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Cofre J, Saalfeld K. The first embryo, the origin of cancer and animal phylogeny. I. A presentation of the neoplastic process and its connection with cell fusion and germline formation. Front Cell Dev Biol 2023; 10:1067248. [PMID: 36684435 PMCID: PMC9846517 DOI: 10.3389/fcell.2022.1067248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/16/2022] [Indexed: 01/05/2023] Open
Abstract
The decisive role of Embryology in understanding the evolution of animal forms is founded and deeply rooted in the history of science. It is recognized that the emergence of multicellularity would not have been possible without the formation of the first embryo. We speculate that biophysical phenomena and the surrounding environment of the Ediacaran ocean were instrumental in co-opting a neoplastic functional module (NFM) within the nucleus of the first zygote. Thus, the neoplastic process, understood here as a biological phenomenon with profound embryologic implications, served as the evolutionary engine that favored the formation of the first embryo and cancerous diseases and allowed to coherently create and recreate body shapes in different animal groups during evolution. In this article, we provide a deep reflection on the Physics of the first embryogenesis and its contribution to the exaptation of additional NFM components, such as the extracellular matrix. Knowledge of NFM components, structure, dynamics, and origin advances our understanding of the numerous possibilities and different innovations that embryos have undergone to create animal forms via Neoplasia during evolutionary radiation. The developmental pathways of Neoplasia have their origins in ctenophores and were consolidated in mammals and other apical groups.
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Affiliation(s)
- Jaime Cofre
- Laboratório de Embriologia Molecular e Câncer, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil,*Correspondence: Jaime Cofre,
| | - Kay Saalfeld
- Laboratório de Filogenia Animal, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
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2
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Hirai J, Urayama SI, Takaki Y, Hirai M, Nagasaki K, Nunoura T. RNA Virosphere in a Marine Zooplankton Community in the Subtropical Western North Pacific. Microbes Environ 2022; 37:ME21066. [PMID: 34980753 PMCID: PMC9763039 DOI: 10.1264/jsme2.me21066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Zooplankton and viruses play a key role in marine ecosystems; however, their interactions have not been examined in detail. In the present study, the diversity of viruses associated with zooplankton collected using a plankton net (mesh size: 100 μm) in the subtropical western North Pacific was investigated by fragmented and primer ligated dsRNA sequencing. We obtained 21 and 168 operational taxonomic units (OTUs) of ssRNA and dsRNA viruses, respectively, containing RNA-dependent RNA polymerase (RdRp). These OTUs presented average amino acid similarities of 43.5 and 44.0% to the RdRp genes of known viruses in ssRNA viruses and dsRNA viruses, respectively. Dominant OTUs mainly belonged to narna-like and picorna-like ssRNA viruses and chryso-like, partiti-like, picobirna-like, reo-like, and toti-like dsRNA viruses. Phylogenetic ana-lyses of the RdRp gene revealed that OTUs were phylogenetically diverse and clustered into distinct clades from known viral groups. The community structure of the same zooplankton sample was investigated using small subunit (SSU) rRNA sequences assembled from the metatranscriptome of single-stranded RNA. More than 90% of the sequence reads were derived from metazoan zooplankton; copepods comprised approximately 70% of the sequence reads. Although this ana-lysis provided no direct evidence of the host species of RNA viruses, these dominant zooplankton are expected to be associated with the RNA viruses detected in the present study. The present results indicate that zooplankton function as a reservoir of diverse RNA viruses and suggest that investigations of zooplankton viruses will provide a more detailed understanding of the role of viruses in marine ecosystems.
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Affiliation(s)
- Junya Hirai
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa, Chiba 277–8564, Japan, Corresponding author. E-mail: ; Tel: +81–4–7136–6163; Fax: +81–4–7136–6172
| | - Syun-ichi Urayama
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan,Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan,Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Yoshiro Takaki
- Super-cuttingedge Grand and Advanced Research (SUGAR) Program, JAMSTEC, 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Miho Hirai
- Super-cuttingedge Grand and Advanced Research (SUGAR) Program, JAMSTEC, 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Keizo Nagasaki
- Faculty of Science and Technology, Kochi University, 200 Monobe Otsu, Nankoku, Kochi 783–8502, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
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3
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Tochetto C, Cibulski SP, Muterle Varela AP, Cerva C, Alves de Lima D, Fumaco Teixeira T, Quoos Mayer F, Roehe PM. A variety of highly divergent eukaryotic ssDNA viruses in sera of pigs. J Gen Virol 2021; 102. [PMID: 34928204 DOI: 10.1099/jgv.0.001706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Over the last decade, viral metagenomics has been established as a non-targeted approach for identifying viruses in stock animals, including pigs. This has led to the identification of a vast diversity of small circular ssDNA viruses. The present study focuses on the investigation of eukaryotic circular Rep-encoding single-stranded (CRESS) DNA viral genomes present in serum of commercially reared pigs from southern Brazil. Several CRESS DNA viral genomes were detected, including representatives of the families Smacoviridae (n=5), Genomoviridae (n=3), Redondoviridae (n=1), Nenyaviridae (n=1) and other yet unclassified genomes (n=9), plus a circular DNA molecule, which probably belongs to the phylum Cressdnaviricota. A novel genus within the family Smacoviridae, tentatively named 'Suismacovirus', comprising 21 potential new species, is proposed. Although the reported genomes were recovered from pigs with clinical signs of respiratory disease, further studies should examine their potential role as pathogens. Nonetheless, these findings highlight the diversity of circular ssDNA viruses in serum of domestic pigs, expand the knowledge on CRESS DNA viruses' genetic diversity and distribution and contribute to the global picture of the virome of commercially reared pigs.
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Affiliation(s)
- Caroline Tochetto
- Laboratório de Virologia, Departamento de Microbiologia Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Samuel Paulo Cibulski
- Centro de Biotecnologia - CBiotec, Laboratório de Biotecnologia Celular e Molecular, Universidade Federal da Paraíba - UFPB, João Pessoa, Paraíba, Brazil
| | - Ana Paula Muterle Varela
- Laboratório de Virologia, Departamento de Microbiologia Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Cristine Cerva
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor(IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria de Agricultura, Pecuária e Desenvolvimento Rural, Eldorado do Sul, Rio Grande do Sul, Brazil
| | - Diane Alves de Lima
- Laboratório de Microbiologia do Centro Clínico Veterinário, Centro Universitário da Serra Gaúcha - FSG, Caxias do Sul, Rio Grande do Sul, Brazil
| | - Thais Fumaco Teixeira
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor(IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria de Agricultura, Pecuária e Desenvolvimento Rural, Eldorado do Sul, Rio Grande do Sul, Brazil
| | - Fabiana Quoos Mayer
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor(IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria de Agricultura, Pecuária e Desenvolvimento Rural, Eldorado do Sul, Rio Grande do Sul, Brazil
| | - Paulo Michel Roehe
- Laboratório de Virologia, Departamento de Microbiologia Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
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Hewson I, Johnson MR, Tibbetts IR. An Unconventional Flavivirus and Other RNA Viruses in the Sea Cucumber (Holothuroidea; Echinodermata) Virome. Viruses 2020; 12:v12091057. [PMID: 32972018 PMCID: PMC7551563 DOI: 10.3390/v12091057] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/11/2022] Open
Abstract
Sea cucumbers (Holothuroidea; Echinodermata) are ecologically significant constituents of benthic marine habitats. We surveilled RNA viruses inhabiting eight species (representing four families) of holothurian collected from four geographically distinct locations by viral metagenomics, including a single specimen of Apostichopus californicus affected by a hitherto undocumented wasting disease. The RNA virome comprised genome fragments of both single-stranded positive sense and double stranded RNA viruses, including those assigned to the Picornavirales, Ghabrivirales, and Amarillovirales. We discovered an unconventional flavivirus genome fragment which was most similar to a shark virus. Ghabivirales-like genome fragments were most similar to fungal totiviruses in both genome architecture and homology and had likely infected mycobiome constituents. Picornavirales, which are commonly retrieved in host-associated viral metagenomes, were similar to invertebrate transcriptome-derived picorna-like viruses. The greatest number of viral genome fragments was recovered from the wasting A. californicus library compared to the asymptomatic A. californicus library. However, reads from the asymptomatic library recruited to nearly all recovered wasting genome fragments, suggesting that they were present but not well represented in the grossly normal specimen. These results expand the known host range of flaviviruses and suggest that fungi and their viruses may play a role in holothurian ecology.
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Affiliation(s)
- Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA;
- Correspondence: ; Tel.: +1-607-255-0151
| | | | - Ian R. Tibbetts
- School of Biological Sciences, University of Queensland, St Lucia, Brisbane, QLD 4072, Australia;
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Traylor-Knowles N, Vandepas LE, Browne WE. Still Enigmatic: Innate Immunity in the Ctenophore Mnemiopsis leidyi. Integr Comp Biol 2020; 59:811-818. [PMID: 31251332 DOI: 10.1093/icb/icz116] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Innate immunity is an ancient physiological response critical for protecting metazoans from invading pathogens. It is the primary pathogen defense mechanism among invertebrates. While innate immunity has been studied extensively in diverse invertebrate taxa, including mollusks, crustaceans, and cnidarians, this system has not been well characterized in ctenophores. The ctenophores comprise an exclusively marine, non-bilaterian lineage that diverged early during metazoan diversification. The phylogenetic position of ctenophore lineage suggests that characterization of the ctenophore innate immune system will reveal important features associated with the early evolution of the metazoan innate immune system. Here, we review current understanding of the ctenophore immune repertoire and identify innate immunity genes recovered from three ctenophore species. We also isolate and characterize Mnemiopsis leidyi cells that display macrophage-like behavior when challenged with bacteria. Our results indicate that ctenophores possess cells capable of phagocytosing microbes and that two distantly related ctenophores, M. leidyi and Hormiphora californiensis, possess many candidate innate immunity proteins.
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Affiliation(s)
- Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, FL 33149, USA
| | - Lauren E Vandepas
- Benaroya Research Institute, 1201 9th Avenue, Seattle, WA 98101, USA.,Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - William E Browne
- Department of Biology, University of Miami, Cox Science Building, 1301 Memorial Drive, Miami, FL 33146, USA
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Shiganova TA, Mikaelyan AS, Moncheva S, Stefanova K, Chasovnikov VK, Mosharov SA, Mosharova IN, Slabakova N, Mavrodieva R, Stefanova E, Zasko DN, Dzhurova B. Effect of invasive ctenophores Mnemiopsis leidyi and Beroe ovata on low trophic webs of the Black Sea ecosystem. MARINE POLLUTION BULLETIN 2019; 141:434-447. [PMID: 30955754 DOI: 10.1016/j.marpolbul.2019.02.049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 02/23/2019] [Indexed: 06/09/2023]
Abstract
The study focuses on the impact of life excretion and mucus released by the "biological pollutants" invasive ctenophore Mnemiopsis leidyi and its predator Beroe ovata on the marine environment and lower trophic levels of the Black Sea ecosystem (bacteria, pico-phytoplankton, nano-autotrophic/heterotrophic flagellates, micro-phytoplankton, chlorophyll a, primary production (PP), micro-zooplankton). The chemical and biological variables were analysed in two sets of lab experiments with natural communities from mesotrophic (Gelendzhik) and eutrophic (Varna) coastal waters. While both species altered the chemical properties of experimental media, exerting structural and functional changes in the low food-web biological compartments, the results showed a stronger effect of B. ovata, most likely related to the measured higher rate of excretion and amount of released mucus. In addition the alterations in the Gelendzhik experiment were more pronounced, indicating that environmental implications on lower food-web are more conspicuous in mesotrophic than in eutrophic coastal waters.
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Affiliation(s)
- T A Shiganova
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36, Nahimovskiy prospekt, Moscow 117997, Russia.
| | - A S Mikaelyan
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36, Nahimovskiy prospekt, Moscow 117997, Russia.
| | - S Moncheva
- Institute of Oceanology BAS, 40 Parvi Mai street, 9000 Varna, Bulgaria
| | - K Stefanova
- Institute of Oceanology BAS, 40 Parvi Mai street, 9000 Varna, Bulgaria
| | - V K Chasovnikov
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36, Nahimovskiy prospekt, Moscow 117997, Russia
| | - S A Mosharov
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36, Nahimovskiy prospekt, Moscow 117997, Russia
| | - I N Mosharova
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36, Nahimovskiy prospekt, Moscow 117997, Russia
| | - N Slabakova
- Institute of Oceanology BAS, 40 Parvi Mai street, 9000 Varna, Bulgaria
| | - R Mavrodieva
- Institute of Oceanology BAS, 40 Parvi Mai street, 9000 Varna, Bulgaria
| | - E Stefanova
- Institute of Oceanology BAS, 40 Parvi Mai street, 9000 Varna, Bulgaria
| | - D N Zasko
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36, Nahimovskiy prospekt, Moscow 117997, Russia
| | - B Dzhurova
- Institute of Oceanology BAS, 40 Parvi Mai street, 9000 Varna, Bulgaria
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Zhao L, Rosario K, Breitbart M, Duffy S. Eukaryotic Circular Rep-Encoding Single-Stranded DNA (CRESS DNA) Viruses: Ubiquitous Viruses With Small Genomes and a Diverse Host Range. Adv Virus Res 2018; 103:71-133. [PMID: 30635078 DOI: 10.1016/bs.aivir.2018.10.001] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA viruses in most environments and in association with diverse hosts. In particular, circular ssDNA viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA viruses (CRESS DNA) viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA viruses, and speculates on future research horizons.
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Affiliation(s)
- Lele Zhao
- Department of Ecology, Evolution and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ, United States
| | - Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ, United States.
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8
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Bistolas KSI, Rudstam LG, Hewson I. Gene expression of benthic amphipods (genus: Diporeia) in relation to a circular ssDNA virus across two Laurentian Great Lakes. PeerJ 2017; 5:e3810. [PMID: 28966890 PMCID: PMC5621510 DOI: 10.7717/peerj.3810] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/23/2017] [Indexed: 01/15/2023] Open
Abstract
Circular rep-encoding ssDNA (CRESS-DNA) viruses are common constituents of invertebrate viral consortia. Despite their ubiquity and sequence diversity, the effects of CRESS-DNA viruses on invertebrate biology and ecology remain largely unknown. This study assessed the relationship between the transcriptional profile of benthic amphipods of genus Diporeia and the presence of the CRESS-DNA virus, LM29173, in the Laurentian Great Lakes to provide potential insight into the influence of these viruses on invertebrate gene expression. Twelve transcriptomes derived from Diporeia were compared, representing organisms from two amphipod haplotype clades (Great Lakes Michigan and Superior, defined by COI barcode sequencing) with varying viral loads (up to 3 × 106 genome copies organism−1). Read recruitment to de novo assembled transcripts revealed 2,208 significantly over or underexpressed contigs in transcriptomes with above average LM29173 load. Of these contigs, 31.5% were assigned a putative function. The greatest proportion of annotated, differentially expressed transcripts were associated with functions including: (1) replication, recombination, and repair, (2) cell structure/biogenesis, and (3) post-translational modification, protein turnover, and chaperones. Contigs putatively associated with innate immunity displayed no consistent pattern of expression, though several transcripts were significantly overexpressed in amphipods with high viral load. Quantitation (RT-qPCR) of target transcripts, non-muscular myosin heavy chain, β-actin, and ubiquitin-conjugating enzyme E2, corroborated transcriptome analysis and indicated that Lake Michigan and Lake Superior amphipods with high LM29173 load exhibit lake-specific trends in gene expression. While this investigation provides the first comparative survey of the transcriptional profile of invertebrates of variable CRESS-DNA viral load, additional inquiry is required to define the scope of host-specific responses to potential infection.
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Affiliation(s)
| | - Lars G Rudstam
- Department of Natural Resources and the Cornell Biological Field Station, Cornell University, Bridgeport, NY, USA
| | - Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY, USA
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9
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Tijssen P, Pénzes JJ, Yu Q, Pham HT, Bergoin M. Reprint of: Diversity of small, single-stranded DNA viruses of invertebrates and their chaotic evolutionary past. J Invertebr Pathol 2017; 147:23-36. [PMID: 32781498 DOI: 10.1016/j.jip.2017.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/14/2016] [Accepted: 09/19/2016] [Indexed: 11/25/2022]
Abstract
A wide spectrum of invertebrates is susceptible to various single-stranded DNA viruses. Their relative simplicity of replication and dependence on actively dividing cells makes them highly pathogenic for many invertebrates (Hexapoda, Decapoda, etc.). We present their taxonomical classification and describe the evolutionary relationships between various groups of invertebrate-infecting viruses, their high degree of recombination, and their relationship to viruses infecting mammals or other vertebrates. They share characteristics of the viruses within the various families, including structure of the virus particle, genome properties, and gene expression strategy.
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Affiliation(s)
- Peter Tijssen
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Judit J Pénzes
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Qian Yu
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Hanh T Pham
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Max Bergoin
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada; Laboratoire de Pathologie Comparée, Faculté des Sciences, Université Montpellier, Place Eugène Bataillon, 34095 Montpellier, France
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10
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Jackson EW, Bistolas KSI, Button JB, Hewson I. Novel Circular Single-Stranded DNA Viruses among an Asteroid, Echinoid and Holothurian (Phylum: Echinodermata). PLoS One 2016; 11:e0166093. [PMID: 27855181 PMCID: PMC5113903 DOI: 10.1371/journal.pone.0166093] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/21/2016] [Indexed: 11/24/2022] Open
Abstract
Echinoderms are prone to large population fluctuations that can be mediated by pervasive disease events. For the majority of echinoderm disease events the causative pathogen is unknown. Viruses have only recently been explored as potential pathogens using culture-independent techniques though little information currently exists on echinoderm viruses. In this study, ten circular ssDNA viruses were discovered in tissues among an asteroid (Asterias forbesi), an echinoid (Strongylocentrotus droebachiensis) and a holothurian (Parastichopus californicus) using viral metagenomics. Genome architecture and sequence similarity place these viruses among the rapidly expanding circular rep-encoding single stranded (CRESS) DNA viral group. Multiple genomes from the same tissue were no more similar in sequence identity to each other than when compared to other known CRESS DNA viruses. The results from this study are the first to describe a virus from a holothurian and continue to show the ubiquity of these viruses among aquatic invertebrates.
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Affiliation(s)
- Elliot W. Jackson
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
- * E-mail:
| | - Kalia S. I. Bistolas
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | - Jason B. Button
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | - Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
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11
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Tijssen P, Pénzes JJ, Yu Q, Pham HT, Bergoin M. Diversity of small, single-stranded DNA viruses of invertebrates and their chaotic evolutionary past. J Invertebr Pathol 2016; 140:83-96. [PMID: 27663091 DOI: 10.1016/j.jip.2016.09.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/14/2016] [Accepted: 09/19/2016] [Indexed: 11/19/2022]
Abstract
A wide spectrum of invertebrates is susceptible to various single-stranded DNA viruses. Their relative simplicity of replication and dependence on actively dividing cells makes them highly pathogenic for many invertebrates (Hexapoda, Decapoda, etc.). We present their taxonomical classification and describe the evolutionary relationships between various groups of invertebrate-infecting viruses, their high degree of recombination, and their relationship to viruses infecting mammals or other vertebrates. They share characteristics of the viruses within the various families, including structure of the virus particle, genome properties, and gene expression strategy.
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Affiliation(s)
- Peter Tijssen
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Judit J Pénzes
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Qian Yu
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Hanh T Pham
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Max Bergoin
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada; Laboratoire de Pathologie Comparée, Faculté des Sciences, Université Montpellier, Place Eugène Bataillon, 34095 Montpellier, France
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12
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Ryan JF, Schnitzler CE, Tamm SL. Meeting report of Ctenopalooza: the first international meeting of ctenophorologists. EvoDevo 2016. [PMCID: PMC4997693 DOI: 10.1186/s13227-016-0057-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Here we present a report on Ctenopalooza: A meeting of ctenophorologists held at the Whitney Laboratory for Marine Bioscience in St. Augustine, FL, USA, on March 14–15, 2016. In this report, we provide a summary of each of the sessions that occurred during this two-day meeting, which touched on most of the relevant areas of ctenophore biology. The report includes some major themes regarding the future of ctenophore research that emerged during Ctenopalooza. More information can be found at the meeting Web site: http://ctenopalooza.whitney.ufl.edu.
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Steel O, Kraberger S, Sikorski A, Young LM, Catchpole RJ, Stevens AJ, Ladley JJ, Coray DS, Stainton D, Dayaram A, Julian L, van Bysterveldt K, Varsani A. Circular replication-associated protein encoding DNA viruses identified in the faecal matter of various animals in New Zealand. INFECTION GENETICS AND EVOLUTION 2016; 43:151-64. [PMID: 27211884 DOI: 10.1016/j.meegid.2016.05.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 12/13/2022]
Abstract
In recent years, innovations in molecular techniques and sequencing technologies have resulted in a rapid expansion in the number of known viral sequences, in particular those with circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA genomes. CRESS DNA viruses are present in the virome of many ecosystems and are known to infect a wide range of organisms. A large number of the recently identified CRESS DNA viruses cannot be classified into any known viral families, indicating that the current view of CRESS DNA viral sequence space is greatly underestimated. Animal faecal matter has proven to be a particularly useful source for sampling CRESS DNA viruses in an ecosystem, as it is cost-effective and non-invasive. In this study a viral metagenomic approach was used to explore the diversity of CRESS DNA viruses present in the faeces of domesticated and wild animals in New Zealand. Thirty-eight complete CRESS DNA viral genomes and two circular molecules (that may be defective molecules or single components of multicomponent genomes) were identified from forty-nine individual animal faecal samples. Based on shared genome organisations and sequence similarities, eighteen of the isolates were classified as gemycircularviruses and twelve isolates were classified as smacoviruses. The remaining eight isolates lack significant sequence similarity with any members of known CRESS DNA virus groups. This research adds significantly to our knowledge of CRESS DNA viral diversity in New Zealand, emphasising the prevalence of CRESS DNA viruses in nature, and reinforcing the suggestion that a large proportion of CRESS DNA viruses are yet to be identified.
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Affiliation(s)
- Olivia Steel
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Simona Kraberger
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Alyssa Sikorski
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Laura M Young
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Ryan J Catchpole
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Aaron J Stevens
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Jenny J Ladley
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Dorien S Coray
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Daisy Stainton
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Anisha Dayaram
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Laurel Julian
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Katherine van Bysterveldt
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Arvind Varsani
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Structural Biology Research Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory 7700, South Africa; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, USA.
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Diverse circular replication-associated protein encoding viruses circulating in invertebrates within a lake ecosystem. INFECTION GENETICS AND EVOLUTION 2016; 39:304-316. [PMID: 26873065 DOI: 10.1016/j.meegid.2016.02.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/30/2016] [Accepted: 02/07/2016] [Indexed: 11/24/2022]
Abstract
Over the last five years next-generation sequencing has become a cost effective and efficient method for identifying known and unknown microorganisms. Access to this technique has dramatically changed the field of virology, enabling a wide range of environmental viral metagenome studies to be undertaken of organisms and environmental samples from polar to tropical regions. These studies have led to the discovery of hundreds of highly divergent single stranded DNA (ssDNA) virus-like sequences encoding replication-associated proteins. Yet, few studies have explored how viruses might be shared in an ecosystem through feeding relationships. Here we identify 169 circular molecules (160 CRESS DNA molecules, nine circular molecules) recovered from a New Zealand freshwater lake, that we have tentatively classified into 51 putatively novel species and five previously described species (DflaCV-3, -5, -6, -8, -10). The CRESS DNA viruses identified in this study were recovered from molluscs (Echyridella menzeisii, Musculium novaezelandiae, Potamopyrgus antipodarum and Physella acuta) and insect larvae (Procordulia grayi, Xanthocnemis zealandica, and Chironomus zealandicus) collected from Lake Sarah, as well as from the lake water and benthic sediments. Extensive diversity was observed across most CRESS DNA molecules recovered. The putative capsid protein of one viral species was found to be most similar to those of members of the Tombusviridae family, thus expanding the number of known RNA-DNA hybrid viruses in nature. We noted a strong association between the CRESS DNA viruses and circular molecules identified in the water and browser organisms (C. zealandicus, P. antipodarum and P. acuta), and between water sediments and undefended prey species (C. zealandicus). However, we were unable to find any significant correlation of viral assemblages to the potential feeding relationships of the host aquatic invertebrates.
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Male MF, Kraberger S, Stainton D, Kami V, Varsani A. Cycloviruses, gemycircularviruses and other novel replication-associated protein encoding circular viruses in Pacific flying fox (Pteropus tonganus) faeces. INFECTION GENETICS AND EVOLUTION 2016; 39:279-292. [PMID: 26873064 DOI: 10.1016/j.meegid.2016.02.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/27/2016] [Accepted: 02/06/2016] [Indexed: 12/13/2022]
Abstract
Viral metagenomic studies have demonstrated that animal faeces can be a good sampling source for exploring viral diversity associated with the host and its environment. As part of an continuing effort to identify novel circular replication-associated protein encoding single-stranded (CRESS) DNA viruses circulating in the Tongan archipelago, coupled with the fact that bats are a reservoir species of a large number of viruses, we used a metagenomic approach to investigate the CRESS DNA virus diversity in Pacific flying fox (Pteropus tonganus) faeces. Faecal matter from four roosting sites located in Ha'avakatolo, Kolovai, Ha'ateiho and Lapaha on Tongatapu Island was collected in April 2014 and January 2015. From these samples we identified five novel cycloviruses representing three putative species, 25 gemycircularviruses representing at least 14 putative species, 17 other CRESS DNA viruses (15 putative species), two circular DNA molecules and a putative novel multi-component virus for which we have identified three cognate molecules. This study demonstrates that there exists a large diversity of CRESS DNA viruses in Pacific flying fox faeces.
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Affiliation(s)
- Maketalena F Male
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Simona Kraberger
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Daisy Stainton
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | | | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Structural Biology Research Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory 7700, South Africa; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, USA.
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