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Deng S, Tian X, Belshaw R, Zhou J, Zhang S, Yang Y, Huang C, Chen W, Qiu H, Choo SW. An RNA-Seq analysis of coronavirus in the skin of the Pangolin. Sci Rep 2024; 14:910. [PMID: 38195813 PMCID: PMC10776870 DOI: 10.1038/s41598-024-51261-x] [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: 10/26/2023] [Accepted: 01/02/2024] [Indexed: 01/11/2024] Open
Abstract
Protection of the Critically Endangered East Asian Pangolin species is hampered by the vulnerability of captive individuals to infection. Studies have previously shown the pangolin to have a unique pseudogenisation of many immunity genes (including IFNE, IFIH1, cGAS, STING, TLR5, and TLR11), and we suspected that these losses could account for this vulnerability. Here we used RNA-Seq data to show the effect of these gene losses on the transcriptional response to a viral skin infection in a deceased pangolin. This virus is very closely related to the one causing the current COVID-19 pandemic in the human population (SARS-CoV2), and we found the most upregulated pathway was the same one previously identified in the lungs of SARS-CoV2-infected humans. As predicted, we found that the pathways downstream of the lost genes were not upregulated. For example, the pseudogenised interferon epsilon (IFNE) is known to be particularly important in epithelial immunity, and we show that interferon-related responses were not upregulated in the infected pangolin skin. We suggest that the pangolin's innate gene pseudogenisation is indeed likely to be responsible for the animal's vulnerability to infection.
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Affiliation(s)
- Siwei Deng
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China
| | - Xuechen Tian
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Centre, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China
| | - Robert Belshaw
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China
| | - Jinfeng Zhou
- China Biodiversity Conservation and Green Development Foundation (CBCGDF), Empark International Apartment, No. 69, Banding Road, Haidian District, Beijing, China
| | - Siyuan Zhang
- China Biodiversity Conservation and Green Development Foundation (CBCGDF), Empark International Apartment, No. 69, Banding Road, Haidian District, Beijing, China
| | - Yixin Yang
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Centre, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China
- Dorothy and George Hennings College of Science, Mathematics and Technology, Kean University, 1000 Morris Ave, Union, NJ, 07083, USA
| | - Chang Huang
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China
| | - Weikang Chen
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China
| | - Hailu Qiu
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China
| | - Siew Woh Choo
- Department of Biology, College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China.
- Zhejiang Bioinformatics International Science and Technology Cooperation Centre, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China.
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang, 325060, China.
- Dorothy and George Hennings College of Science, Mathematics and Technology, Kean University, 1000 Morris Ave, Union, NJ, 07083, USA.
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Zhang X, Xie T, Li X, Feng M, Mo G, Zhang Q, Zhang X. Transcriptome Sequencing Reveals That Intact Expression of the Chicken Endogenous Retrovirus chERV3 In Vitro Can Possibly Block the Key Innate Immune Pathway. Animals (Basel) 2023; 13:2720. [PMID: 37684986 PMCID: PMC10486640 DOI: 10.3390/ani13172720] [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: 07/17/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
Endogenous retroviruses (ERVs) are viral sequences that have integrated into the genomes of vertebrates. Our preliminary transcriptome sequencing analysis revealed that chERV3 is active and is located on chromosome 1:32602284-32615631. We hypothesized that chERV3 may have a role in the host innate immune response to viral infection. In this study, using reverse genetics, we constructed the puc57-chERV3 full-length reverse cloning plasmid in vitro. We measured the p27 content in culture supernatant by enzyme-linked immunosorbent assay (ELISA). Finally, transcriptome analysis was performed to analyze the function of chERV3 in innate immunity. The results showed that chERV3 may generate p27 viral particles. We found that compared to the negative control (NC) group (transfected with pMD18T-EGFP), the chERV3 group exhibited 2538 up-regulated differentially expressed genes (DEGs) and 1828 down-regulated DEGs at 24 hours (h) and 1752 up-regulated DEGs and 1282 down-regulated DEGs at 48 h. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, the down-regulated DEGs were enriched mainly in immune-related processes such as the inflammatory response, innate immune response, and Toll-like receptor signaling pathway. GSEA showed that the Toll-like receptor signaling pathway was suppressed by chERV3 at both time points. We hypothesized that chERV3 can influence the activation of the innate immune pathway by blocking the Toll-like receptor signaling pathway to achieve immune evasion.
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Affiliation(s)
- Xi Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.Z.)
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Tingting Xie
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.Z.)
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Xiaoqi Li
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.Z.)
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Min Feng
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.Z.)
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Guodong Mo
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.Z.)
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Qihong Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.Z.)
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Xiquan Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.Z.)
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
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3
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Dai M, Xie T, Feng M, Zhang X. Endogenous retroviruses transcriptomes in response to four avian pathogenic microorganisms infection in chicken. Genomics 2022; 114:110371. [PMID: 35462029 DOI: 10.1016/j.ygeno.2022.110371] [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: 10/13/2021] [Revised: 02/20/2022] [Accepted: 04/17/2022] [Indexed: 01/14/2023]
Abstract
The impact of Endogenous retroviruses (ERVs) on chicken disease is not well understood. Here, we systematically identified 436 relatively complete ChERVs from the chicken genome. Subsequently, ChERV transcriptomes were analyzed in chicken after subgroup J avian leukosis virus (ALV-J), avian influenza virus (AIV), Marek's disease virus (MDV) and avian pathogenic Escherichia coli (APEC) infection. We found that about 50%-68% of ChERVs were transcriptionally active in infected and uninfected-samples, although the abundance of most ChERVs is relatively low. Moreover, compared to uninfected-samples, 49, 18, 66 and 17 ChERVs were significantly differentially expressed in ALV-J, AIV, MDV and APEC infected-samples, respectively. These findings may be of significance for understanding the role and function of ChERVs to response the pathogenic microorganism infection.
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Affiliation(s)
- Manman Dai
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Tingting Xie
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Min Feng
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Xiquan Zhang
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
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Middlebrook EA, Stark DL, Cornwall DH, Kubinak JL, Potts WK. Deep Sequencing of MHC-Adapted Viral Lines Reveals Complex Recombinational Exchanges With Endogenous Retroviruses Leading to High-Frequency Variants. Front Genet 2021; 12:716623. [PMID: 34512727 PMCID: PMC8430262 DOI: 10.3389/fgene.2021.716623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/05/2021] [Indexed: 12/03/2022] Open
Abstract
Experimental evolution (serial passage) of Friend virus complex (FVC) in mice demonstrates phenotypic adaptation to specific host major histocompatibility complex (MHC) genotypes. These evolved viral lines show increased fitness and virulence in their host-genotype-of-passage, but display fitness and virulence tradeoffs when infecting unfamiliar host MHC genotypes. Here, we deep sequence these viral lines in an attempt to discover the genetic basis of FVC adaptation. The principal prediction for genotype-specific adaptation is that unique mutations would rise to high frequency in viral lines adapted to each host MHC genotype. This prediction was not supported by our sequencing data as most observed high-frequency variants were present in each of our independently evolved viral lines. However, using a multi-variate approach to measure divergence between viral populations, we show that populations of replicate evolved viral lines from the same MHC congenic mouse strain were more similar to one another than to lines derived from different MHC congenic mouse strains, suggesting that MHC genotype does predictably act on viral evolution in our model. Sequence analysis also revealed rampant recombination with endogenous murine leukemia virus sequences (EnMuLVs) that are encoded within the BALB/c mouse genome. The highest frequency variants in all six lines contained a 12 bp insertion from a recombinant EnMuLV source, suggesting such recombinants were either being favored by selection or were contained in a recombinational hotspot. Interestingly, they did not reach fixation, as if they are low fitness. The amount of background mutations linked to FVC/EnMuLV variable sites indicated that FVC/EnMuLV recombinants had not reached mutation selection equilibrium and thus, that EnMuLV sequences are likely continuously introgressing into the replicating viral population. These discoveries raise the question: is the expression of EnMuLV sequences in mouse splenocytes that permit recombination with exogenous FVC a pathogen or host adaptation?
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Affiliation(s)
- Earl A. Middlebrook
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
- Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Derek L. Stark
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
| | - Douglas H. Cornwall
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
- Department of Pathology, University of Utah, Salt Lake City, UT, United States
| | - Jason L. Kubinak
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States
| | - Wayne K. Potts
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
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5
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Gemmell P, Hein J, Katzourakis A. The Exaptation of HERV-H: Evolutionary Analyses Reveal the Genomic Features of Highly Transcribed Elements. Front Immunol 2019; 10:1339. [PMID: 31338090 PMCID: PMC6629862 DOI: 10.3389/fimmu.2019.01339] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 05/28/2019] [Indexed: 12/25/2022] Open
Abstract
HERV-H endogenous retroviruses are thought to be essential to stem cell identity in humans. We embrace several decades of HERV-H research in order to relate the transcription of HERV-H loci to their genomic structure. We find that highly transcribed HERV-H loci are younger, more fragmented, and less likely to be present in other primate genomes. We also show that repeats in HERV-H LTRs are correlated to where loci are transcribed: type-I LTRs associate with stem cells while type-II repeats associate with embryonic cells. Our findings are generally in line with what is known about endogenous retrovirus biology but we find that the presence of the zinc finger motif containing region of gag is positively correlated with transcription. This leads us to suggest a possible explanation for why an unusually large proportion of HERV-H loci have been preserved in non-solo-LTR form.
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Affiliation(s)
- Patrick Gemmell
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Jotun Hein
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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6
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Feng M, Ren F, Zhou Y, Zhang N, Lu Q, Swevers L, Sun J. Correlation in Expression between LTR Retrotransposons and Potential Host Cis-Targets during Infection of Antherea pernyi with ApNPV Baculovirus. Viruses 2019; 11:v11050421. [PMID: 31064084 PMCID: PMC6563192 DOI: 10.3390/v11050421] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 05/04/2019] [Indexed: 12/14/2022] Open
Abstract
The published genome sequence of Antheraeayamamai (Saturnnidae) was used to construct a library of long terminal repeat (LTR)-retrotransposons that is representative of the wild silkmoth (Antherea) genus, and that includes 22,666 solo LTRs and 541 full-length LTRs. The LTR retrotransposons of Antheraeayamamai (AyLTRs) could be classified into the three canonical groups of Gypsy, Copia and Belpao. Eleven AyLTRs contained the env gene element, but the relationship with the env element of baculovirus, particularly A. yamamai and pernyi nucleopolyhedrovirus (AyNPV and ApNPV), was distant. A total of 251 “independent” full-length AyLTRs were identified that were located within 100 kb distance (downstream or upstream) of 406 neighboring genes in A. yamamai. Regulation of these genes might occur in cis by the AyLTRs, and the neighboring genes were found to be enriched in GO terms such as “response to stimulus”, and KEGG terms such as “mTOR signaling pathway” among others. Furthermore, the library of LTR-retrotransposons and the A. yamamai genome were used to identify and analyze the expression of LTR-retrotransposons and genes in ApNPV-infected and non-infected A. pernyi larval midguts, using raw data of a published transcriptome study. Our analysis demonstrates that 93 full-length LTR-retrotransposons are transcribed in the midgut of A. pernyi of which 12 significantly change their expression after ApNPV infection (differentially expressed LTR-retrotransposons or DELs). In addition, the expression of differentially expressed genes (DEGs) and neighboring DELs on the chromosome following ApNPV infection suggests the possibility of regulation of expression of DEGs by DELs through a cis mechanism, which will require experimental verification. When examined in more detail, it was found that genes involved in Notch signaling and stress granule (SG) formation were significantly up-regulated in ApNPV-infected A. pernyi larval midgut. Moreover, several DEGs in the Notch and SG pathways were found to be located in the neighborhood of particular DELs, indicating the possibility of DEG-DEL cross-regulation in cis for these two pathways.
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Affiliation(s)
- Min Feng
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research Demokritos, Aghia Paraskevi, Athens 15341, Greece.
| | - Feifei Ren
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Yaohong Zhou
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Nan Zhang
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Qiuyuan Lu
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research Demokritos, Aghia Paraskevi, Athens 15341, Greece.
| | - Jingchen Sun
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
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Complete Endogenous Retrovirus Genome Sequence from a Brazilian Vampire Bat (Desmodus rotundus). Microbiol Resour Announc 2019; 8:MRA01497-18. [PMID: 30643896 PMCID: PMC6328669 DOI: 10.1128/mra.01497-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 11/26/2018] [Indexed: 12/12/2022] Open
Abstract
The strain Desmodus rotundusendogenous retrovirus (DrERV) QR09 was obtained from a bat tissue sample collected from Desmodus rotundus in the Brazilian rain forest. The complete genome was sequenced using the next-generation sequencing strategy. The strain Desmodus rotundusendogenous retrovirus (DrERV) QR09 was obtained from a bat tissue sample collected from Desmodus rotundus in the Brazilian rain forest. The complete genome was sequenced using the next-generation sequencing strategy. The full-length genome of DrERV QR09 is 8,256 nucleotides in length and showed high similarity with other DrERVs.
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8
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Cell-Derived Viral Genes Evolve under Stronger Purifying Selection in Rhadinoviruses. J Virol 2018; 92:JVI.00359-18. [PMID: 29997213 DOI: 10.1128/jvi.00359-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/01/2018] [Indexed: 12/20/2022] Open
Abstract
Like many other large double-stranded DNA (dsDNA) viruses, herpesviruses are known to capture host genes to evade host defenses. Little is known about the detailed natural history of such genes, nor do we fully understand their evolutionary dynamics. A major obstacle is that they are often highly divergent, maintaining very low sequence similarity to host homologs. Here we use the herpesvirus genus Rhadinovirus as a model system to develop an analytical approach that combines complementary evolutionary and bioinformatic techniques, offering results that are both detailed and robust for a range of genes. Using a systematic phylogenetic strategy, we identify the original host lineage of viral genes with high confidence. We show that although host immunomodulatory genes evolve rapidly compared to other host genes, they undergo a clear increase in purifying selection once captured by a virus. To characterize this shift in detail, we developed a novel technique to identify changes in selection pressure that can be attributable to particular domains. These findings will inform us on how viruses develop strategies to evade the immune system, and our synthesis of techniques can be reapplied to other viruses or biological systems with similar analytical challenges.IMPORTANCE Viruses and hosts have been shown to capture genes from one another as part of the evolutionary arms race. Such genes offer a natural experiment on the effects of evolutionary pressure, since the same gene exists in vastly different selective environments. However, sequences of viral homologs often bear little similarity to the original sequence, complicating the reconstruction of their shared evolutionary history with host counterparts. In this study, we use a genus of herpesviruses as a model system to comprehensively investigate the evolution of host-derived viral genes, using a synthesis of genomics, phylogenetics, selection analysis, and nucleotide and amino acid modeling.
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Aswad A, Katzourakis A. A novel viral lineage distantly related to herpesviruses discovered within fish genome sequence data. Virus Evol 2017; 3:vex016. [PMID: 28798873 PMCID: PMC5544889 DOI: 10.1093/ve/vex016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Pathogenic viruses represent a small fraction of viral diversity, and emerging diseases are frequently the result of cross-species transmissions. Therefore, we need to develop high-throughput techniques to investigate a broader range of viral biodiversity across a greater number of species. This is especially important in the context of new practices in agriculture that have arisen to tackle the challenges of global food security, including the rising number of marine and freshwater species that are used in aquaculture. In this study, we demonstrate the utility of combining evolutionary approaches with bioinformatics to mine non-viral genome data for viruses, by adapting methods from paleovirology. We report the discovery of a new lineage of dsDNA viruses that are associated with at least fifteen different species of fish. This approach also enabled us to simultaneously identify sequences that likely represent endogenous viral elements, which we experimentally confirmed in commercial salmon samples. Moreover, genomic analysis revealed that the endogenous sequences have co-opted PiggyBac-like transposable elements, possibly as a mechanism of intragenomic proliferation. The identification of novel viruses from genome data shows that our approach has applications in genomics, virology, and the development of best practices for aquaculture and farming.
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Affiliation(s)
- Amr Aswad
- Department of Zoology, University of Oxford, South Parks Road, OX1 3PS Oxford, UK
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, South Parks Road, OX1 3PS Oxford, UK
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10
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Abstract
This paper reports on the various nuances of the origins of life on Earth and highlights the latest findings in that arena as reported at the Network of Researchers on Horizontal Gene Transfer and the Last Universal Common Ancestor (NoR HGT and LUCA) which was held from the 3–4th November 2016 at the Open University, UK. Although the answers to the question of the origin of life on Earth will not be fathomable anytime soon, a wide variety of subject matter was able to be covered, ranging from examining what constitutes a LUCA, looking at viral connections and “from RNA to DNA”, i.e., could DNA have been formed simultaneously with RNA, rather than RNA first and then describing the emergence of DNA from RNA. Also discussed are proteins and the origins of genomes as well as various ideas that purport to explain the origin of life here on Earth and potentially further afield elsewhere on other planets.
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Affiliation(s)
- Sohan Jheeta
- Network of Researchers on Horizontal Gene Transfer and the Last Universal Common Ancestor (NoR HGT & LUCA), Leeds LS7 3RB, UK.
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11
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Koonin EV, Krupovic M. Virology: A parasite's parasite saves host's neighbours. Nature 2017; 540:204-205. [PMID: 27929010 DOI: 10.1038/540204a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Mart Krupovic
- Department of Microbiology, Institut Pasteur, Paris 75015, France
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12
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Rosani U, Gerdol M. A bioinformatics approach reveals seven nearly-complete RNA-virus genomes in bivalve RNA-seq data. Virus Res 2016; 239:33-42. [PMID: 27769778 DOI: 10.1016/j.virusres.2016.10.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/17/2016] [Accepted: 10/17/2016] [Indexed: 01/17/2023]
Abstract
Viral metagenomics (viromics) can provide a great contribution in expanding the knowledge of viruses and the relationship with their hosts. Viromic studies on marine organisms are still at a very early stage and only little efforts have been spent in the identification of viruses associated to marine invertebrates to date, leaving the complexity of marine viromes associated to bivalve hosts almost completely unexplored. However, the potential use of viromic approaches in the management of viral diseases affecting aquacultured species has been recently evidenced by the flourishing of studies on the Ostreid herpesvirus type-1, which has been associated with bivalve mortality events. Herein we discuss an effective pipeline to retrieve and reconstruct nearly complete and previously unreported viral genomes from existing host RNA-seq data. As a case study, we report the identification of seven RNA-virus genomes within the frame of a highly diversified viral community that characterizes both Crassostrea gigas and Mytilus galloprovincialis samples collected from the lagoon of Goro (Italy).
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Affiliation(s)
- Umberto Rosani
- Dept. of Biology, University of Padua, Via U. Bassi 58/B, 35121 Padova Italy.
| | - Marco Gerdol
- Dept. of Life Sciences, University of Trieste, Via L. Giorgieri 5, 34127 Trieste Italy
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