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Bai Y, Xi Y, He X, Twumasi G, Ma S, Tao Q, Xu M, Jiang S, Zhang T, Lu Y, Han X, Qi J, Li L, Bai L, Liu H. Genome-wide characterization and comparison of endogenous retroviruses among 3 duck reference genomes. Poult Sci 2024; 103:103543. [PMID: 38447307 PMCID: PMC11067759 DOI: 10.1016/j.psj.2024.103543] [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: 11/21/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 03/08/2024] Open
Abstract
Endogenous retroviruses (ERV) are viral genomes integrated into the host genome and can be stably inherited. Although ERV sequences have been reported in some avian species' genome, the duck endogenous retroviruses (DERV) genome has yet to be quantified. This study aimed to identify ERV sequences and characterize genes near ERVs in the duck genome by utilizing LTRhavest and LTRdigest tools to forecast the duck genome and analyze the distribution of ERV copies. The results revealed 1,607, 2,031, and 1,908 full-length ERV copies in the Pekin duck (ZJU1.0), Mallard (CAU_wild_1.0), and Shaoxing duck (CAU_laying_1.0) genomes, respectively, with average lengths of 7,046, 7,027, and 6,945 bp. ERVs are mainly distributed on the 1, 2, and sex chromosomes. Phylogenetic analysis demonstrated the presence of Betaretrovirus in 3 duck genomes, whereas Alpharetrovirus was exclusively identified in the Shaoxing duck genome. Through screening, 596, 315, and 343 genes adjacent to ERV were identified in 3 duck genomes, respectively, and their functions of ERV neighboring genes were predicted. Functional enrichment analysis of ERV-adjacent genes revealed enrichment for Focal adhesion, Calcium signaling pathway, and Adherens junction in 3 duck genomes. The overlapped genes were highly expressed in 8 tissues (brain, fat, heart, kidney, liver, lung, skin, and spleen) of 8-wk-old Mallard, revealing their important expression in different tissues. Our study provides a new perspective for understanding the quantity and function of DERVs, and may also provide important clues for regulating nearby genes and affecting the traits of organisms.
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Affiliation(s)
- Yuan Bai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Yang Xi
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Xinxin He
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Grace Twumasi
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Shengchao Ma
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Qiuyu Tao
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Mengru Xu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Shuaixue Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Tao Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Yinjuan Lu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Xu Han
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Jingjing Qi
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Liang Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Lili Bai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China
| | - Hehe Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, P. R. Chengdu 613000, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, P. R. Chengdu 613000, China.
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Mo G, Wei P, Hu B, Nie Q, Zhang X. Advances on genetic and genomic studies of ALV resistance. J Anim Sci Biotechnol 2022; 13:123. [PMID: 36217167 PMCID: PMC9550310 DOI: 10.1186/s40104-022-00769-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/14/2022] [Indexed: 12/01/2022] Open
Abstract
Avian leukosis (AL) is a general term for a variety of neoplastic diseases in avian caused by avian leukosis virus (ALV). No vaccine or drug is currently available for the disease. Therefore, the disease can result in severe economic losses in poultry flocks. Increasing the resistance of poultry to ALV may be one effective strategy. In this review, we provide an overview of the roles of genes associated with ALV infection in the poultry genome, including endogenous retroviruses, virus receptors, interferon-stimulated genes, and other immune-related genes. Furthermore, some methods and techniques that can improve ALV resistance in poultry are discussed. The objectives are willing to provide some valuable references for disease resistance breeding in poultry.
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Affiliation(s)
- Guodong Mo
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Ping Wei
- Institute for Poultry Science and Health, Guangxi University, Nanning, 530001, Guangxi, China
| | - Bowen Hu
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Qinghua Nie
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Xiquan Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China. .,Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China. .,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, 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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4
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Warmuth VM, Weissensteiner MH, Wolf J. Ineffective silencing of transposable elements on an avian W Chromosome. Genome Res 2022; 32:671-681. [PMID: 35149543 PMCID: PMC8997356 DOI: 10.1101/gr.275465.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 02/08/2022] [Indexed: 11/24/2022]
Abstract
One of the defining features of transposable elements (TEs) is their ability to move to new locations in the host genome. To minimise the potentially deleterious effects of de novo TE insertions, hosts have evolved several mechanisms to control TE activity, including recombination-mediated removal and epigenetic silencing; however, increasing evidence suggests that silencing of TEs is often incomplete. The crow family experienced a recent radiation of LTR retrotransposons (LTRs), offering an opportunity to gain insight into the regulatory control of young, potentially still active TEs. We quantified the abundance of TE-derived transcripts across several tissues in 15 Eurasian crows (Corvus (corone) spp.) raised under common garden conditions and find evidence for ineffective TE suppression on the female-specific W Chromosome. Using RNA-seq data, we show that ~ 9.5% of all transcribed TEs had considerably greater (average: 16-fold) transcript abundance in female crows, and that more than 85% of these female-biased TEs originated on the W Chromosome. After accounting for differences in TE density among chromosomal classes, W-linked TEs were significantly more highly expressed than TEs residing on other chromosomes, consistent with ineffective silencing on the former. Together, our results suggest that the crow W Chromosome acts as a source of transcriptionally active TEs, with possible negative fitness consequences for female birds analogous to Drosophila (an X/Y system), where overexpression of Y-linked TEs is associated with male-specific aging and fitness loss ('toxic Y').
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Genome-Wide Characterization of Zebrafish Endogenous Retroviruses Reveals Unexpected Diversity in Genetic Organizations and Functional Potentials. Microbiol Spectr 2021; 9:e0225421. [PMID: 34908463 PMCID: PMC8672886 DOI: 10.1128/spectrum.02254-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Endogenous retroviruses (ERVs) occupy a substantial fraction of mammalian genomes. However, whether ERVs extensively exist in ancient vertebrates remains unexplored. Here, we performed a genome-wide characterization of ERVs in a zebrafish (Danio rerio) model. Approximately 3,315 ERV-like elements (DrERVs) were identified as Gypsy, Copia, Bel, and class I−III groups. DrERVs accounted for approximately 2.3% of zebrafish genome and were distributed in all 25 chromosomes, with a remarkable bias on chromosome 4. Gypsy and class I are the two most abundant groups with earlier insertion times. The vast majority of the DrERVs have varied structural defects. A total of 509 gag and 71 env genes with coding potentials were detected. The env-coding elements were well-characterized and classified into four subgroups. A ERV-E4.8.43-DanRer element shows high similarity with HERV9NC-int in humans and analogous sequences were detected in species spanning from fish to mammals. RNA-seq data showed that hundreds of DrERVs were expressed in embryos and tissues under physiological conditions, and most of them exhibited stage and tissue specificity. Additionally, 421 DrERVs showed strong responsiveness to virus infection. A unique group of DrERVs with immune-relevant genes, such as fga, ddx41, ftr35, igl1c3, and tbk1, instead of intrinsic viral genes were identified. These DrERVs are regulated by transcriptional factors binding at the long terminal repeats. This study provided a survey of the composition, phylogeny, and potential functions of ERVs in a fish model, which benefits the understanding of the evolutionary history of ERVs from fish to mammals. IMPORTANCE Endogenous retroviruses (ERVs) are relics of past infection that constitute up to 8% of the human genome. Understanding the genetic evolution of the ERV family and the interplay of ERVs and encoded RNAs and proteins with host function has become a new frontier in biology. Fish, as the most primitive vertebrate host for retroviruses, is an indispensable integral part for such investigations. In the present study, we report the genome-wide characterization of ERVs in zebrafish, an attractive model organism of ancient vertebrates from multiple perspectives, including composition, genomic organization, chromosome distribution, classification, phylogeny, insertion time, characterization of gag and env genes, and expression profiles in embryos and tissues. The result helps uncover the evolutionarily conserved and fish-specific ERVs, as well as the immune-relevant ERVs in response to virus infection. This study demonstrates the previously unrecognized abundance, diversification, and extensive activity of ERVs at the early stage of ERV evolution.
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Liu T, Xing Y, Fan X, Chen Z, Zhao C, Liu L, Zhao M, Hu X, Dong B, Wang J, Cui H, Gong D, Geng T. Fasting and overfeeding affect the expression of the immunity- or inflammation-related genes in the liver of poultry via endogenous retrovirus. Poult Sci 2021; 100:973-981. [PMID: 33518151 PMCID: PMC7858184 DOI: 10.1016/j.psj.2020.11.057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 11/06/2020] [Accepted: 11/22/2020] [Indexed: 12/19/2022] Open
Abstract
It is known that nutrition and immunity are connected, but the mechanism is not very clear. Endogenous retroviruses (ERV) account for 8 to 10% of the human and mouse genomes and play an important role in some biological processes of animals. Recent studies indicate that the activation of ERV can affect the expression of the immunity- or inflammation-related genes, and the activities of ERV are subjected to regulation of many factors including nutritional factors. Therefore, we hypothesize that nutritional status can affect the expression of the immunity- or inflammation-related genes via ERV. To verify this hypothesis, the nutritional status of animals was altered by fasting or overfeeding, and the expression of intact ERV (ERVK18P, ERVK25P) and immunity- or inflammation-related genes (DDX41, IFIH1, IFNG, IRF7, STAT3) in the liver was determined by quantitative PCR, followed by overexpressing ERVK25P in goose primary hepatocytes and determining the expression of the immunity- or inflammation-related genes. The data showed that compared with the control group (no fasting), the expression of ERV and the immunity- or inflammation-related genes was increased in the liver of the fasted chickens but decreased in the liver of the fasted geese. Moreover, compared with the control group (routinely fed), the expression of ERV and the immunity- or inflammation-related genes was increased in the liver of the overfed geese. In addition, overexpression of ERVK25P in goose primary hepatocytes can induce the expression of the immunity- or inflammation-related genes. In conclusion, these findings suggest that ERV mediate the effects of fasting and overfeeding on the expression of the immunity- or inflammation-related genes, the mediation varied with poultry species, and ERV and the immunity- or inflammation-related genes may be involved in the development of goose fatty liver. This study provides a potential mechanism for the connection between nutrition and immunity.
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Affiliation(s)
- Tongjun Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Ya Xing
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xue Fan
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhenzhen Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Chao Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Long Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Minmeng Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xuming Hu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Biao Dong
- Department of Animal Science and Technology, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou 225300, China
| | - Jian Wang
- Department of Animal Science and Technology, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou 225300, China
| | - Hengmi Cui
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Daoqing Gong
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Tuoyu Geng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
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Sacco MA, Crosetti A. GGERV20, a recently integrated, segregating endogenous retrovirus in Gallus gallus. J Gen Virol 2020; 101:299-308. [PMID: 31916930 DOI: 10.1099/jgv.0.001379] [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] [Indexed: 11/18/2022] Open
Abstract
Endogenous retroviruses (ERVs) are widespread in vertebrate genomes. The recent availability of whole eukaryotic genomes has enabled their characterization in many organisms, including Gallus gallus (red jungle fowl), the progenitor of the domesticated chicken. Our bioinformatics analysis of a G. gallus ERV previously designated GGERV20 identified 35 proviruses with complete long terminal repeats (LTRs) and gag-pol open reading frames (ORFs) in the Genome Reference Consortium Chicken Build 6a, of which 8 showed potential for translation of functional retroviral polyproteins, including the integrase and reverse transcriptase enzymes. No elements were discovered with an env gene. Fifteen loci had LTR sequences with 100 % identity, indicative of recent integration. Chicken embryo fibroblast RNA-seq datasets showed reads representing the entire length of the GGERV20 provirus, supporting their potential for expressing viral proteins. To investigate the possibility that GGERV20 elements may not be fixed in the genome, we assessed the integration status of five loci in a meat-type chicken. PCRs targeting a GGERV20 locus on G. gallus chromosome one (GGERV201-1) reproducibly amplified both LTRs and the preintegration state, indicating that the bird from which the DNA was sampled was hemizygous at this locus. The four other loci examined only produced the preintegration state amplicons. These results reveal that GGERV20 is not fixed in the G. gallus population, and taken together with the lack of mutations seen in several provirus LTRs and their transcriptional activity, suggest that GGERV20 retroviruses have recently been and continue to be active in the chicken genome.
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Affiliation(s)
- Melanie Ann Sacco
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University, Fullerton, CA 92834-6850, USA
| | - Anna Crosetti
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University, Fullerton, CA 92834-6850, USA
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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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Whole-Genome Analysis of Domestic Chicken Selection Lines Suggests Segregating Variation in ERV Makeups. Genes (Basel) 2019; 10:genes10020162. [PMID: 30791656 PMCID: PMC6410134 DOI: 10.3390/genes10020162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/13/2019] [Accepted: 02/15/2019] [Indexed: 01/04/2023] Open
Abstract
Retroviruses have invaded vertebrate hosts for millions of years and left an extensive endogenous retrovirus (ERV) record in the host genomes, which provides a remarkable source for an evolutionary perspective on retrovirus-host associations. Here we identified ERV variation across whole-genomes from two chicken lines, derived from a common founder population subjected to 50 years of bi-directional selection on body weight, and a distantly related domestic chicken line as a comparison outgroup. Candidate ERV loci, where at least one of the chicken lines indicated distinct differences, were analyzed for adjacent host genomic landscapes, selective sweeps, and compared by sequence associations to reference assembly ERVs in phylogenetic analyses. Current data does not support selection acting on specific ERV loci in the domestic chicken lines, as determined by presence inside selective sweeps or composition of adjacent host genes. The varying ERV records among the domestic chicken lines associated broadly across the assembly ERV phylogeny, indicating that the observed insertion differences result from pre-existing and segregating ERV loci in the host populations. Thus, data suggest that the observed differences between the host lineages are best explained by substantial standing ERV variation within host populations, and indicates that even truncated, presumably old, ERVs have not yet become fixed in the host population.
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Xu X, Zhao H, Gong Z, Han GZ. Endogenous retroviruses of non-avian/mammalian vertebrates illuminate diversity and deep history of retroviruses. PLoS Pathog 2018; 14:e1007072. [PMID: 29902269 PMCID: PMC6001957 DOI: 10.1371/journal.ppat.1007072] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/03/2018] [Indexed: 02/06/2023] Open
Abstract
The deep history and early diversification of retroviruses remains elusive, largely because few retroviruses have been characterized in vertebrates other than mammals and birds. Endogenous retroviruses (ERVs) documented past retroviral infections and thus provide ‘molecular fossils’ for studying the deep history of retroviruses. Here we perform a comprehensive phylogenomic analysis of ERVs within the genomes of 92 non-avian/mammalian vertebrates, including 72 fishes, 4 amphibians, and 16 reptiles. We find that ERVs are present in all the genomes of jawed vertebrates, revealing the ubiquitous presence of ERVs in jawed vertebrates. We identify a total of >8,000 ERVs and reconstruct ~450 complete or partial ERV genomes, which dramatically expands the phylogenetic diversity of retroviruses and suggests that the diversity of exogenous retroviruses might be much underestimated in non-avian/mammalian vertebrates. Phylogenetic analyses show that retroviruses cluster into five major groups with different host distributions, providing important insights into the classification and diversification of retroviruses. Moreover, we find retroviruses mainly underwent frequent host switches in non-avian/mammalian vertebrates, with exception of spumavirus-related viruses that codiverged with their ray-finned fish hosts. Interestingly, ray-finned fishes and turtles appear to serve as unappreciated hubs for the transmission of retroviruses. Finally, we find retroviruses underwent many independent water-land transmissions, indicating the water-land interface is not a strict barrier for retrovirus transmission. Our analyses provide unprecedented insights into and valuable resources for studying the diversification, key evolutionary transitions, and macroevolution of retroviruses. Retroviruses infect a wide range of vertebrates and cause many diseases, such as AIDS and cancers. To date, retroviruses have been rarely characterized in vertebrates other than mammals and birds, impeding our understanding of the diversity and early evolution of retroviruses. Retroviruses can occasionally integrate into host genomes and become endogenous retroviruses (ERVs), which provide molecular fossils for studying the long-term evolution of retroviruses. Here we performed comparative genomic and evolutionary analyses of ERVs within 92 non-avian/mammalian vertebrates (fishes, amphibians, and reptiles) and uncovered extraordinary diversity of retroviruses in non-avian/mammalian vertebrates. Our analyses reveal an ancient aquatic origin of retroviruses and retroviruses underwent frequent host-switching. Our findings have important implications in understanding the deep history and evolutionary mode of retroviruses.
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Affiliation(s)
- Xiaoyu Xu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Huayao Zhao
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Zhen Gong
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Guan-Zhu Han
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
- * E-mail:
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Greenwood AD, Ishida Y, O'Brien SP, Roca AL, Eiden MV. Transmission, Evolution, and Endogenization: Lessons Learned from Recent Retroviral Invasions. Microbiol Mol Biol Rev 2018; 82:e00044-17. [PMID: 29237726 PMCID: PMC5813887 DOI: 10.1128/mmbr.00044-17] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Viruses of the subfamily Orthoretrovirinae are defined by the ability to reverse transcribe an RNA genome into DNA that integrates into the host cell genome during the intracellular virus life cycle. Exogenous retroviruses (XRVs) are horizontally transmitted between host individuals, with disease outcome depending on interactions between the retrovirus and the host organism. When retroviruses infect germ line cells of the host, they may become endogenous retroviruses (ERVs), which are permanent elements in the host germ line that are subject to vertical transmission. These ERVs sometimes remain infectious and can themselves give rise to XRVs. This review integrates recent developments in the phylogenetic classification of retroviruses and the identification of retroviral receptors to elucidate the origins and evolution of XRVs and ERVs. We consider whether ERVs may recurrently pressure XRVs to shift receptor usage to sidestep ERV interference. We discuss how related retroviruses undergo alternative fates in different host lineages after endogenization, with koala retrovirus (KoRV) receiving notable interest as a recent invader of its host germ line. KoRV is heritable but also infectious, which provides insights into the early stages of germ line invasions as well as XRV generation from ERVs. The relationship of KoRV to primate and other retroviruses is placed in the context of host biogeography and the potential role of bats and rodents as vectors for interspecies viral transmission. Combining studies of extant XRVs and "fossil" endogenous retroviruses in koalas and other Australasian species has broadened our understanding of the evolution of retroviruses and host-retrovirus interactions.
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Affiliation(s)
- Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin e.V., Berlin, Germany
| | - Yasuko Ishida
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Sean P O'Brien
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Alfred L Roca
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Maribeth V Eiden
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin e.V., Berlin, Germany
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Sun YH, Xie LH, Zhuo X, Chen Q, Ghoneim D, Zhang B, Jagne J, Yang C, Li XZ. Domestic chickens activate a piRNA defense against avian leukosis virus. eLife 2017; 6. [PMID: 28384097 PMCID: PMC5383398 DOI: 10.7554/elife.24695] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/04/2017] [Indexed: 12/12/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) protect the germ line by targeting transposable elements (TEs) through the base-pair complementarity. We do not know how piRNAs co-evolve with TEs in chickens. Here we reported that all active TEs in the chicken germ line are targeted by piRNAs, and as TEs lose their activity, the corresponding piRNAs erode away. We observed de novo piRNA birth as host responds to a recent retroviral invasion. Avian leukosis virus (ALV) has endogenized prior to chicken domestication, remains infectious, and threatens poultry industry. Domestic fowl produce piRNAs targeting ALV from one ALV provirus that was known to render its host ALV resistant. This proviral locus does not produce piRNAs in undomesticated wild chickens. Our findings uncover rapid piRNA evolution reflecting contemporary TE activity, identify a new piRNA acquisition modality by activating a pre-existing genomic locus, and extend piRNA defense roles to include the period when endogenous retroviruses are still infectious. DOI:http://dx.doi.org/10.7554/eLife.24695.001 Viruses called retroviruses can infect animal cells and merge their genetic information with those of the animal causing damage to the animal’s genetic blueprints. Once retroviruses are integrated into a cell they can sometimes get passed down through the generations over the centuries. Almost half of the human genetic code, for example, is made from ancient retroviruses and other foreign sequences. Over time many of these ancient viruses lost the ability to infect other cells and became trapped within cells but they can still jump out and damage the animal’s genetic code under certain circumstances. These trapped foreign sequences are called transposable elements. Animal cells produce molecules called piRNAs to shut down transposable elements. Most piRNAs are produced from genetic information that originally came from integrated retroviruses and that has been hijacked to defend the cell, a similar strategy as Crisper system in bacteria. Domestic chickens produce piRNAs against a virus called avian leukosis virus (or ALV for short) – which commonly infects domestic fowl. The virus also infected the wild ancestors of chickens, known as red jungle fowl, but these birds do not produce piRNAs. This provides an ideal setting to study the evolution of piRNAs in an animal that is not too distantly related to humans (chickens and humans both have backbones, and are therefore both warm-blooded vertebrates). Sun et al. examined cells from the testicles of domestic chickens and red jungle fowl as an example of the role of piRNAs in protecting genetic information in vertebrates. The investigation revealed that piRNAs against all previously trapped viruses in the chicken’s genetic code are produced in chickens to stop them from causing more damage. Sun et al. also observed the creation of piRNAs in chickens in response to ALV that had not yet become trapped in the chicken’s genetic code. Importantly, the piRNAs could control these retroviruses while they were still infectious. The experiments also revealed that piRNAs against ALV are produced from a single copy of ALV that is found in both domestic and wild chickens. The results showed that cells can produce new piRNAs using these pre-existing viral copies within their own genetics. This illustrates that production of piRNA from existing genetic material can be activated in response to certain cues. Further work will seek to discover how existing genetic information becomes a source of piRNAs. In the United States, 8 billion domestic chickens are consumed each year, and a better understanding of how these birds defend themselves against viral infections could increase the productivity of the poultry industry around the world. Moreover, because other viruses trapped in the chicken’s genetic code are related to similar viruses in humans, future discoveries made in this area could help to guide research that will benefit human health as well. DOI:http://dx.doi.org/10.7554/eLife.24695.002
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Affiliation(s)
- Yu Huining Sun
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, Department of Urology, University of Rochester Medical Center, Rochester, United States
| | - Li Huitong Xie
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, Department of Urology, University of Rochester Medical Center, Rochester, United States
| | - Xiaoyu Zhuo
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, United States
| | - Qiang Chen
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, Department of Urology, University of Rochester Medical Center, Rochester, United States
| | - Dalia Ghoneim
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, Department of Urology, University of Rochester Medical Center, Rochester, United States
| | - Bin Zhang
- Department of Pathology and Laboratory Medicine, Department of Pediatrics, University of Rochester Medical Center, Rochester, United States
| | - Jarra Jagne
- Animal Health Diagnostic Center, Cornell University College of Veterinary Medicine, Ithaca, United States
| | - Chengbo Yang
- Department of Animal Science, University of Manitoba, Winnipeg, Canada
| | - Xin Zhiguo Li
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, Department of Urology, University of Rochester Medical Center, Rochester, United States
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Abstract
Genome size in mammals and birds shows remarkably little interspecific variation compared with other taxa. However, genome sequencing has revealed that many mammal and bird lineages have experienced differential rates of transposable element (TE) accumulation, which would be predicted to cause substantial variation in genome size between species. Thus, we hypothesize that there has been covariation between the amount of DNA gained by transposition and lost by deletion during mammal and avian evolution, resulting in genome size equilibrium. To test this model, we develop computational methods to quantify the amount of DNA gained by TE expansion and lost by deletion over the last 100 My in the lineages of 10 species of eutherian mammals and 24 species of birds. The results reveal extensive variation in the amount of DNA gained via lineage-specific transposition, but that DNA loss counteracted this expansion to various extents across lineages. Our analysis of the rate and size spectrum of deletion events implies that DNA removal in both mammals and birds has proceeded mostly through large segmental deletions (>10 kb). These findings support a unified "accordion" model of genome size evolution in eukaryotes whereby DNA loss counteracting TE expansion is a major determinant of genome size. Furthermore, we propose that extensive DNA loss, and not necessarily a dearth of TE activity, has been the primary force maintaining the greater genomic compaction of flying birds and bats relative to their flightless relatives.
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Chicken ( Gallus gallus) endogenous retrovirus generates genomic variations in the chicken genome. Mob DNA 2017; 8:2. [PMID: 28138342 PMCID: PMC5260121 DOI: 10.1186/s13100-016-0085-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 12/27/2016] [Indexed: 01/08/2023] Open
Abstract
Background Transposable elements (TEs) comprise ~10% of the chicken (Gallus gallus) genome. The content of TEs is much lower than that of mammalian genomes, where TEs comprise around half of the genome. Endogenous retroviruses are responsible for ~1.3% of the chicken genome. Among them is Gallus gallus endogenous retrovirus 10 (GGERV10), one of the youngest endogenous retrovirus families, which emerged in the chicken genome around 3 million years ago. Results We identified a total of 593 GGERV10 elements in the chicken reference genome using UCSC genome database and RepeatMasker. While most of the elements were truncated, 49 GGERV10 elements were full-length retaining 5′ and 3′ LTRs. We examined in detail their structural features, chromosomal distribution, genomic environment, and phylogenetic relationships. We compared LTR sequence among five different GGERV10 subfamilies and found sequence variations among the LTRs. Using a traditional PCR assay, we examined a polymorphism rate of the 49 full-length GGERV10 elements in three different chicken populations of the Korean domestic chicken, Leghorn, and Araucana. The result found a breed-specific GGERV10B insertion locus in the Korean domestic chicken, which could be used as a Korean domestic chicken-specific marker. Conclusions GGERV10 family is the youngest ERV family and thus might have contributed to recent genomic variations in different chicken populations. The result of this study showed that one of GGERV10 elements integrated into the chicken genome after the divergence of Korean domestic chicken from other closely related chicken populations, suggesting that GGERV10 could be served as a molecular marker for chicken breed identification. Electronic supplementary material The online version of this article (doi:10.1186/s13100-016-0085-5) contains supplementary material, which is available to authorized users.
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Expression patterns of endogenous avian retrovirus ALVE1 and its response to infection with exogenous avian tumour viruses. Arch Virol 2016; 162:89-101. [PMID: 27686071 DOI: 10.1007/s00705-016-3086-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 09/21/2016] [Indexed: 02/01/2023]
Abstract
Endogenous retroviruses (ERVs) are genomic elements that are present in a wide range of vertebrates and have been implicated in a variety of human diseases, including cancer. However, the characteristic expression patterns of ERVs, particularly in virus-induced tumours, is not fully clear. DNA methylation was analysed by bisulfite pyrosequencing, and gene expression was analysed by RT-qPCR. In this study, we first found that the endogenous avian retrovirus ALVE1 was highly expressed in some chicken tissues (including the heart, bursa, thymus, and spleen) at 2 days of age, but its expression was markedly decreased at 35 days of age. In contrast, the CpG methylation level of ALVE1 was significantly lower in heart and bursa at 2 days than at 35 days of age. Moreover, we found that the expression of ALVE1 was significantly inhibited in chicken embryo fibroblast cells (CEFs) and MSB1 cells infected with avian leukosis virus subgroup J (ALVJ) and reticuloendotheliosis virus (REV) at the early stages of infection. In contrast, the expression of the ALVE1 env gene was significantly induced in CEFs and MSB1 cells infected with Marek's disease virus (MDV). However, the methylation and expression levels of the ALVE1 long terminal repeat (LTR) did not show obvious alterations in response to viral infection. The present study revealed the expression patterns of ALVE1 in a variety of chicken organs and tissues and in chicken cells in response to avian tumour virus infection. These findings may be of significance for understanding the role and function of ERVs that are present in the host genome.
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Mason AS, Fulton JE, Hocking PM, Burt DW. A new look at the LTR retrotransposon content of the chicken genome. BMC Genomics 2016; 17:688. [PMID: 27577548 PMCID: PMC5006616 DOI: 10.1186/s12864-016-3043-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 08/24/2016] [Indexed: 11/23/2022] Open
Abstract
Background LTR retrotransposons contribute approximately 10 % of the mammalian genome, but it has been previously reported that there is a deficit of these elements in the chicken relative to both mammals and other birds. A novel LTR retrotransposon classification pipeline, LocaTR, was developed and subsequently utilised to re-examine the chicken LTR retrotransposon annotation, and determine if the proposed chicken deficit is biologically accurate or simply a technical artefact. Results Using LocaTR 3.01 % of the chicken galGal4 genome assembly was annotated as LTR retrotransposon-derived elements (nearly double the previous annotation), including 1,073 that were structurally intact. Element distribution is significantly correlated with chromosome size and is non-random within each chromosome. Elements are significantly depleted within coding regions and enriched in gene sparse areas of the genome. Over 40 % of intact elements are found in clusters, unrelated by age or genera, generally in poorly recombining regions. The transcription of most LTR retrotransposons were suppressed or incomplete, but individual domain and full length retroviral transcripts were produced in some cases, although mostly with regularly interspersed stop codons in all reading frames. Furthermore, RNAseq data from 23 diverse tissues enabled greater characterisation of the co-opted endogenous retrovirus Ovex1. This gene was shown to be expressed ubiquitously but at variable levels across different tissues. LTR retrotransposon content was found to be very variable across the avian lineage and did not correlate with either genome size or phylogenetic position. However, the extent of previous, species-specific LTR retrotransposon annotation appears to be a confounding factor. Conclusions Use of the novel LocaTR pipeline has nearly doubled the annotated LTR retrotransposon content of the chicken genome compared to previous estimates. Further analysis has described element distribution, clustering patterns and degree of expression in a variety of adult tissues, as well as in three embryonic stages. This study also enabled better characterisation of the co-opted gamma retroviral envelope gene Ovex1. Additionally, this work suggests that there is no deficit of LTR retrotransposons within the Galliformes relative to other birds, or to mammalian genomes when scaled for the three-fold difference in genome size. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3043-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew S Mason
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - Janet E Fulton
- Hy-Line International, 1915 Sugar Grove Avenue, Dallas Grove, IA, 50063, USA
| | - Paul M Hocking
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - David W Burt
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
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Rutherford K, Meehan CJ, Langille MGI, Tyack SG, McKay JC, McLean NL, Benkel K, Beiko RG, Benkel B. Discovery of an expanded set of avian leukosis subgroup E proviruses in chickens using Vermillion, a novel sequence capture and analysis pipeline [corrected]. Poult Sci 2016; 95:2250-8. [PMID: 27354549 DOI: 10.3382/ps/pew194] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/08/2016] [Indexed: 01/26/2023] Open
Abstract
Transposable elements (TEs), such as endogenous retroviruses (ERVs), are common in the genomes of vertebrates. ERVs result from retroviral infections of germ-line cells, and once integrated into host DNA they become part of the host's heritable genetic material. ERVs have been ascribed positive effects on host physiology such as the generation of novel, adaptive genetic variation and resistance to infection, as well as negative effects as agents of tumorigenesis and disease. The avian leukosis virus subgroup E family (ALVE) of endogenous viruses of chickens has been used as a model system for studying the effects of ERVs on host physiology, and approximately 30 distinct ALVE proviruses have been described in the Gallus gallus genome. In this report we describe the development of a software tool, which we call Vermillion, and the use of this tool in combination with targeted next-generation sequencing (NGS) to increase the number of known proviruses belonging to the ALVE family of ERVs in the chicken genome by 4-fold, including expanding the number of known ALVE elements on chromosome 1 (Gga1) from the current 9 to a total of 40. Although we focused on the discovery of ALVE elements in chickens, with appropriate selection of target sequences Vermillion can be used to develop profiles of other families of ERVs and TEs in chickens as well as in species other than the chicken.
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Affiliation(s)
- K Rutherford
- Dalhousie University, Faculty of Computer Science, 6050 University Avenue, Halifax, NS, Canada, B3H 4R2
| | - C J Meehan
- Dalhousie University, Faculty of Computer Science, 6050 University Avenue, Halifax, NS, Canada, B3H 4R2 Institute of Tropical Medicine, Department of Biomedical Sciences, Antwerp 2000, Belgium
| | - M G I Langille
- Dalhousie University, Faculty of Computer Science, 6050 University Avenue, Halifax, NS, Canada, B3H 4R2 Dalhousie University, Faculty of Medicine, Department of Pharmacology, 5850 College St, Halifax, NS, Canada, B3H 4R2
| | - S G Tyack
- EW GROUP, 1 Hogenboegen, Visbek, Germany
| | - J C McKay
- EW GROUP, 1 Hogenboegen, Visbek, Germany
| | - N L McLean
- Dalhousie University, Faculty of Agriculture, Department of Plant and Animal Sciences, Box 550, Truro, NS, B2N 5E3
| | - K Benkel
- Dalhousie University, Faculty of Agriculture, Department of Plant and Animal Sciences, Box 550, Truro, NS, B2N 5E3
| | - R G Beiko
- Dalhousie University, Faculty of Computer Science, 6050 University Avenue, Halifax, NS, Canada, B3H 4R2
| | - B Benkel
- Dalhousie University, Faculty of Agriculture, Department of Plant and Animal Sciences, Box 550, Truro, NS, B2N 5E3
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Vargiu L, Rodriguez-Tomé P, Sperber GO, Cadeddu M, Grandi N, Blikstad V, Tramontano E, Blomberg J. Classification and characterization of human endogenous retroviruses; mosaic forms are common. Retrovirology 2016; 13:7. [PMID: 26800882 PMCID: PMC4724089 DOI: 10.1186/s12977-015-0232-y] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 12/16/2015] [Indexed: 02/06/2023] Open
Abstract
Background Human endogenous retroviruses (HERVs) represent the inheritance of ancient germ-line cell infections by exogenous retroviruses and the subsequent transmission of the integrated proviruses to the descendants. ERVs have the same internal structure as exogenous retroviruses. While no replication-competent HERVs have been recognized, some retain up to three of four intact ORFs. HERVs have been classified before, with varying scope and depth, notably in the RepBase/RepeatMasker system. However, existing classifications are bewildering. There is a need for a systematic, unifying and simple classification. We strived for a classification which is traceable to previous classifications and which encompasses HERV variation within a limited number of clades. Results The human genome assembly GRCh 37/hg19 was analyzed with RetroTector, which primarily detects relatively complete Class I and II proviruses. A total of 3173 HERV sequences were identified. The structure of and relations between these proviruses was resolved through a multi-step classification procedure that involved a novel type of similarity image analysis (“Simage”) which allowed discrimination of heterogeneous (noncanonical) from homogeneous (canonical) HERVs. Of the 3173 HERVs, 1214 were canonical and segregated into 39 canonical clades (groups), belonging to class I (Gamma- and Epsilon-like), II (Beta-like) and III (Spuma-like). The groups were chosen based on (1) sequence (nucleotide and Pol amino acid), similarity, (2) degree of fit to previously published clades, often from RepBase, and (3) taxonomic markers. The groups fell into 11 supergroups. The 1959 noncanonical HERVs contained 31 additional, less well-defined groups. Simage analysis revealed several types of mosaicism, notably recombination and secondary integration. By comparing flanking sequences, LTRs and completeness of gene structure, we deduced that some noncanonical HERVs proliferated after the recombination event. Groups were further divided into envelope subgroups (altogether 94) based on sequence similarity and characteristic “immunosuppressive domain” motifs. Intra and inter(super)group, as well as intraclass, recombination involving envelope genes (“env snatching”) was a common event. LTR divergence indicated that HERV-K(HML2) and HERVFC had the most recent integrations, HERVL and HUERSP3 the oldest. Conclusions A comprehensive HERV classification and characterization approach was undertaken. It should be applicable for classification of all ERVs. Recombination was common among HERV ancestors. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0232-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laura Vargiu
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy. .,Center for Advanced Studies, Research and Development in Sardinia, CRS4, Pula, Italy. .,Nurideas S.r.l., Cagliari, Italy.
| | - Patricia Rodriguez-Tomé
- Center for Advanced Studies, Research and Development in Sardinia, CRS4, Pula, Italy. .,Nurideas S.r.l., Cagliari, Italy.
| | - Göran O Sperber
- Physiology Unit, Department of Neuroscience, Uppsala University, Uppsala, Sweden.
| | - Marta Cadeddu
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy.
| | - Nicole Grandi
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy.
| | - Vidar Blikstad
- Department of Medical Sciences, Uppsala University Hospital, Dag Hammarskjölds Väg 17, Uppsala, 751 85, Sweden.
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy.
| | - Jonas Blomberg
- Department of Medical Sciences, Uppsala University Hospital, Dag Hammarskjölds Väg 17, Uppsala, 751 85, Sweden.
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Infectious Entry Pathway Mediated by the Human Endogenous Retrovirus K Envelope Protein. J Virol 2016; 90:3640-9. [PMID: 26792739 DOI: 10.1128/jvi.03136-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/12/2016] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED Endogenous retroviruses (ERVs), the majority of which exist as degraded remnants of ancient viruses, comprise approximately 8% of the human genome. The youngest human ERVs (HERVs) belong to the HERV-K(HML-2) subgroup and were endogenized within the past 1 million years. The viral envelope protein (ENV) facilitates the earliest events of endogenization (cellular attachment and entry), and here, we characterize the requirements for HERV-K ENV to mediate infectious cell entry. Cell-cell fusion assays indicate that a minimum of two events are required for fusion, proteolytic processing by furin-like proteases and exposure to acidic pH. We generated an infectious autonomously replicating recombinant vesicular stomatitis virus (VSV) in which the glycoprotein was replaced by HERV-K ENV. HERV-K ENV imparts an endocytic entry pathway that requires dynamin-mediated membrane scission and endosomal acidification but is distinct from clathrin-dependent or macropinocytic uptake pathways. The lack of impediments to the replication of the VSV core in eukaryotic cells allowed us to broadly survey the HERV-K ENV-dictated tropism. Unlike extant betaretroviral envelopes, which impart a narrow species tropism, we found that HERV-K ENV mediates broad tropism encompassing cells from multiple mammalian and nonmammalian species. We conclude that HERV-K ENV dictates an evolutionarily conserved entry pathway and that the restriction of HERV-K to primate genomes reflects downstream stages of the viral replication cycle. IMPORTANCE Approximately 8% of the human genome is of retroviral origin. While many of those viral genomes have become inactivated, some copies of the most recently endogenized human retrovirus, HERV-K, can encode individual functional proteins. Here, we characterize the envelope protein (ENV) of the virus to define how it mediates infection of cells. We demonstrate that HERV-K ENV undergoes a proteolytic processing step and triggers membrane fusion in response to acidic pH--a strategy common to many viral fusogens. Our data suggest that the infectious entry pathway mediated by this ENV requires endosomal acidification and the GTPase dynamin but does not require clathrin-dependent uptake. In marked contrast to other betaretroviruses, HERV-K ENV imparts broad species tropism in cultured cells. This work provides new insights into the entry pathway of an extinct human virus and provides a powerful tool to further probe the endocytic route by which HERV-K infects cells.
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Wragg D, Mason AS, Yu L, Kuo R, Lawal RA, Desta TT, Mwacharo JM, Cho CY, Kemp S, Burt DW, Hanotte O. Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken. BMC Genomics 2015; 16:784. [PMID: 26466991 PMCID: PMC4607243 DOI: 10.1186/s12864-015-1954-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/02/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND EAV-HP is an ancient retrovirus pre-dating Gallus speciation, which continues to circulate in modern chicken populations, and led to the emergence of avian leukosis virus subgroup J causing significant economic losses to the poultry industry. We mapped EAV-HP integration sites in Ethiopian village chickens, a Silkie, Taiwan Country chicken, red junglefowl Gallus gallus and several inbred experimental lines using whole-genome sequence data. RESULTS An average of 75.22 ± 9.52 integration sites per bird were identified, which collectively group into 279 intervals of which 5 % are common to 90 % of the genomes analysed and are suggestive of pre-domestication integration events. More than a third of intervals are specific to individual genomes, supporting active circulation of EAV-HP in modern chickens. Interval density is correlated with chromosome length (P < 2.31(-6)), and 27 % of intervals are located within 5 kb of a transcript. Functional annotation clustering of genes reveals enrichment for immune-related functions (P < 0.05). CONCLUSIONS Our results illustrate a non-random distribution of EAV-HP in the genome, emphasising the importance it may have played in the adaptation of the species, and provide a platform from which to extend investigations on the co-evolutionary significance of endogenous retroviral genera with their hosts.
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Affiliation(s)
- David Wragg
- Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
- Institut National de la Recherche Agronomique (INRA), UMR 1338 GenPhySE, 31326, Castanet-Tolosan, France.
| | - Andrew S Mason
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, Edinburgh, UK.
| | - Le Yu
- GAIC Co. Ltd. Jing Chen Buiding, Science Park, South Street, Chao Yang District, Beijing, People's Republic Popular of China.
| | - Richard Kuo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, Edinburgh, UK.
| | - Raman A Lawal
- Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
| | - Takele Taye Desta
- Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
| | - Joram M Mwacharo
- Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
- International Centre for Agricultural Research in Dry Areas, c/o International Livestock Research Institute, Addis Ababa, Ethiopia.
| | - Chang-Yeon Cho
- Animal Genetic Resources Station, National Institute of Animal Science, Namwon, Republic of Korea.
| | - Steve Kemp
- International Livestock Research Institute, Naivasha Road, P.O. Box 30709, Nairobi, Kenya.
| | - David W Burt
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, Edinburgh, UK.
| | - Olivier Hanotte
- Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
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Abstract
Endogenous retroviruses comprise millions of discrete genetic loci distributed within the genomes of extant vertebrates. These sequences, which are clearly related to exogenous retroviruses, represent retroviral infections of the deep past, and their abundance suggests that retroviruses were a near-constant presence throughout the evolutionary history of modern vertebrates. Endogenous retroviruses contribute in myriad ways to the evolution of host genomes, as mutagens and as sources of genetic novelty (both coding and regulatory) to be acted upon by the twin engines of random genetic drift and natural selection. Importantly, the richness and complexity of endogenous retrovirus data can be used to understand how viruses spread and adapt on evolutionary timescales by combining population genetics and evolutionary theory with a detailed understanding of retrovirus biology (gleaned from the study of extant retroviruses). In addition to revealing the impact of viruses on organismal evolution, such studies can help us better understand, by looking back in time, how life-history traits, as well as ecological and geological events, influence the movement of viruses within and between populations.
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Affiliation(s)
- Welkin E Johnson
- Biology Department, Boston College, Chestnut Hill, Massachusetts 02467;
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22
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Weiss RA. What's the host and what's the microbe? The Marjory Stephenson Prize Lecture 2015. J Gen Virol 2015; 96:2501-2510. [PMID: 26296666 DOI: 10.1099/jgv.0.000220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The interchange between retroviruses and their hosts is an intimate one because retroviruses integrate proviral DNA into host chromosomal DNA as an obligate step in the replication cycle. This has resulted in the occasional transduction of host genes into retroviral genomes as oncogenes, and also led to the integration of viral genomes into the host germ line that gives rise to endogenous retroviruses. I shall reflect on the evolutionary consequences of these events for virus and host. Then, I shall discuss the emergence of non-viral infections of host origin, namely, how malignant cells can give rise to eukaryotic single cell 'parasites' that colonize new hosts and how these in turn have been colonized by host mitochondria.
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Affiliation(s)
- Robin A Weiss
- Division of Infection & Immunity, University College London, Gower Street, London WC1E 6BT, UK
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Seim I, Jeffery PL, Herington AC, Chopin LK. Comparative analysis reveals loss of the appetite-regulating peptide hormone ghrelin in falcons. Gen Comp Endocrinol 2015; 216:98-102. [PMID: 25500363 DOI: 10.1016/j.ygcen.2014.11.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 11/10/2014] [Accepted: 11/21/2014] [Indexed: 12/22/2022]
Abstract
Ghrelin and leptin are key peripherally secreted appetite-regulating hormones in vertebrates. Here we consider the ghrelin gene (GHRL) of birds (class Aves), where it has been reported that ghrelin inhibits rather than augments feeding. Thirty-one bird species were compared, revealing that most species harbour a functional copy of GHRL and the coding region for its derived peptides ghrelin and obestatin. We provide evidence for loss of GHRL in saker and peregrine falcons, and this is likely to result from the insertion of an ERVK retrotransposon in intron 0. We hypothesise that the loss of anorexigenic ghrelin is a predatory adaptation that results in increased food-seeking behaviour and feeding in falcons.
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Affiliation(s)
- Inge Seim
- Ghrelin Research Group, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, 37 Kent St., Woolloongabba, Queensland 4102, Australia; Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology and Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Penny L Jeffery
- Ghrelin Research Group, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, 37 Kent St., Woolloongabba, Queensland 4102, Australia; Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology and Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Adrian C Herington
- Ghrelin Research Group, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, 37 Kent St., Woolloongabba, Queensland 4102, Australia; Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology and Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Lisa K Chopin
- Ghrelin Research Group, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, 37 Kent St., Woolloongabba, Queensland 4102, Australia; Australian Prostate Cancer Research Centre - Queensland, Queensland University of Technology and Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia.
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Mata H, Gongora J, Eizirik E, Alves BM, Soares MA, Ravazzolo AP. Identification and characterization of diverse groups of endogenous retroviruses in felids. Retrovirology 2015; 12:26. [PMID: 25808580 PMCID: PMC4373062 DOI: 10.1186/s12977-015-0152-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 02/23/2015] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Endogenous retroviruses (ERVs) are genetic elements with a retroviral origin that are integrated into vertebrate genomes. In felids (Mammalia, Carnivora, Felidae), ERVs have been described mostly in the domestic cat, and only rarely in wild species. To gain insight into the origins and evolutionary dynamics of endogenous retroviruses in felids, we have identified and characterized partial pro/pol ERV sequences from eight Neotropical wild cat species, belonging to three distinct lineages of Felidae. We also compared them with publicly available genomic sequences of Felis catus and Panthera tigris, as well as with representatives of other vertebrate groups, and performed phylogenetic and molecular dating analyses to investigate the pattern and timing of diversification of these retroviral elements. RESULTS We identified a high diversity of ERVs in the sampled felids, with a predominance of Gammaretrovirus-related sequences, including class I ERVs. Our data indicate that the identified ERVs arose from at least eleven horizontal interordinal transmissions from other mammals. Furthermore, we estimated that the majority of the Gamma-like integrations took place during the diversification of modern felids. Finally, our phylogenetic analyses indicate the presence of a genetically divergent group of sequences whose position in our phylogenetic tree was difficult to establish confidently relative to known retroviruses, and another lineage identified as ERVs belonging to class II. CONCLUSIONS Retroviruses have circulated in felids along with their evolution. The majority of the deep clades of ERVs exist since the primary divergence of felids' base and cluster with retroviruses of divergent mammalian lineages, suggesting horizontal interordinal transmission. Our findings highlight the importance of additional studies on the role of ERVs in the genome landscaping of other carnivore species.
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Aiewsakun P, Katzourakis A. Endogenous viruses: Connecting recent and ancient viral evolution. Virology 2015; 479-480:26-37. [PMID: 25771486 DOI: 10.1016/j.virol.2015.02.011] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 12/15/2014] [Accepted: 02/04/2015] [Indexed: 12/17/2022]
Abstract
The rapid rates of viral evolution allow us to reconstruct the recent history of viruses in great detail. This feature, however, also results in rapid erosion of evolutionary signal within viral molecular data, impeding studies of their deep history. Thus, the further back in time, the less accurate the inference becomes. Furthermore, reconstructing complex histories of transmission can be challenging, especially where extinct viral lineages are concerned. This problem has been partially solved by the discovery of viruses embedded in host genomes, known as endogenous viral elements (EVEs). Some of these endogenous viruses are derived from ancient relatives of extant viruses, allowing us to better examine ancient viral host range, geographical distribution and transmission routes. Moreover, our knowledge of viral evolutionary timescales and rate dynamics has also been greatly improved by their discovery, thereby bridging the gap between recent and ancient viral evolution.
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Affiliation(s)
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.
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26
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Chong AY, Kojima KK, Jurka J, Ray DA, Smit AFA, Isberg SR, Gongora J. Evolution and gene capture in ancient endogenous retroviruses - insights from the crocodilian genomes. Retrovirology 2014; 11:71. [PMID: 25499090 PMCID: PMC4299795 DOI: 10.1186/s12977-014-0071-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 08/07/2014] [Indexed: 01/12/2023] Open
Abstract
Background Crocodilians are thought to be hosts to a diverse and divergent complement of endogenous retroviruses (ERVs) but a comprehensive investigation is yet to be performed. The recent sequencing of three crocodilian genomes provides an opportunity for a more detailed and accurate representation of the ERV diversity that is present in these species. Here we investigate the diversity, distribution and evolution of ERVs from the genomes of three key crocodilian species, and outline the key processes driving crocodilian ERV proliferation and evolution. Results ERVs and ERV related sequences make up less than 2% of crocodilian genomes. We recovered and described 45 ERV groups within the three crocodilian genomes, many of which are species specific. We have also revealed a new class of ERV, ERV4, which appears to be common to crocodilians and turtles, and currently has no characterised exogenous counterpart. For the first time, we formally describe the characteristics of this ERV class and its classification relative to other recognised ERV and retroviral classes. This class shares some sequence similarity and sequence characteristics with ERV3, although it is phylogenetically distinct from the other ERV classes. We have also identified two instances of gene capture by crocodilian ERVs, one of which, the capture of a host KIT-ligand mRNA has occurred without the loss of an ERV domain. Conclusions This study indicates that crocodilian ERVs comprise a wide variety of lineages, many of which appear to reflect ancient infections. In particular, ERV4 appears to have a limited host range, with current data suggesting that it is confined to crocodilians and some lineages of turtles. Also of interest are two ERV groups that demonstrate evidence of host gene capture. This study provides a framework to facilitate further studies into non-mammalian vertebrates and highlights the need for further studies into such species. Electronic supplementary material The online version of this article (doi:10.1186/s12977-014-0071-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amanda Y Chong
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Kenji K Kojima
- Genetic Information Research Institute, Los Altos, CA, 94022, USA.
| | - Jerzy Jurka
- Genetic Information Research Institute, Los Altos, CA, 94022, USA.
| | - David A Ray
- Department of Biochemistry, Molecular Biology, Plant Pathology and Entomology, Mississippi State University, Starkville, Mississippi State, 39762, USA. .,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, Mississippi State, 39762, USA. .,Current Address: Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA.
| | - Arian F A Smit
- Institute for Systems Biology, Seattle, WA, 98109-5234, USA.
| | - Sally R Isberg
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW, 2006, Australia. .,Centre for Crocodile Research, Noonamah, NT, 0837, Australia.
| | - Jaime Gongora
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW, 2006, Australia.
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27
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Garcia-Etxebarria K, Jugo BM. Genomic environment and digital expression of bovine endogenous retroviruses. Gene 2014; 548:14-21. [DOI: 10.1016/j.gene.2014.06.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 02/08/2014] [Accepted: 06/23/2014] [Indexed: 10/25/2022]
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Garcia-Etxebarria K, Sistiaga-Poveda M, Jugo BM. Endogenous retroviruses in domestic animals. Curr Genomics 2014; 15:256-65. [PMID: 25132796 PMCID: PMC4133949 DOI: 10.2174/1389202915666140520003503] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 05/14/2014] [Accepted: 05/16/2014] [Indexed: 01/15/2023] Open
Abstract
Endogenous retroviruses (ERVs) are genomic elements that are present in a wide range of vertebrates. Although the study of ERVs has been carried out mainly in humans and model organisms, recently, domestic animals have become important, and some species have begun to be analyzed to gain further insight into ERVs. Due to the availability of complete genomes and the development of new computer tools, ERVs can now be analyzed from a genome-wide viewpoint. In addition, more experimental work is being carried out to analyze the distribution, expression and interplay of ERVs within a host genome. Cats, cattle, chicken, dogs, horses, pigs and sheep have been scrutinized in this manner, all of which are interesting species in health and economic terms. Furthermore, several studies have noted differences in the number of endogenous retroviruses and in the variability of these elements among different breeds, as well as their expression in different tissues and the effects of their locations, which, in some cases, are near genes. These findings suggest a complex, intriguing relationship between ERVs and host genomes. In this review, we summarize the most important in silico and experimental findings, discuss their implications and attempt to predict future directions for the study of these genomic elements.
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Affiliation(s)
- Koldo Garcia-Etxebarria
- Genetika, Antropologia Fisikoa eta Animalien Fisiologia Saila. Zientzia eta Teknologia Fakultatea. Euskal Herriko Unibertsitatea (UPV/EHU). 644 Postakutxa , E-48080 Bilbao, Spain
| | - Maialen Sistiaga-Poveda
- Genetika, Antropologia Fisikoa eta Animalien Fisiologia Saila. Zientzia eta Teknologia Fakultatea. Euskal Herriko Unibertsitatea (UPV/EHU). 644 Postakutxa , E-48080 Bilbao, Spain
| | - Begoña Marina Jugo
- Genetika, Antropologia Fisikoa eta Animalien Fisiologia Saila. Zientzia eta Teknologia Fakultatea. Euskal Herriko Unibertsitatea (UPV/EHU). 644 Postakutxa , E-48080 Bilbao, Spain
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Sacco MA, Nair VK. Prototype endogenous avian retroviruses of the genus Gallus. J Gen Virol 2014; 95:2060-2070. [PMID: 24903328 DOI: 10.1099/vir.0.066852-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ancient endogenous retroviruses (ERVs), designated endogenous avian retrovirus (EAVs), are present in all Gallus spp. including the chicken, and resemble the modern avian sarcoma and leukosis viruses (ASLVs). The EAVs comprise several distinct retroviruses, including EAV-0, EAV-E51 and EAV-HP, as well as a putative member previously named the avian retrotransposon of chickens (ART-CH). Thus far, only the EAV-HP elements have been well characterized. Here, we determined sequences of representative EAV-0 and EAV-E51 proviruses by cloning and data mining of the 2011 assembly of the Gallus gallus genome. Although the EAV-0 elements are primarily deleted in the env region, we identified two complete EAV-0 env genes within the G. gallus genome and prototype elements sharing identity with an EAV-E51-related clone previously designated EAV-E33. Prototype EAV-0, EAV-E51 and EAV-E33 gag, pol and env gene sequences used for phylogenetic analysis of deduced proteins showed that the EAVs formed three distinct clades, with EAV-0 sharing the last common ancestor with the ASLVs. The EAV-E51 clade showed the greatest level of divergence compared with other EAVs or ASLVs, suggesting that these ERVs represented exogenous retroviruses that evolved and integrated into the germline over a long period of time. Moreover, the degree of divergence between the chicken and red jungle fowl EAV-E51 sequences suggested that they were more ancient than the other EAVs and may have diverged through mutations that accumulated post-integration. Finally, we showed that the ART-CH elements were chimeric defective ERVs comprising portions of EAV-E51 and EAV-HP rather than authentic retrotransposons.
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Affiliation(s)
- Melanie Ann Sacco
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92834-6850, USA
| | - Venugopal K Nair
- Pirbright Institute, Compton Laboratory, Newbury, Berkshire RG20 7NN, UK
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Cui J, Zhao W, Huang Z, Jarvis ED, Gilbert MTP, Walker PJ, Holmes EC, Zhang G. Low frequency of paleoviral infiltration across the avian phylogeny. Genome Biol 2014; 15:539. [PMID: 25496498 PMCID: PMC4272516 DOI: 10.1186/s13059-014-0539-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 11/10/2014] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Mammalian genomes commonly harbor endogenous viral elements. Due to a lack of comparable genome-scale sequence data, far less is known about endogenous viral elements in avian species, even though their small genomes may enable important insights into the patterns and processes of endogenous viral element evolution. RESULTS Through a systematic screening of the genomes of 48 species sampled across the avian phylogeny we reveal that birds harbor a limited number of endogenous viral elements compared to mammals, with only five viral families observed: Retroviridae, Hepadnaviridae, Bornaviridae, Circoviridae, and Parvoviridae. All nonretroviral endogenous viral elements are present at low copy numbers and in few species, with only endogenous hepadnaviruses widely distributed, although these have been purged in some cases. We also provide the first evidence for endogenous bornaviruses and circoviruses in avian genomes, although at very low copy numbers. A comparative analysis of vertebrate genomes revealed a simple linear relationship between endogenous viral element abundance and host genome size, such that the occurrence of endogenous viral elements in bird genomes is 6- to 13-fold less frequent than in mammals. CONCLUSIONS These results reveal that avian genomes harbor relatively small numbers of endogenous viruses, particularly those derived from RNA viruses, and hence are either less susceptible to viral invasions or purge them more effectively.
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Affiliation(s)
- Jie Cui
- />Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006 Australia
- />Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, 169857 Singapore
| | - Wei Zhao
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Zhiyong Huang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Erich D Jarvis
- />Howard Hughes Medical Institute, Duke University Medical Center, Department of Neurobiology, Box 3209, Durham, North Carolina 27710 USA
| | - M Thomas P Gilbert
- />Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen, Denmark
- />Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102 Australia
| | - Peter J Walker
- />CSIRO Animal, Food and Health Sciences, Australian Animal Health Laboratory, Geelong, Victoria 3220 Australia
| | - Edward C Holmes
- />Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006 Australia
| | - Guojie Zhang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
- />Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
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A novel recombinant retrovirus in the genomes of modern birds combines features of avian and mammalian retroviruses. J Virol 2013; 88:2398-405. [PMID: 24352464 DOI: 10.1128/jvi.02863-13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Endogenous retroviruses (ERVs) represent ancestral sequences of modern retroviruses or their extinct relatives. The majority of ERVs cluster alongside exogenous retroviruses into two main groups based on phylogenetic analyses of the reverse transcriptase (RT) enzyme. Class I includes gammaretroviruses, and class II includes lentiviruses and alpha-, beta-, and deltaretroviruses. However, analyses of the transmembrane subunit (TM) of the envelope glycoprotein (env) gene result in a different topology for some retroviruses, suggesting recombination events in which heterologous env sequences have been acquired. We previously demonstrated that the TM sequences of five of the six genera of orthoretroviruses can be divided into three types, each of which infects a distinct set of vertebrate classes. Moreover, these classes do not always overlap the host range of the associated RT classes. Thus, recombination resulting in acquisition of a heterologous env gene could in theory facilitate cross-species transmissions across vertebrate classes, for example, from mammals to reptiles. Here we characterized a family of class II avian ERVs, "TgERV-F," that acquired a mammalian gammaretroviral env sequence. Although TgERV-F clusters near a sister clade to alpharetroviruses, its genome also has some features of betaretroviruses. We offer evidence that this unusual recombinant has circulated among several avian orders and may still have infectious members. In addition to documenting the infection of a nongalliform avian species by a mammalian retrovirus, TgERV-F also underscores the importance of env sequences in reconstructing phylogenies and supports a possible role for env swapping in allowing cross-species transmissions across wide taxonomic distances. IMPORTANCE Retroviruses can sometimes acquire an envelope gene (env) from a distantly related retrovirus. Since env is a key determinant of host range, such an event affects the host range of the recombinant virus and can lead to the creation of novel retroviral lineages. Retroviruses insert viral DNA into the host DNA during infection, and therefore vertebrate genomes contain a "fossil record" of endogenous retroviral sequences thought to represent past infections of germ cells. We examined endogenous retroviral sequences in avian genomes for evidence of recombination events involving env. Although cross-species transmissions of retroviruses between vertebrate classes (from mammals to birds, for example) are thought to be rare, we here characterized a group of avian retroviruses that acquired an env sequence from a mammalian retrovirus. We offer evidence that this unusual recombinant circulated among songbirds 2 to 4 million years ago and has remained active into the recent past.
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Allison AB, Kevin Keel M, Philips JE, Cartoceti AN, Munk BA, Nemeth NM, Welsh TI, Thomas JM, Crum JM, Lichtenwalner AB, Fadly AM, Zavala G, Holmes EC, Brown JD. Avian oncogenesis induced by lymphoproliferative disease virus: a neglected or emerging retroviral pathogen? Virology 2013; 450-451:2-12. [PMID: 24503062 DOI: 10.1016/j.virol.2013.11.037] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 11/07/2013] [Accepted: 11/25/2013] [Indexed: 10/25/2022]
Abstract
Lymphoproliferative disease virus (LPDV) is an exogenous oncogenic retrovirus that induces lymphoid tumors in some galliform species of birds. Historically, outbreaks of LPDV have been reported from Europe and Israel. Although the virus has previously never been detected in North America, herein we describe the widespread distribution, genetic diversity, pathogenesis, and evolution of LPDV in the United States. Characterization of the provirus genome of the index LPDV case from North America demonstrated an 88% nucleotide identity to the Israeli prototype strain. Although phylogenetic analysis indicated that the majority of viruses fell into a single North American lineage, a small subset of viruses from South Carolina were most closely related to the Israeli prototype. These results suggest that LPDV was transferred between continents to initiate outbreaks of disease. However, the direction (New World to Old World or vice versa), mechanism, and time frame of the transcontinental spread currently remain unknown.
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Affiliation(s)
- Andrew B Allison
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA; Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
| | - M Kevin Keel
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Jamie E Philips
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Andrew N Cartoceti
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Brandon A Munk
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Nicole M Nemeth
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Trista I Welsh
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Jesse M Thomas
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - James M Crum
- West Virginia Division of Natural Resources, Elkins, WV 26241, USA
| | - Anne B Lichtenwalner
- Department of Animal and Veterinary Sciences, University of Maine Animal Health Laboratory, University of Maine, Orono, ME 04469, USA
| | - Aly M Fadly
- United States Department of Agriculture, Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI 48823, USA
| | - Guillermo Zavala
- Poultry Diagnostic Research Center, Department of Population Health, University of Georgia, Athens, GA 30602, USA
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Biological Sciences and Sydney Medical School, University of Sydney, NSW 2006, Australia
| | - Justin D Brown
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
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Avian retroviral replication. Curr Opin Virol 2013; 3:664-9. [PMID: 24011707 DOI: 10.1016/j.coviro.2013.08.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 08/14/2013] [Accepted: 08/15/2013] [Indexed: 12/17/2022]
Abstract
Avian retroviruses were originally identified as cancer-inducting filterable agents in chicken neoplasms at the beginning of the 20th century. Since their discovery, the study of these simple retroviruses has contributed greatly to our understanding of viral replication and cancer. Avian retroviruses continue to evolve and have great economic importance in the poultry industry worldwide. The aim of this review is to provide a broad overview of the genome, pathology, and replication of avian retroviruses. Notable gaps in our current knowledge are highlighted, and areas where avian retroviruses differ from other retroviruses are emphasized.
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Wragg D, Mwacharo JM, Alcalde JA, Wang C, Han JL, Gongora J, Gourichon D, Tixier-Boichard M, Hanotte O. Endogenous retrovirus EAV-HP linked to blue egg phenotype in Mapuche fowl. PLoS One 2013; 8:e71393. [PMID: 23990950 PMCID: PMC3747184 DOI: 10.1371/journal.pone.0071393] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 07/02/2013] [Indexed: 12/03/2022] Open
Abstract
Oocyan or blue/green eggshell colour is an autosomal dominant trait found in native chickens (Mapuche fowl) of Chile and in some of their descendants in European and North American modern breeds. We report here the identification of an endogenous avian retroviral (EAV-HP) insertion in oocyan Mapuche fowl and European breeds. Sequencing data reveals 100% retroviral identity between the Mapuche and European insertions. Quantitative real-time PCR analysis of European oocyan chicken indicates over-expression of the SLCO1B3 gene (P<0.05) in the shell gland and oviduct. Predicted transcription factor binding sites in the long terminal repeats (LTR) indicate AhR/Ar, a modulator of oestrogen, as a possible promoter/enhancer leading to reproductive tissue-specific over-expression of the SLCO1B3 gene. Analysis of all jungle fowl species Gallus sp. supports the retroviral insertion to be a post-domestication event, while identical LTR sequences within domestic chickens are in agreement with a recent de novo mutation.
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Affiliation(s)
- David Wragg
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Joram M. Mwacharo
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, University Park, Nottingham, United Kingdom
| | - José A. Alcalde
- Pontificia Universidad Catolica de Chile, Facultad de Agronomia e Ingenieria Forestal, Santiago, Chile
| | - Chen Wang
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Jaime Gongora
- The University of Sydney, Faculty of Veterinary Science, Sydney, New South Wales, Australia
| | - David Gourichon
- Institut National de la Recherche Agronomique, UE1295 Poultry Experimental Platform of Tours, Nouzilly, France
| | - Michèle Tixier-Boichard
- Institut National de la Recherche Agronomique, AgroParisTech, UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas, France
| | - Olivier Hanotte
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, University Park, Nottingham, United Kingdom
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Abstract
The majority of retroviral envelope glycoproteins characterized to date are typical of type I viral fusion proteins, having a receptor binding subunit associated with a fusion subunit. The fusion subunits of lentiviruses and alpha-, beta-, delta- and gammaretroviruses have a very conserved domain organization and conserved features of secondary structure, making them suitable for phylogenetic analyses. Such analyses, along with sequence comparisons, reveal evidence of numerous recombination events in which retroviruses have acquired envelope glycoproteins from heterologous sequences. Thus, the envelope gene (env) can have a history separate from that of the polymerase gene (pol), which is the most commonly used gene in phylogenetic analyses of retroviruses. Focusing on the fusion subunits of the genera listed above, we describe three distinct types of retroviral envelope glycoproteins, which we refer to as gamma-type, avian gamma-type and beta-type. By tracing these types within the ‘fossil record’ provided by endogenous retroviruses, we show that they have surprisingly distinct evolutionary histories and dynamics, with important implications for cross-species transmissions and the generation of novel lineages. These findings validate the utility of env sequences in contributing phylogenetic signal that enlarges our understanding of retrovirus evolution.
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Affiliation(s)
- Jamie E Henzy
- Biology Department, Boston College, , Chestnut Hill, MA 02467, USA
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Abstract
Endogenous retrovirus (ERV) genomes integrated into the chromosomal DNA of the host were first detected in chickens and mice as Mendelian determinants of Gag and Env proteins and of the release of infectious virus particles. The presence of ERV was confirmed by DNA hybridization. With complete host genomes available for analysis, we can now see the great extent of viral invasion into the genomes of numerous vertebrate species, including humans. ERVs are found at many loci in host DNA and also in the genomes of large DNA viruses, such as herpesviruses and poxviruses. The evolution of xenotropism and cross-species infection is discussed in the light of the dynamic relationship between exogenous and endogenous retroviruses.
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Affiliation(s)
- Robin A Weiss
- Division of Infection and Immunity, Wohl Virion Centre, University College London, , Cruciform Building, Gower Street, London WC1 6BT, UK
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Kucerová D, Plachy J, Reinisová M, Senigl F, Trejbalová K, Geryk J, Hejnar J. Nonconserved tryptophan 38 of the cell surface receptor for subgroup J avian leukosis virus discriminates sensitive from resistant avian species. J Virol 2013; 87:8399-407. [PMID: 23698309 PMCID: PMC3719790 DOI: 10.1128/jvi.03180-12] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 05/14/2013] [Indexed: 11/20/2022] Open
Abstract
Subgroup J avian leukosis virus (ALV-J) is unique among the avian sarcoma and leukosis viruses in using the multimembrane-spanning cell surface protein Na(+)/H(+) exchanger type 1 (NHE1) as a receptor. The precise localization of amino acids critical for NHE1 receptor activity is key in understanding the virus-receptor interaction and potential interference with virus entry. Because no resistant chicken lines have been described until now, we compared the NHE1 amino acid sequences from permissive and resistant galliform species. In all resistant species, the deletion or substitution of W38 within the first extracellular loop was observed either alone or in the presence of other incidental amino acid changes. Using the ectopic expression of wild-type or mutated chicken NHE1 in resistant cells and infection with a reporter recombinant retrovirus of subgroup J specificity, we studied the effect of individual mutations on the NHE1 receptor capacity. We suggest that the absence of W38 abrogates binding of the subgroup J envelope glycoprotein to ALV-J-resistant cells. Altogether, we describe the functional importance of W38 for virus entry and conclude that natural polymorphisms in NHE1 can be a source of host resistance to ALV-J.
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Affiliation(s)
- Dana Kucerová
- Department of Cellular and Viral Genetics, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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38
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The avian XPR1 gammaretrovirus receptor is under positive selection and is disabled in bird species in contact with virus-infected wild mice. J Virol 2013; 87:10094-104. [PMID: 23843647 DOI: 10.1128/jvi.01327-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Xenotropic mouse leukemia viruses (X-MLVs) are broadly infectious for mammals except most of the classical strains of laboratory mice. These gammaretroviruses rely on the XPR1 receptor for entry, and the unique resistance of laboratory mice is due to two mutations in different putative XPR1 extracellular loops. Cells from avian species differ in susceptibility to X-MLVs, and 2 replacement mutations in the virus-resistant chicken XPR1 (K496Q and Q579E) distinguish it from the more permissive duck and quail receptors. These substitutions align with the two mutations that disable the laboratory mouse XPR1. Mutagenesis of the chicken and duck genes confirms that residues at both sites are critical for virus entry. Among 32 avian species, the 2 disabling XPR1 mutations are found together only in the chicken, an omnivorous, ground-dwelling fowl that was domesticated in India and/or Southeast Asia, which is also where X-MLV-infected house mice evolved. The receptor-disabling mutations are also present separately in 5 additional fowl and raptor species, all of which are native to areas of Asia populated by the virus-infected subspecies Mus musculus castaneus. Phylogenetic analysis showed that the avian XPR1 gene is under positive selection at sites implicated in receptor function, suggesting a defensive role for XPR1 in the avian lineage. Contact between bird species and virus-infected mice may thus have favored selection of mouse virus-resistant receptor orthologs in the birds, and our data suggest that similar receptor-disabling mutations were fixed in mammalian and avian species exposed to similar virus challenges.
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Song N, Jo H, Choi M, Kim JH, Seo HG, Cha SY, Seo K, Park C. Identification and classification of feline endogenous retroviruses in the cat genome using degenerate PCR and in silico data analysis. J Gen Virol 2013; 94:1587-1596. [PMID: 23515024 DOI: 10.1099/vir.0.051862-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this study was to identify and classify endogenous retroviruses (ERVs) in the cat genome. Pooled DNA from five domestic cats was subjected to degenerate PCR with primers specific to the conserved retroviral pro/pol region. The 59 amplified retroviral sequences were used for in silico analysis of the cat genome (Felis_catus-6.2). We identified 219 ERV γ and β elements from cat genome contigs, which were classified into 42 ERV γ and 4 β families and further analysed. Among them, 99 γ and 5 β ERV elements contained the complete retroviral structure. Furthermore, we identified 757 spuma-like ERV elements based on the sequence homology to murine (Mu)ERV-L and human (H)ERV-L. To the best of our knowledge, this is the first detailed genome-scale analysis examining Felis catus endogenous retroviruses (FcERV) and providing advanced insights into their structural characteristics, localization in the genome, and diversity.
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Affiliation(s)
- Ning Song
- Department of Animal Biotechnology, Konkuk University, Hwayang-dong, Kwangjin-gu, Seoul, South Korea
| | - Haiin Jo
- Department of Animal Biotechnology, Konkuk University, Hwayang-dong, Kwangjin-gu, Seoul, South Korea
| | - Minkyeung Choi
- Department of Animal Biotechnology, Konkuk University, Hwayang-dong, Kwangjin-gu, Seoul, South Korea
| | - Jin-Hoi Kim
- Department of Animal Biotechnology, Konkuk University, Hwayang-dong, Kwangjin-gu, Seoul, South Korea
| | - Han Geuk Seo
- Department of Animal Biotechnology, Konkuk University, Hwayang-dong, Kwangjin-gu, Seoul, South Korea
| | - Se-Yeoun Cha
- College of Veterinary Medicine, Chonbuk National University, Jeonju, South Korea
| | - Kunho Seo
- Colleges of Veterinary Medicine, Konkuk University, Seoul, South Korea
| | - Chankyu Park
- Department of Animal Biotechnology, Konkuk University, Hwayang-dong, Kwangjin-gu, Seoul, South Korea
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