
| | - Aaron T Irving
- Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.,Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining 314400, China
| | - Samuel C Forster
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Molecular and Translational Sciences, Monash University, Melbourne, Victoria, Australia
| | - Benjamin J Marsland
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute, Sydney, NSW 2050, Australia.,Centre for Inflammation, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Paul J Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Molecular and Translational Sciences, Monash University, Melbourne, Victoria, Australia
| | - Claudia A Nold-Petry
- Department of Paediatrics, Monash University, Melbourne, Victoria 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne, Victoria 3168, Australia
| | - Marcel F Nold
- Department of Paediatrics, Monash University, Melbourne, Victoria 3168, Australia.,Ritchie Centre, Hudson Institute of Medical Research, Melbourne, Victoria 3168, Australia.,Monash Newborn, Monash Children's Hospital, Melbourne, Victoria, Australia
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26
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Vandewege MW, Sotero-Caio CG, Phillips CD. Positive Selection and Gene Expression Analyses from Salivary Glands Reveal Discrete Adaptations within the Ecologically Diverse Bat Family Phyllostomidae. Genome Biol Evol 2021; 12:1419-1428. [PMID: 32697843 PMCID: PMC7487161 DOI: 10.1093/gbe/evaa151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2020] [Indexed: 12/15/2022] Open
Abstract
The leaf-nosed bats (Phyllostomidae) are outliers among chiropterans with respect to the unusually high diversity of dietary strategies within the family. Salivary glands, owing to their functions and high ultrastructural variability among lineages, are proposed to have played an important role during the phyllostomid radiation. To identify genes underlying salivary gland functional diversification, we sequenced submandibular gland transcriptomes from phyllostomid species representative of divergent dietary strategies. From the assembled transcriptomes, we performed an array of selection tests and gene expression analyses to identify signatures of adaptation. Overall, we identified an enrichment of immunity-related gene ontology terms among 53 genes evolving under positive selection. Lineage-specific selection tests revealed several endomembrane system genes under selection in the vampire bat. Many genes that respond to insulin were under selection and differentially expressed genes pointed to modifications of amino acid synthesis pathways in plant-visitors. Results indicate salivary glands have diversified in various ways across a functional diverse clade of mammals in response to niche specializations.
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27
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Chazal N. Coronavirus, the King Who Wanted More Than a Crown: From Common to the Highly Pathogenic SARS-CoV-2, Is the Key in the Accessory Genes? Front Microbiol 2021; 12:682603. [PMID: 34335504 PMCID: PMC8317507 DOI: 10.3389/fmicb.2021.682603] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/22/2021] [Indexed: 12/14/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), that emerged in late 2019, is the etiologic agent of the current "coronavirus disease 2019" (COVID-19) pandemic, which has serious health implications and a significant global economic impact. Of the seven human coronaviruses, all of which have a zoonotic origin, the pandemic SARS-CoV-2, is the third emerging coronavirus, in the 21st century, highly pathogenic to the human population. Previous human coronavirus outbreaks (SARS-CoV-1 and MERS-CoV) have already provided several valuable information on some of the common molecular and cellular mechanisms of coronavirus infections as well as their origin. However, to meet the new challenge caused by the SARS-CoV-2, a detailed understanding of the biological specificities, as well as knowledge of the origin are crucial to provide information on viral pathogenicity, transmission and epidemiology, and to enable strategies for therapeutic interventions and drug discovery. Therefore, in this review, we summarize the current advances in SARS-CoV-2 knowledges, in light of pre-existing information of other recently emerging coronaviruses. We depict the specificity of the immune response of wild bats and discuss current knowledge of the genetic diversity of bat-hosted coronaviruses that promotes viral genome expansion (accessory gene acquisition). In addition, we describe the basic virology of coronaviruses with a special focus SARS-CoV-2. Finally, we highlight, in detail, the current knowledge of genes and accessory proteins which we postulate to be the major keys to promote virus adaptation to specific hosts (bat and human), to contribute to the suppression of immune responses, as well as to pathogenicity.
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Affiliation(s)
- Nathalie Chazal
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS, Montpellier, France
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28
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Franzen J, Soto S, Fasel NJ, Rüegg-van den Broek P, Veiga IB. Malignant Peripheral Nerve Sheath Tumour in a Seba's Short-Tailed Bat (Carollia perspicillata). J Comp Pathol 2021; 184:72-76. [PMID: 33894882 DOI: 10.1016/j.jcpa.2021.02.004] [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: 11/11/2020] [Revised: 01/04/2021] [Accepted: 02/19/2021] [Indexed: 10/21/2022]
Abstract
There are few reports of tumours in bats, despite the fact that members of the Chiroptera order include 22.4% of all currently known mammal species. We now describe a case of malignant peripheral nerve sheath tumour (MPNST) in an adult female Seba's short-tailed bat (Carollia perspicillata) from a private zoo in Switzerland. The macroscopical and histological findings indicated that the MPNST originated from a dorsal spinal nerve root sheath in the lumbar region and metastasized to the spleen. Immunohistochemical labelling for glial fibrillary acid protein, S100 protein, neuron specific enolase and synaptophysin was negative. The cytoplasm of a few neoplastic cells labelled for smooth muscle actin and desmin. To our knowledge, this is the first report of a PNST in a member of the Chiroptera order.
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Affiliation(s)
- Jan Franzen
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
| | - Sara Soto
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nicolas J Fasel
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Inês B Veiga
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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29
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Irving AT, Ahn M, Goh G, Anderson DE, Wang LF. Lessons from the host defences of bats, a unique viral reservoir. Nature 2021; 589:363-370. [PMID: 33473223 DOI: 10.1038/s41586-020-03128-0] [Citation(s) in RCA: 170] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 12/03/2020] [Indexed: 01/30/2023]
Abstract
There have been several major outbreaks of emerging viral diseases, including Hendra, Nipah, Marburg and Ebola virus diseases, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS)-as well as the current pandemic of coronavirus disease 2019 (COVID-19). Notably, all of these outbreaks have been linked to suspected zoonotic transmission of bat-borne viruses. Bats-the only flying mammal-display several additional features that are unique among mammals, such as a long lifespan relative to body size, a low rate of tumorigenesis and an exceptional ability to host viruses without presenting clinical disease. Here we discuss the mechanisms that underpin the host defence system and immune tolerance of bats, and their ramifications for human health and disease. Recent studies suggest that 64 million years of adaptive evolution have shaped the host defence system of bats to balance defence and tolerance, which has resulted in a unique ability to act as an ideal reservoir host for viruses. Lessons from the effective host defence of bats would help us to better understand viral evolution and to better predict, prevent and control future viral spillovers. Studying the mechanisms of immune tolerance in bats could lead to new approaches to improving human health. We strongly believe that it is time to focus on bats in research for the benefit of both bats and humankind.
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Affiliation(s)
- Aaron T Irving
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore. .,Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China. .,Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Matae Ahn
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Geraldine Goh
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore. .,SingHealth Duke-NUS Global Health Institute, Singapore, Singapore.
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30
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Donnik IM, Popov IV, Sereda SV, Popov IV, Chikindas ML, Ermakov AM. Coronavirus Infections of Animals: Future Risks to Humans. BIOL BULL+ 2021; 48:26-37. [PMID: 33679117 PMCID: PMC7917535 DOI: 10.1134/s1062359021010052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/27/2020] [Accepted: 07/17/2020] [Indexed: 01/31/2023]
Abstract
Coronaviruses have tremendous evolutionary potential, and three major outbreaks of new human coronavirus infections have occurred in the recent history of humankind. In this paper, the patterns of occurrence of new zoonotic coronavirus infections and the role of bioveterinary control in preventing their potential outbreaks in the future are determined. The possibility of SARS-CoV-2 infection in companion animals is considered. Diverse human activities may trigger various interactions between animal species and their viruses, sometimes causing the emergence of new viral pathogens. In addition, the possibility of using probiotics for the control of viral infections in animals is discussed.
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Affiliation(s)
- I. M. Donnik
- Russian Academy of Sciences, 119991 Moscow, Russia
| | - Ig. V. Popov
- Don State Technical University, 344000 Rostov-on-Don, Russia ,Rostov State Medical University, 344022 Rostov-on-Don, Russia
| | - S. V. Sereda
- Don State Technical University, 344000 Rostov-on-Don, Russia
| | - Il. V. Popov
- Rostov State Medical University, 344022 Rostov-on-Don, Russia
| | - M. L. Chikindas
- Don State Technical University, 344000 Rostov-on-Don, Russia ,Health Promoting Naturals Laboratory, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, 08901 New Brunswick, NJ USA
| | - A. M. Ermakov
- Don State Technical University, 344000 Rostov-on-Don, Russia
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31
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Clayton E, Munir M. Fundamental Characteristics of Bat Interferon Systems. Front Cell Infect Microbiol 2020; 10:527921. [PMID: 33363045 PMCID: PMC7759481 DOI: 10.3389/fcimb.2020.527921] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 11/09/2020] [Indexed: 12/24/2022] Open
Abstract
Interferons are an essential component of the innate arm of the immune system and are arguably one of the most important lines of defence against viruses. The human IFN system and its functionality has already been largely characterized and studied in detail. However, the IFN systems of bats have only been marginally examined to date up until the recent developments of the Bat1k project which have now opened new opportunities in research by identifying six new bat genomes to possess novel genes that are likely associated with viral tolerance exhibited in bats. Interestingly, bats have been hypothesized to possess the ability to establish a host-virus relationship where despite being infected, they exhibit limited signs of disease and still retain the ability to transmit the disease into other susceptible hosts. Bats are one of the most abundant and widespread vertebrates on the planet and host many zoonotic viruses that are highly pathogenic to humans. Several genomics, immunological, and biological features are thought to underlie novel antiviral mechanisms of bats. This review aims to explore the bat IFN system and developments in its diverse IFN features, focusing mainly on the model species, the Australian black flying fox (Pteropus alecto), while also highlighting bat innate immunity as an exciting and fruitful area of research to understand their ability to control viral-mediated pathogenesis.
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Affiliation(s)
- Emily Clayton
- Department of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
| | - Muhammad Munir
- Department of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
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32
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Herculano-Houzel S, da Cunha FB, Reed JL, Kaswera-Kyamakya C, Gillissen E, Manger PR. Microchiropterans have a diminutive cerebral cortex, not an enlarged cerebellum, compared to megachiropterans and other mammals. J Comp Neurol 2020; 528:2978-2993. [PMID: 32656795 DOI: 10.1002/cne.24985] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 06/14/2020] [Accepted: 06/16/2020] [Indexed: 11/11/2022]
Abstract
Small echolocating bats are set apart from most other mammals by their relatively large cerebellum, a feature that has been associated to echolocation, as it is presumed to indicate a relatively enlarged number of neurons in the cerebellum in comparison to other brain structures. Here we quantify the neuronal composition of the cerebral cortex, cerebellum and remaining brain structures of seven species of large Pteropodid bats (formerly classified as megachiropterans), one of which echolocates, and six species of small bats (formerly classified as microchiropterans), all of which echolocate. This chiropteran data is compared to 60 mammalian species in our dataset to determine whether the relatively large cerebellum of the small echolocating bats, and possibly that of the echolocating Pteropodid, contains a relatively enlarged number of neurons. We find no evidence that the distribution of neurons differs between microchiropterans and megachiropterans, but our data indicate that microchiropterans, like the smallest shrew in our dataset, have diminutive cerebral cortices, which makes the cerebellum appear relatively large. We propose that, in agreement with the diminutive brain size of the earliest fossil mammals, this is a plesiomorphic, not a derived, feature of microchiropteran brains. The results of this study also reveal important neural characteristics related to the phylogenetic affinities and relationships of the chiropterans.
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Affiliation(s)
- Suzana Herculano-Houzel
- Department of Psychology, Vanderbilt University, Nashville, Tennessee, USA.,Department Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA.,Vanderbilt Brain Institute, Vanderbilt University, Nashville, Tennessee, USA
| | - Felipe Barros da Cunha
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,University of Lethbridge, Lethbridge, Canada
| | - Jamie L Reed
- Department of Psychology, Vanderbilt University, Nashville, Tennessee, USA
| | | | - Emmanuel Gillissen
- Department of African Zoology, Royal Museum for Central Africa, Tervuren, Belgium.,Laboratory of Histology and Neuropathology, Université Libre de Bruxelles, Brussels, Belgium.,Department of Anthropology, University of Arkansas, Fayetteville, Arkansas, USA
| | - Paul R Manger
- School of Anatomical Sciences, University of the Witwatersrand, South Africa
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33
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RTP4 Is a Potent IFN-Inducible Anti-flavivirus Effector Engaged in a Host-Virus Arms Race in Bats and Other Mammals. Cell Host Microbe 2020; 28:712-723.e9. [PMID: 33113352 DOI: 10.1016/j.chom.2020.09.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/19/2020] [Accepted: 09/15/2020] [Indexed: 12/17/2022]
Abstract
Among mammals, bats are particularly rich in zoonotic viruses, including flaviviruses. Certain bat species can be productively yet asymptomatically infected with viruses that cause overt disease in other species. However, little is known about the antiviral effector repertoire in bats relative to other mammals. Here, we report the black flying fox receptor transporter protein 4 (RTP4) as a potent interferon (IFN)-inducible inhibitor of human pathogens in the Flaviviridae family, including Zika, West Nile, and hepatitis C viruses. Mechanistically, RTP4 associates with the flavivirus replicase, binds viral RNA, and suppresses viral genome amplification. Comparative approaches revealed that RTP4 undergoes positive selection, that a flavivirus can mutate to escape RTP4-imposed restriction, and that diverse mammalian RTP4 orthologs exhibit striking patterns of specificity against distinct Flaviviridae members. Our findings reveal an antiviral mechanism that has likely adapted over 100 million years of mammalian evolution to accommodate unique host-virus genetic conflicts.
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34
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Complementary regulation of caspase-1 and IL-1β reveals additional mechanisms of dampened inflammation in bats. Proc Natl Acad Sci U S A 2020; 117:28939-28949. [PMID: 33106404 DOI: 10.1073/pnas.2003352117] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Bats have emerged as unique mammalian vectors harboring a diverse range of highly lethal zoonotic viruses with minimal clinical disease. Despite having sustained complete genomic loss of AIM2, regulation of the downstream inflammasome response in bats is unknown. AIM2 sensing of cytoplasmic DNA triggers ASC aggregation and recruits caspase-1, the central inflammasome effector enzyme, triggering cleavage of cytokines such as IL-1β and inducing GSDMD-mediated pyroptotic cell death. Restoration of AIM2 in bat cells led to intact ASC speck formation, but intriguingly resulted in a lack of caspase-1 or consequent IL-1β activation. We further identified two residues undergoing positive selection pressures in Pteropus alecto caspase-1 that abrogate its enzymatic function and are crucial in human caspase-1 activity. Functional analysis of another bat lineage revealed a targeted mechanism for loss of Myotis davidii IL-1β cleavage and elucidated an inverse complementary relationship between caspase-1 and IL-1β, resulting in overall diminished signaling across bats of both suborders. Thus we report strategies that additionally undermine downstream inflammasome signaling in bats, limiting an overactive immune response against pathogens while potentially producing an antiinflammatory state resistant to diseases such as atherosclerosis, aging, and neurodegeneration.
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35
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Crespi B. Evolutionary medical insights into the SARS-CoV-2 pandemic. Evol Med Public Health 2020; 2020:314-322. [PMID: 33335737 PMCID: PMC7665492 DOI: 10.1093/emph/eoaa036] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/28/2020] [Indexed: 12/13/2022] Open
Abstract
The author apply concepts and tools from evolutionary medicine to understanding the SARS-CoV-2 pandemic. The pandemic represents a mismatched conflict, with dynamics and pathology apparently driven by three main factors: (i) bat immune systems that rely on low inflammation but high efficacy of interferon-based defenses; (ii) viral tactics that differentially target the human interferon system, leading to substantial asymptomatic and pre-symptomatic transmission; and (ii) high mortality caused by hyper-inflammatory and hyper-coagulatory phenotypes, that represent dysregulated tradeoffs whereby collateral immune-induced damage becomes systemic and severe. This framework can explain the association of mortality with age (which involves immune life-history shifts towards higher inflammation and coagulation and reduced adaptive immunity), and sex (since males senesce faster than females). Genetic-risk factors for COVID-19 mortality can be shown, from a phenome-wide association analysis of the relevant SNPs, to be associated with inflammation and coagulation; the phenome-wide association study also provides evidence, consistent with several previous studies, that the calcium channel blocking drug amlodipine mediates risk of mortality. Lay Summary: SARS-CoV-2 is a bat virus that jumped into humans. The virus is adapted to bat immune systems, where it evolved to suppress the immune defenses (interferons) that mammals use to tell that they are infected. In humans, the virus can apparently spread effectively in the body with a delay in the production of symptoms and the initiation of immune responses. This delay may then promote overactive immune responses, when the virus is detected, that damage the body as a side effect. Older people are more vulnerable to the virus because they are less adapted to novel infectious agents, and invest less in immune defense, compared to younger people. Genes that increase risk of mortality from SARS-CoV-2 are functionally associated with a drug called amlodipine, which may represent a useful treatment.
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Affiliation(s)
- Bernard Crespi
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
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36
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Picard L, Ganivet Q, Allatif O, Cimarelli A, Guéguen L, Etienne L. DGINN, an automated and highly-flexible pipeline for the detection of genetic innovations on protein-coding genes. Nucleic Acids Res 2020; 48:e103. [PMID: 32941639 PMCID: PMC7544217 DOI: 10.1093/nar/gkaa680] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 06/29/2020] [Accepted: 09/04/2020] [Indexed: 12/13/2022] Open
Abstract
Adaptive evolution has shaped major biological processes. Finding the protein-coding genes and the sites that have been subjected to adaptation during evolutionary time is a major endeavor. However, very few methods fully automate the identification of positively selected genes, and widespread sources of genetic innovations such as gene duplication and recombination are absent from most pipelines. Here, we developed DGINN, a highly-flexible and public pipeline to Detect Genetic INNovations and adaptive evolution in protein-coding genes. DGINN automates, from a gene's sequence, all steps of the evolutionary analyses necessary to detect the aforementioned innovations, including the search for homologs in databases, assignation of orthology groups, identification of duplication and recombination events, as well as detection of positive selection using five methods to increase precision and ranking of genes when a large panel is analyzed. DGINN was validated on nineteen genes with previously-characterized evolutionary histories in primates, including some engaged in host-pathogen arms-races. Our results confirm and also expand results from the literature, including novel findings on the Guanylate-binding protein family, GBPs. This establishes DGINN as an efficient tool to automatically detect genetic innovations and adaptive evolution in diverse datasets, from the user's gene of interest to a large gene list in any species range.
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Affiliation(s)
- Lea Picard
- CIRI - Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
- Laboratoire de Biologie et Biométrie Evolutive, CNRS UMR 5558, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Quentin Ganivet
- Laboratoire de Biologie et Biométrie Evolutive, CNRS UMR 5558, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Omran Allatif
- CIRI - Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Andrea Cimarelli
- CIRI - Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Laurent Guéguen
- Laboratoire de Biologie et Biométrie Evolutive, CNRS UMR 5558, Université Claude Bernard Lyon 1, Villeurbanne, France
- Swedish Collegium for Advanced Study, Uppsala, Sweden
| | - Lucie Etienne
- CIRI - Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
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37
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Sackton TB. Studying Natural Selection in the Era of Ubiquitous Genomes. Trends Genet 2020; 36:792-803. [DOI: 10.1016/j.tig.2020.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 01/15/2023]
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38
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Sun H, Chen W, Wang J, Zhang L, Rossiter SJ, Mao X. Echolocation call frequency variation in horseshoe bats: molecular basis revealed by comparative transcriptomics. Proc Biol Sci 2020; 287:20200875. [PMID: 32900318 DOI: 10.1098/rspb.2020.0875] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Recently diverged taxa with contrasting phenotypes offer opportunities for unravelling the genetic basis of phenotypic variation in nature. Horseshoe bats are a speciose group that exhibit a derived form of high-duty cycle echolocation in which the inner ear is finely tuned to echoes of the narrowband call frequency. Here, by focusing on three recently diverged subspecies of the intermediate horseshoe bat (Rhinolophus affinis) that display divergent echolocation call frequencies, we aim to identify candidate loci putatively involved in hearing frequency variation. We used de novo transcriptome sequencing of two mainland taxa (himalayanus and macrurus) and one island taxon (hainanus) to compare expression profiles of thousands of genes. By comparing taxa with divergent call frequencies (around 15 kHz difference), we identified 252 differentially expressed genes, of which six have been shown to be involved in hearing or deafness in human/mouse. To obtain further validation of these results, we applied quantitative reverse transcription-PCR to the candidate gene FBXL15 and found a broad association between the level of expression and call frequency across taxa. The genes identified here represent strong candidate loci associated with hearing frequency variation in bats.
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Affiliation(s)
- Haijian Sun
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, People's Republic of China
| | - Wenli Chen
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, People's Republic of China
| | - Jiaying Wang
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, People's Republic of China
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou 510260, People's Republic of China
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, People's Republic of China.,Institute of Eco-Chongming (IEC), East China Normal University, Shanghai 200062, People's Republic of China
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39
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Affiliation(s)
- Omoshola Aleru
- Institute of Ecology & Evolution, University of Oregon, Eugene, Oregon, United States of America
- Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Matthew F. Barber
- Institute of Ecology & Evolution, University of Oregon, Eugene, Oregon, United States of America
- Department of Biology, University of Oregon, Eugene, Oregon, United States of America
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40
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Fouret J, Brunet FG, Binet M, Aurine N, Enchéry F, Croze S, Guinier M, Goumaidi A, Preininger D, Volff JN, Bailly-Bechet M, Lachuer J, Horvat B, Legras-Lachuer C. Sequencing the Genome of Indian Flying Fox, Natural Reservoir of Nipah Virus, Using Hybrid Assembly and Conservative Secondary Scaffolding. Front Microbiol 2020; 11:1807. [PMID: 32849415 PMCID: PMC7403528 DOI: 10.3389/fmicb.2020.01807] [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: 01/15/2020] [Accepted: 07/09/2020] [Indexed: 11/20/2022] Open
Abstract
Indian fruit bats, flying fox Pteropus medius was identified as an asymptomatic natural host of recently emerged Nipah virus, which is known to induce a severe infectious disease in humans. The absence of P. medius genome sequence presents an important obstacle for further studies of virus–host interactions and better understanding of mechanisms of zoonotic viral emergence. Generation of the high-quality genome sequence is often linked to a considerable effort associated to elevated costs. Although secondary scaffolding methods have reduced sequencing expenses, they imply the development of new tools for the integration of different data sources to achieve more reliable sequencing results. We initially sequenced the P. medius genome using the combination of Illumina paired-end and Nanopore sequencing, with a depth of 57.4x and 6.1x, respectively. Then, we introduced the novel scaff2link software to integrate multiple sources of information for secondary scaffolding, allowing to remove the association with discordant information among two sources. Different quality metrics were next produced to validate the benefits from secondary scaffolding. The P. medius genome, assembled by this method, has a length of 1,985 Mb and consists of 33,613 contigs and 16,113 scaffolds with an NG50 of 19 Mb. At least 22.5% of the assembled sequences is covered by interspersed repeats already described in other species and 19,823 coding genes are annotated. Phylogenetic analysis demonstrated the clustering of P. medius genome with two other Pteropus bat species, P. alecto and P. vampyrus, for which genome sequences are currently available. SARS-CoV entry receptor ACE2 sequence of P. medius was 82.7% identical with ACE2 of Rhinolophus sinicus bats, thought to be the natural host of SARS-CoV. Altogether, our results confirm that a lower depth of sequencing is enough to obtain a valuable genome sequence, using secondary scaffolding approaches and demonstrate the benefits of the scaff2link application. The genome sequence is now available to the scientific community to (i) proceed with further genomic analysis of P. medius, (ii) to characterize the underlying mechanism allowing Nipah virus maintenance and perpetuation in its bat host, and (iii) to monitor their evolutionary pathways toward a better understanding of bats’ ability to control viral infections.
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Affiliation(s)
- Julien Fouret
- CIRI, International Center for Infectiology Research, Team Immunobiology of Viral Infections, Univ Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Viroscan3D, Trévoux, France
| | - Frédéric G Brunet
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Martin Binet
- CIRI, International Center for Infectiology Research, Team Immunobiology of Viral Infections, Univ Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Viroscan3D, Trévoux, France
| | - Noémie Aurine
- CIRI, International Center for Infectiology Research, Team Immunobiology of Viral Infections, Univ Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Francois Enchéry
- CIRI, International Center for Infectiology Research, Team Immunobiology of Viral Infections, Univ Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Séverine Croze
- Plateforme Profilexpert, Université Claude Bernard Lyon 1, Lyon, France
| | | | | | | | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | | | - Joël Lachuer
- Cancer Research Center of Lyon, INSERM 1052/CNRS 5286, Université de Lyon, Lyon, France.,Plateforme Profilexpert, Université Claude Bernard Lyon 1, Lyon, France
| | - Branka Horvat
- CIRI, International Center for Infectiology Research, Team Immunobiology of Viral Infections, Univ Lyon, INSERM U1111, CNRS UMR 5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Catherine Legras-Lachuer
- Viroscan3D, Trévoux, France.,Ecologie Microbienne, CNRS UMR 5557, LEM, INRA, VetAgro Sup, Université Claude Bernard Lyon 1, Villeurbanne, France
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41
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Tuo Y, Chu W, Zhang J, Cheng J, Chen L, Bao L, Xiao T. Analysis of Natural Selection of Immune Genes in Spinibarbus caldwelli by Transcriptome Sequencing. Front Genet 2020; 11:714. [PMID: 32793279 PMCID: PMC7393255 DOI: 10.3389/fgene.2020.00714] [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: 09/24/2019] [Accepted: 06/11/2020] [Indexed: 12/03/2022] Open
Abstract
Spinibarbus caldwelli is an omnivorous cyprinid fish that is distributed widely in China. To investigate the adaptive evolution of S. caldwelli, the muscle transcriptome was sequenced by Illumina HiSeq 4000 platform. A total of 80,447,367 reads were generated by next-generation sequencing. Also, 211,386 unigenes were obtained by de novo assembly. Additionally, we calculated that the divergence time between S. caldwelli and Sinocyclocheilus grahami is 23.14 million years ago (Mya). And both of them diverged from Ctenopharyngodon idellus 46.95 Mya. Furthermore, 38 positive genes were identified by calculating Ka/Ks ratios from 9225 orthologs. Among them, several immune-related genes were identified as positively selected, such as POLR3B, PIK3C3, TOPORS, FASTKD3, CYPLP1A1, and UACA. Our results throw light on the nature of the natural selection of S. caldwelli and contribute to future immunological and transcriptome studies.
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Affiliation(s)
- Yun Tuo
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, China.,College of Life Science and Resources Environment, Yichun University, Yichun, China
| | - Wuying Chu
- Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Jianshe Zhang
- Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Jia Cheng
- Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Lin Chen
- Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Lingsheng Bao
- Department of Biological and Environmental Engineering, Changsha University, Changsha, China
| | - Tiaoyi Xiao
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, China
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42
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Wcisel DJ, Howard JT, Yoder JA, Dornburg A. Transcriptome Ortholog Alignment Sequence Tools (TOAST) for phylogenomic dataset assembly. BMC Evol Biol 2020; 20:41. [PMID: 32228442 PMCID: PMC7106827 DOI: 10.1186/s12862-020-01603-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 03/11/2020] [Indexed: 01/05/2023] Open
Abstract
Background Advances in next-generation sequencing technologies have reduced the cost of whole transcriptome analyses, allowing characterization of non-model species at unprecedented levels. The rapid pace of transcriptomic sequencing has driven the public accumulation of a wealth of data for phylogenomic analyses, however lack of tools aimed towards phylogeneticists to efficiently identify orthologous sequences currently hinders effective harnessing of this resource. Results We introduce TOAST, an open source R software package that can utilize the ortholog searches based on the software Benchmarking Universal Single-Copy Orthologs (BUSCO) to assemble multiple sequence alignments of orthologous loci from transcriptomes for any group of organisms. By streamlining search, query, and alignment, TOAST automates the generation of locus and concatenated alignments, and also presents a series of outputs from which users can not only explore missing data patterns across their alignments, but also reassemble alignments based on user-defined acceptable missing data levels for a given research question. Conclusions TOAST provides a comprehensive set of tools for assembly of sequence alignments of orthologs for comparative transcriptomic and phylogenomic studies. This software empowers easy assembly of public and novel sequences for any target database of candidate orthologs, and fills a critically needed niche for tools that enable quantification and testing of the impact of missing data. As open-source software, TOAST is fully customizable for integration into existing or novel custom informatic pipelines for phylogenomic inference. Software, a detailed manual, and example data files are available through github carolinafishes.github.io
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Affiliation(s)
- Dustin J Wcisel
- Department of Molecular Biomedical Sciences, NC State University, Raleigh, NC, USA
| | - J Thomas Howard
- Department of Molecular Biomedical Sciences, NC State University, Raleigh, NC, USA
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, NC State University, Raleigh, NC, USA.,Comparative Medicine Institute, NC State University, Raleigh, NC, USA.,Center for Human Health and the Environment, NC State University, Raleigh, NC, USA
| | - Alex Dornburg
- Department of Molecular Biomedical Sciences, NC State University, Raleigh, NC, USA.
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43
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Banerjee A, Baker ML, Kulcsar K, Misra V, Plowright R, Mossman K. Novel Insights Into Immune Systems of Bats. Front Immunol 2020; 11:26. [PMID: 32117225 PMCID: PMC7025585 DOI: 10.3389/fimmu.2020.00026] [Citation(s) in RCA: 157] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/08/2020] [Indexed: 11/13/2022] Open
Abstract
In recent years, viruses similar to those that cause serious disease in humans and other mammals have been detected in apparently healthy bats. These include filoviruses, paramyxoviruses, and coronaviruses that cause severe diseases such as Ebola virus disease, Marburg haemorrhagic fever and severe acute respiratory syndrome (SARS) in humans. The evolution of flight in bats seem to have selected for a unique set of antiviral immune responses that control virus propagation, while limiting self-damaging inflammatory responses. Here, we summarize our current understanding of antiviral immune responses in bats and discuss their ability to co-exist with emerging viruses that cause serious disease in other mammals. We highlight how this knowledge may help us to predict viral spillovers into new hosts and discuss future directions for the field.
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Affiliation(s)
- Arinjay Banerjee
- Department of Pathology and Molecular Medicine, Michael DeGroote Institute for Infectious Disease Research, McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | - Michelle L Baker
- Health and Biosecurity Business Unit, Australian Animal Health Laboratory, CSIRO, Geelong, VIC, Australia
| | - Kirsten Kulcsar
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Vikram Misra
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Raina Plowright
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Karen Mossman
- Department of Pathology and Molecular Medicine, Michael DeGroote Institute for Infectious Disease Research, McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
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