Alphasatellitidae : a new family with two subfamilies for the classification of geminivirus- and nanovirus-associated alphasatellites

Published on May 9, 2018in Archives of Virology2.243
· DOI :10.1007/S00705-018-3854-2
Rob W. Briddon67
Estimated H-index: 67
(National Institute for Biotechnology and Genetic Engineering),
Darren P. Martin (UCT: University of Cape Town)+ 6 AuthorsArvind Varsani63
Estimated H-index: 63
(ASU: Arizona State University)
Sources
Abstract
Nanoviruses and geminiviruses are circular, single stranded DNA viruses that infect many plant species around the world. Nanoviruses and certain geminiviruses that belong to the Begomovirus and Mastrevirus genera are associated with additional circular, single stranded DNA molecules (~ 1-1.4 kb) that encode a replication-associated protein (Rep). These Rep-encoding satellite molecules are commonly referred to as alphasatellites and here we communicate the establishment of the family Alphasatellitidae to which these have been assigned. Within the Alphasatellitidae family two subfamilies, Geminialphasatellitinae and Nanoalphasatellitinae, have been established to respectively accommodate the geminivirus- and nanovirus-associated alphasatellites. Whereas the pairwise nucleotide sequence identity distribution of all the known geminialphasatellites (n = 628) displayed a troughs at ~ 70% and 88% pairwise identity, that of the known nanoalphasatellites (n = 54) had a troughs at ~ 67% and ~ 80% pairwise identity. We use these pairwise identity values as thresholds together with phylogenetic analyses to establish four genera and 43 species of geminialphasatellites and seven genera and 19 species of nanoalphasatellites. Furthermore, a divergent alphasatellite associated with coconut foliar decay disease is assigned to a species but not a subfamily as it likely represents a new alphasatellite subfamily that could be established once other closely related molecules are discovered.
Figures & Tables
Download
📖 Papers frequently viewed together
229 Citations
20172.82Virology
37 Citations
20113.82Viruses
143 Citations
References53
Newest
#1Qamar Abbas (National Institute for Biotechnology and Genetic Engineering)H-Index: 3
#2Imran Amin (National Institute for Biotechnology and Genetic Engineering)H-Index: 31
Last. Rob W. Briddon (National Institute for Biotechnology and Genetic Engineering)H-Index: 67
view all 6 authors...
Alphasatellites are non-essential satellite-like components associated with geminiviruses. The precise selective advantage to a geminivirus infection of an alphasatellite remains unclear. The ability of the cotton leaf curl Multan alphasatellite (CLCuMuA)-encoded replication-associated protein (Rep) to suppress TGS was investigated by using Nicotiana benthamiana line 16-TGS (16-TGS) harbouring a transcriptionally silenced green fluorescent protein (GFP) transgene. Inoculation of 16-TGS plants wi...
11 CitationsSource
#1Arvind Varsani (ASU: Arizona State University)H-Index: 63
#2Mart Krupovic (Pasteur Institute)H-Index: 59
Smacoviruses have small (∼2.3-2.9 kb), circular single-stranded DNA genomes encoding rolling circle replication-associated proteins (Rep) and unique capsid proteins. Although smacoviruses are prevalent in faecal matter of various vertebrates, including humans, none of these viruses have been cultured thus far. Smacoviruses display ∼45% genome-wide sequence diversity, which is very similar to that found within other families of circular Rep-encoding single-stranded (CRESS) DNA viruses, including ...
42 CitationsSource
#1Romain Gallet (SupAgro)H-Index: 15
#2Simona Kraberger (ASU: Arizona State University)H-Index: 26
Last. Philippe Roumagnac (SupAgro)H-Index: 28
view all 8 authors...
Nanoviruses are multi-component plant-infecting single-stranded DNA viruses. Using a viral metagenomics-informed approach, a new nanovirus and two associated alphasatellite molecules have been identified in an uncultivated asymptomatic Vicia cracca plant in the Rhone region of France. This novel nanovirus genome includes eight genomic components (named DNA-R, DNA-S, DNA-M, DNA-C, DNA-N, DNA-U1, DNA-U2 and DNA-U4) and, across all components, shares < 66% pairwise sequence identity with other nano...
15 CitationsSource
#1Katharina Hipp (University of Stuttgart)H-Index: 10
#2Clemens Grimm (University of Würzburg)H-Index: 14
Last. Bettina Böttcher (University of Würzburg)H-Index: 42
view all 4 authors...
Summary African cassava mosaic virus is a whitefly-transmitted geminivirus which forms unique twin particles of incomplete icosahedra that are joined at five-fold vertices, building an unusual waist. How its 22 capsomers interact within a half-capsid or across the waist is unknown thus far. Using electron cryo-microscopy and image processing, we determined the virion structure with a resolution of 4.2 A and built an atomic model for its capsid protein. The inter-capsomer contacts mediated by the...
23 CitationsSource
#1Talita Bernardon Mar (UFV: Universidade Federal de Viçosa)H-Index: 3
#2Igor Rodrigues Mendes (UFV: Universidade Federal de Viçosa)H-Index: 4
Last. F. Murilo Zerbini (UFV: Universidade Federal de Viçosa)H-Index: 27
view all 7 authors...
The majority of Old World monopartite begomoviruses (family Geminiviridae) are associated with satellite DNAs. Alphasatellites are capable of autonomous replication, but depend on the helper virus for movement, encapsidation and transmission by the insect vector. Recently, Euphorbia yellow mosaic alphasatellite (EuYMA) was found in association with Euphorbia yellow mosaic virus (EuYMV) infecting Euphorbia heterophylla plants in Brazil. The geographical range of EuYMA was assessed in a representa...
19 CitationsSource
#1Subha Kalyaanamoorthy (U of A: University of Alberta)H-Index: 11
#2Bui Quang Minh (Medical University of Vienna)H-Index: 23
Last. Lars S. Jermiin (ANU: Australian National University)H-Index: 42
view all 5 authors...
ModelFinder is a fast model-selection method that greatly improves the accuracy of phylogenetic estimates.
3,311 CitationsSource
#2Mehdi Kamali (SBUK: Shahid Bahonar University of Kerman)
Viruses in the genus Nanovirus of the family Nanoviridae generally have eight individually encapsidated circular genome components and have been predominantly found infecting Fabaceae plants in Europe, Australia, Africa and Asia. For over a decade Sophora alopecuroides L. (Fabaceae) plants have been observed across Iran displaying dwarfing, yellowing, stunted leaves and yellow vein banding. Using a high-throughput sequencing approach, sequences were identified within one such plant that had simi...
18 CitationsSource
#1Peter Simmonds (University of Oxford)H-Index: 145
#2Michael J. AdamsH-Index: 55
Last. F. Murilo Zerbini (UFV: Universidade Federal de Viçosa)H-Index: 27
view all 26 authors...
The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data...
359 CitationsSource
#1Camila Geovana Ferro (UFV: Universidade Federal de Viçosa)H-Index: 4
#2João Paulo Santos da Silva (UFV: Universidade Federal de Viçosa)H-Index: 4
Last. Francisco Murilo Zerbini (UFV: Universidade Federal de Viçosa)H-Index: 23
view all 8 authors...
Begomoviruses (whitefly-transmitted, single-stranded DNA plant viruses) are among the most damaging pathogens causing epidemics in economically important crops worldwide. Besides cultivated plants, many weed and wild hosts act as virus reservoirs where recombination may occur, resulting in new species. The aim of this study was to further characterise the diversity of begomoviruses infecting two major weed genera, Sida and Leonurus. Total DNA was extracted from samples collected in the states of...
18 CitationsSource
#1Arvind Varsani (ASU: Arizona State University)H-Index: 63
#2Philippe Roumagnac (SupAgro)H-Index: 28
Last. Darren P. Martin (UCT: University of Cape Town)H-Index: 52
view all 10 authors...
Geminiviruses are plant-infecting single-stranded DNA viruses that occur in most parts of the world. Currently, there are seven genera within the family Geminiviridae (Becurtovirus, Begomovirus, Curtovirus, Eragrovirus, Mastrevirus, Topocuvirus and Turncurtovirus). The rate of discovery of new geminiviruses has increased significantly over the last decade as a result of new molecular tools and approaches (rolling-circle amplification and deep sequencing) that allow for high-throughput workflows....
135 CitationsSource
Cited By60
Newest
#1Yaqin Wang (ZJU: Zhejiang University)H-Index: 11
#2Xinyue Zhang (ZJU: Zhejiang University)
Last. Xueping Zhou (ZJU: Zhejiang University)H-Index: 54
view all 4 authors...
Malvastrum coromandelianum is a common weed plant frequently found around agricultural fields. Three virus isolates (Y249, Y278 and Y281) were obtained from M. coromandelianum with yellow vein symptoms in Honghe and Baoshan, Yunnan Province, China. Specific 500 bp products were amplified from total DNA extracts using universal primers for members of the genus Begomovirus. The complete viral genome sequences of both Y278 and Y281 were determined to be 2743 nucleotides, and that of Y249 was determ...
Source
Begomoviruses can be found in association with alphasatellites, which are capable of autonomous replication but are dependent on the helper begomovirus for systemic infection, encapsidation and vector transmission. Previous studies suggest that the presence of NW alphasatellites (genus Clecrusatellite) is associated with more severe symptoms. To better understand this interaction, we investigated the effects of two alphasatellites on infectivity, symptom development, viral DNA accumulation and v...
Source
#1Arvind Varsani (ASU: Arizona State University)H-Index: 63
#2Darren P. Martin (UCT: University of Cape Town)H-Index: 52
Last. Philippe Roumagnac (University of Montpellier)H-Index: 28
view all 11 authors...
Alphasatellites (family Alphasatellitidae) are circular, single-stranded DNA molecules (~1–1.4 kb) that encode a replication-associated protein and have commonly been associated with some members of the families Geminiviridae, Nanoviridae, and Metaxyviridae (recently established). Here, we provide a taxonomy update for the family Alphasatellitidae following the International Committee on Taxonomy of Viruses (ICTV) Ratification Vote held in March 2021. The taxonomic update includes the establishm...
1 CitationsSource
#1Lele Zhao (RU: Rutgers University)H-Index: 6
#2Erik Lavington (RU: Rutgers University)H-Index: 6
Last. Siobain Duffy (RU: Rutgers University)H-Index: 28
view all 3 authors...
Until recently, most viruses detected and characterized were of economic significance, associated with agricultural and medical diseases. This was certainly true for the eukaryote-infecting circular Rep (replication-associated protein)-encoding single-stranded DNA (CRESS DNA) viruses, which were thought to be a relatively small group of viruses. With the explosion of metagenomic sequencing over the past decade and increasing use of rolling-circle replication for sequence amplification, scientist...
Source
#1Eugene V. Koonin (NIH: National Institutes of Health)H-Index: 218
#2Valerian V. DoljaH-Index: 72
Last. Jens H. Kuhn (NIH: National Institutes of Health)H-Index: 65
view all 4 authors...
Originally, viruses were defined as miniscule infectious agents that passed through filters that retain even the smallest cells. Subsequently, viruses were considered obligate intracellular parasites whose reproduction depends on their cellular hosts for energy supply and molecular building blocks. However, these features are insufficient to unambiguously define viruses as they are broadly understood today. We outline possible approaches to define viruses and explore the boundaries of the virosp...
Source
#1Arvind Varsani (ASU: Arizona State University)H-Index: 63
#2Tanja Opriessnig (Edin.: University of Edinburgh)H-Index: 64
Last. Simona Kraberger (ASU: Arizona State University)H-Index: 26
view all 10 authors...
Anelloviruses are small negative-sense single-stranded DNA viruses with genomes ranging in size from 1.6 to 3.9 kb. The family Anelloviridae comprised 14 genera before the present changes. However, in the last five years, a large number of diverse anelloviruses have been identified in various organisms. Here, we undertake a global analysis of mammalian anelloviruses whose full genome sequences have been determined and have an intact open reading frame 1 (ORF1). We established new criteria for th...
2 CitationsSource
The genus Gyrovirus was assigned to the family Anelloviridae in 2017 with only one recognized species, Chicken anemia virus. Over the last decade, many diverse viruses related to chicken anemia virus have been identified but not classified. Here, we provide a framework for the classification of new species in the genus Gyrovirus and communicate the establishment of nine new species. We adopted the ‘Genus + freeform epithet’ binomial system for the naming of these species.
2 CitationsSource
#1Elvira Tarasova (CCNY: City College of New York)
#2Sonali Dhindwal (CCNY: City College of New York)H-Index: 10
Last. Reza Khayat (CUNY: City University of New York)H-Index: 23
view all 5 authors...
Circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses infect members from all three domains of life (Archaea, Prokarya, and Eukarya). The replicase (Rep) from these viruses is responsible for initiating rolling circle replication (RCR) of their genomes. Rep is a multifunctional enzyme responsible for nicking and ligating ssDNA and unwinding double-stranded DNA (dsDNA). We report the structure of porcine circovirus 2 (PCV2) Rep bound to ADP and single-stranded DNA (ssDNA), and Rep bound t...
Source
Abstract null null Weeds and ornamental plants serve as a reservoir for geminiviruses and contribute to their dissemination, genome recombination and/or satellite capture. Ornamental sunflower (Helianthus spp.) plants exhibiting mild leaf curl symptoms were subjected to begomovirus and DNA-satellites isolation. The full-length genome of the isolated begomovirus clone (Od1-A) showed 96.8% nucleotide (nt) sequence identity with mesta yellow vein mosaic virus (MeYVMV; accession no. FR772081) wherea...
Source
#1K. V. Ashwathappa (IIHR: Indian Institute of Horticultural Research)H-Index: 3
#2Venkataravanappa Venkataravanappa (IIHR: Indian Institute of Horticultural Research)H-Index: 10
Last. M. Krishna Reddy (IIHR: Indian Institute of Horticultural Research)H-Index: 11
view all 7 authors...
Pseuderanthemum reticulatum (Radlk.) ornamental plant is cultivated in different parts of the world to increase the aesthetic value of the gardens. During the year 2018–2019, the pseuderanthemum ornamental showing typical begomovirus symptoms of vein clearing, complete leaf yellowing, enation and upward curling were observed at Bengaluru rural area, Karnataka (India) and 10 samples five locations (two from each location) were collected. Incidence of the plants showing symptoms was recorded from ...
Source