Biological and Genomic Characterization of a Novel Tobamovirus Infecting Hoya spp.

Foliar symptoms suggestive of virus infection were observed on the ornamental plant hoya (Hoya spp.; commonly known as waxflower) in Florida. An agent that reacted with commercially available tobamovirus detection reagents was mechanically transmitted to Chenopodium quinoa and Nicotiana benthamiana. Rod-shaped particles ∼300 nm in length and typical of tobamoviruses were observed in partially purified virion preparations by electron microscopy. An experimental host range was determined by mechanical inoculation with virions, and systemic infections were observed in plants in the Asclepiadaceae, Apocynaceae, and Solanaceae families. Some species in the Solanaceae and Chenopodiaceae families allowed virus replication only in inoculated leaves, and were thus only local hosts for the virus. Tested plants in the Amaranthaceae, Apiaceae, Brassicaceae, Cucurbitaceae, Fabaceae, and Malvaceae did not support either local or systemic virus infection. The complete genome for the virus was sequenced and shown to have a typical tobamovirus organization. Comparisons of genome nucleotide sequence and individual gene deduced amino acid sequences indicate that it is a novel tobamovirus sharing the highest level of sequence identity with Streptocarpus flower break virus and members of the Brassicaceae-infecting subgroup of tobamoviruses. The virus, for which the name Hoya chlorotic spot virus (HoCSV) is proposed, was detected in multiple hoya plants from different locations in Florida.

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Identification and genomic characterization of a novel fish reovirus, Hubei grass carp disease reovirus, isolated in 2009 in China

Journal of General Virology ◽

10.1099/vir.0.054767-0 ◽

2013 ◽

Vol 94 (10) ◽

pp. 2266-2277 ◽

Cited By ~ 47

Author(s):

Yuding Fan ◽

Shujing Rao ◽

Lingbing Zeng ◽

Jie Ma ◽

Yong Zhou ◽

...

Keyword(s):

Amino Acid ◽

Grass Carp ◽

Sequence Similarity ◽

Amino Acid Level ◽

Amino Acid Sequences ◽

Full Genome Sequence ◽

Total Size ◽

The Family ◽

Genomic Characterization

A novel fish reovirus, Hubei grass carp disease reovirus (HGDRV; formerly grass carp reovirus strain 104, GCRV104), was isolated from diseased grass carp in China in 2009 and the full genome sequence was determined. This reovirus was propagated in a grass carp kidney cell line with a typical cytopathic effect. The total size of the genome was 23 706 bp with a 51 mol% G+C content, and the 11 dsRNA segments encoded 12 proteins (two proteins encoded by segment 11). A nucleotide sequence similarity search using blastn found no significant matches except for segment 2, which partially matched that of the RNA-dependent RNA polymerase (RdRp) from several viruses in the genera Aquareovirus and Orthoreovirus of the family Reoviridae. At the amino acid level, seven segments (Seg-1 to Seg-6, and Seg-8) matched with species in the genera Aquareovirus (15–46 % identities) and Orthoreovirus (12–44 % identities), while for four segments (Seg-7, Seg-9, Seg-10 and Seg-11) no similarities in these genera were found. Conserved terminal sequences, 5′-GAAUU----UCAUC-3′, were found in each HGDRV segment at the 5′ and 3′ ends, and the 5′-terminal nucleotides were different from any known species in the genus Aquareovirus. Phylogenetic analysis based on RdRp amino acid sequences from members of the family Reoviridae showed that HGDRV clustered with aquareoviruses prior to joining a branch common with orthoreoviruses. Based on these observations, we propose that HGDRV is a new species in the genus Aquareovirus that is distantly related to any known species within this genus.

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Occurrence of Lily mottle virus in Escarole

Plant Disease ◽

10.1094/pdis.2002.86.3.329a ◽

2002 ◽

Vol 86 (3) ◽

pp. 329-329 ◽

Cited By ~ 3

Author(s):

V. Lisa ◽

H. J. Vetten ◽

D.-E. Lesemann ◽

P. Gotta

Keyword(s):

Host Range ◽

Chenopodium Quinoa ◽

Mottle Virus ◽

Enzyme Linked Immunosorbent Assay ◽

The Family ◽

Experimental Host Range ◽

Necrotic Spots ◽

Systemic Infections ◽

Differentiation Index ◽

Natural Host Range

Lily mottle virus (LMoV), genus Potyvirus, an important virus of lily that also causes flower-breaking in tulip (1), is considered to have a natural host range restricted to the family Liliaceae. In 1996, escarole (Cichorium endivia L. var. latifolium LAM) plants growing in fields close to Torino, Italy, and showing mosaic and necrotic spots on outer leaves were infected by a potyvirus related to LMoV. The virus was identified by immunoelectron microscopy (IEM) done on experimentally infected Nicotiana benthamiana and Chenopodium quinoa. The virus isolated from escarole (LMoV-E) had an experimental host range similar to that of lily isolates of LMoV, although species within the Liliaceae were not tested. LMoV-E systemically infected all nine escarole cultivars and six of seven endive cultivars (C. endivia L. var. crispum LAM) but did not infect any of six lettuce and two chicory cultivars (C. intybus L. var. foliosum HEGI). Symptoms ranged from mild to severe mosaic and were generally more severe on escarole than on endive. Some of the same escarole, endive, and lettuce cultivars were inoculated with a typical LMoV isolate from lily (Le97/49, from A. F. L. M. Derks, the Netherlands), which induced mild systemic infections in only one escarole and one endive cultivar. Both cultivars were also susceptible to LMoV-E. LMoV-E was purified from N. benthamiana, and an antiserum was prepared. IEM decoration titer experiments were done with LMoV-E and four other LMoV isolates from Liliaceae and their homologous antisera. Heterologous titers ranging from identity to serological differentiation index values of 2 to 4 were obtained, confirming the identity of the escarole isolate as a LMoV strain and indicating considerable serological variability among LMoV isolates. In a field survey of endive and escarole crops in 1998, in the area where LMoV-E was first identified, the virus was again detected by enzyme-linked immunosorbent assay in 4 of 80 escarole plants tested. LMoV-E appears to be a LMoV strain particularly adapted to escarole. To our knowledge, this is the first report of LMoV identified in a naturally infected host outside monocotyledonous plants. Reference: (1) E. L. Dekker et al. J. Gen. Virol. 74:881, 1993.

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First Report of Capsicum chlorosis virus Causing Yellow Stripes on Calla Lilies in Taiwan

Plant Disease ◽

10.1094/pdis-91-9-1201c ◽

2007 ◽

Vol 91 (9) ◽

pp. 1201-1201 ◽

Cited By ~ 9

Author(s):

C. C. Chen ◽

C. H. Huang ◽

T. C. Chen ◽

S. D. Yeh ◽

Y. H. Cheng ◽

...

Keyword(s):

Chenopodium Quinoa ◽

Amino Acid Sequences ◽

N Gene ◽

Impatiens Necrotic Spot Virus ◽

Leaf Extracts ◽

Spot Virus ◽

Chlorotic Spot ◽

Calla Lily ◽

Capsicum Chlorosis Virus ◽

Virus Isolates

Tomato spotted wilt virus (TSWV) and Calla lily chlorotic spot virus (CCSV) are two recognized species of the Tospovirus genus in the family Bunyaviridae infecting calla lily (Zantedeschia spp.). During 2005, 15 virus isolates were collected from different calla lily plants exhibiting yellow stripes on their leaves in Ho-Li, a major calla lily-production township in Taiwan. After three successive local lesion passages on Chenopodium quinoa Willd., diseased leaf tissues individually infected by these isolates were preserved in liquid nitrogen and used for subsequent identification studies. Using the tospovirus genus-specific primers gL3637 and gL4435c designed from the L RNA, an 800-bp DNA fragment was amplified in reverse transcription-PCR from all 15 isolates. Moreover, leaf extracts of the diseased calla lilies and the C. quinoa plants inoculated with the 15 virus isolates reacted with antisera against the nucleocapsid proteins (NP) of Capsicum chlorosis virus (CaCV)-gloxinia and Watermelon silver mottle virus (WSMoV), but not to monoclonal antibodies against the NP of TSWV, CCSV, Peanut chlorotic fan-spot virus (PCFV), or Impatiens necrotic spot virus (INSV) in indirect ELISA. These results indicate that the 15 virus isolates are tospoviruses belonging to the WSMoV serogroup. Additionally, we amplified and sequenced the full-length N gene from these tospovirus isolates using primers WN2328 (5′-CCATTGGTTTGCCTCCG-3′) and WN3534 (5′-CGTCGACAGAGCAATCGAGGC-3′) designed from the S RNA of WSMoV. The deduced amino acid sequences of the N protein from these 15 tospovirus isolates showed a greater than 92% identity to that of CaCV (GenBank Accession No. NC-008301). Furthermore, results of phylogenetic analysis of the 15 isolates on the basis of amino acids sequences, both genetic distance and parsimony trees indicated that they were all genetically clustered within CaCV using INSV, TSWV, and WSMoV as outgroups. The results indicate that the virus causing yellow stripes in calla lilies is a strain of CaCV. To our knowledge, this is the first evidence that CaCV can naturally infect calla lilies and cause yellow stripe symptoms. Reference: (1) F.-H. Chu et al. Phytopathology 91:361, 2001.

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Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution

Genome Biology ◽

10.1186/s13059-021-02459-z ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Ilias Georgakopoulos-Soares ◽

Ofer Yizhar-Barnea ◽

Ioannis Mouratidis ◽

Martin Hemberg ◽

Nadav Ahituv

Keyword(s):

Significant Proportion ◽

Amino Acid Sequences ◽

Human Populations ◽

Functional Categories ◽

Naturally Occurring ◽

A Genome ◽

Genomic Characterization ◽

Single Base Pair ◽

Detrimental Impact

Abstract Nullomers and nullpeptides are short DNA or amino acid sequences that are absent from a genome or proteome, respectively. One potential cause for their absence could be their having a detrimental impact on an organism. Results Here, we identify all possible nullomers and nullpeptides in the genomes and proteomes of thirty eukaryotes and demonstrate that a significant proportion of these sequences are under negative selection. We also identify nullomers that are unique to specific functional categories: coding sequences, exons, introns, 5′UTR, 3′UTR, promoters, and show that coding sequence and promoter nullomers are most likely to be selected against. By analyzing all protein sequences across the tree of life, we further identify 36,081 peptides up to six amino acids in length that do not exist in any known organism, termed primes. We next characterize all possible single base pair mutations that can lead to the appearance of a nullomer in the human genome, observing a significantly higher number of mutations than expected by chance for specific nullomer sequences in transposable elements, likely due to their suppression. We also annotate nullomers that appear due to naturally occurring variants and show that a subset of them can be used to distinguish between different human populations. Analysis of nullomers and nullpeptides across vertebrate evolution shows they can also be used as phylogenetic classifiers. Conclusions We provide a catalog of nullomers and nullpeptides in distinct functional categories, develop methods to systematically study them, and highlight the use of variability in these sequences in other analyses

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Genomic characterization of Calla lily chlorotic spot virus and design of broad-spectrum primers for detection of tospoviruses

Plant Pathology ◽

10.1111/j.1365-3059.2011.02484.x ◽

2011 ◽

Vol 61 (1) ◽

pp. 183-194 ◽

Cited By ~ 26

Author(s):

T.-C. Chen ◽

J.-T. Li ◽

Y.-P. Lin ◽

Y.-C. Yeh ◽

Y.-C. Kang ◽

...

Keyword(s):

Broad Spectrum ◽

Spot Virus ◽

Chlorotic Spot ◽

Calla Lily ◽

Genomic Characterization

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Identification and genome characterization of Heliothis armigera cypovirus types 5 and 14 and Heliothis assulta cypovirus type 14

Journal of General Virology ◽

10.1099/vir.0.81435-0 ◽

2006 ◽

Vol 87 (2) ◽

pp. 387-394 ◽

Cited By ~ 17

Author(s):

Yang Li ◽

Li Tan ◽

Yanqiu Li ◽

Wuguo Chen ◽

Jiamin Zhang ◽

...

Keyword(s):

Amino Acid ◽

Heliothis Armigera ◽

Amino Acid Sequences ◽

Nucleotide Sequencing ◽

Sequencing Analysis ◽

Electrophoretic Patterns ◽

The Family ◽

Genomic Characterization

Genomic characterization of Heliothis armigera cypovirus (HaCPV) isolated from China showed that insects were co-infected with several cypoviruses (CPVs). One of the CPVs (HaCPV-5) could be separated from the others by changing the rearing conditions of the Heliothis armigera larvae. This finding was further confirmed by nucleotide sequencing analysis. Genomic sequences of segments S10–S7 from HaCPV-14, S10 and S7 from HaCPV-5, and S10 from Heliothis assulta CPV-14 were compared. Results from database searches showed that the nucleotide sequences and deduced amino acid sequences of the newly identified CPVs had high levels of identity with those of reported CPVs of the same type, but not with CPVs of different types. Putative amino acid sequences of HaCPV-5 S7 were similar to that of the protein from Rice ragged stunt virus (genus Oryzavirus, family Reoviridae), suggesting that CPVs and oryzaviruses are related more closely than other genera of the family Reoviridae. Conserved motifs were also identified at the ends of each RNA segment of the same virus type: type 14, 5′-AGAAUUU…CAGCU-3′; and type 5, 5′-AGUU…UUGC-3′. Our results are consistent with classification of CPV types based on the electrophoretic patterns of CPV double-stranded RNA.

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Biological and Molecular Characterization of Apple chlorotic leaf spot virus Causing Chlorotic Leaf Spot on Pear (Pyrus pyrifolia) in Taiwan

HortScience ◽

10.21273/hortsci.45.7.1073 ◽

2010 ◽

Vol 45 (7) ◽

pp. 1073-1078 ◽

Cited By ~ 2

Author(s):

Zhong-Bin Wu ◽

Hsin-Mei Ku ◽

Yuh-Kun Chen ◽

Chung-Jan Chang ◽

Fuh-Jyh Jan

Keyword(s):

Amino Acid ◽

Leaf Spot ◽

Phylogenetic Analyses ◽

Amino Acid Sequences ◽

Pyrus Pyrifolia ◽

Spot Virus ◽

Chlorotic Spot ◽

Cp Gene ◽

Chlorotic Leaf

Pear plants (Pyrus pyrifolia var. Hengshen) showing symptoms of chlorotic spots on leaves were observed in orchards in central Taiwan in 2004. The sap of diseased leaves reacted positively to Apple chlorotic leaf spot virus (ACLSV) antiserum. A purified virus isolate (LTS1) from pear was characterized by host range, electron microscopy, phylogenetic analyses, serological property, and back-inoculation experiments to pear. Fifteen of 28 species of tested plants were susceptible to this virus after mechanical inoculation. Pathogenicity of ACLSV isolate LTS1 was verified by back-inoculating to pear seedlings. Filamentous virions of ≈12 × 750 nm were observed in the preparations of purified virus. Virus particles accumulated in the cytoplasm were observed in the ultrathin sections of LTS1-infected pear leaf tissue. Sequence analyses of the coat protein (CP) gene of LTS1 and the CP gene of LTS2, which originated from a distinct symptomatic pear sample, shared 81.4% to 92.6% nucleotide and 87.6% to 98.4% amino acid identities with those of the CP of 35 ACLSV isolates available in GenBank. ACLSV isolates were grouped into four clusters, i.e., Asia I, II, III, and Europe, and isolates LTS1 and LTS2 were classified as members of cluster Asia II and Asia I, respectively, based on phylogenetic data. Moreover, the variability of amino acid sequences of the CP gene of 37 ACLSV isolates showed geographically associated clustering in the phylogenetic tree. To our knowledge, this is the first study on the characterization of ACLSV causing the leaf chlorotic spot disease of pear in Taiwan. This study also provides the phylogenetic relationships among ACLSV populations based on amino acid sequences of CPs, which are correlated with their geographic origins.

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First Report on Co-isolation and Whole-genomic Characterization of Mammalian Orthorubulavirus 5 and Mammalian Orthoreovirus Type-3 From Domestic Pigs in India

10.21203/rs.3.rs-1219383/v1 ◽

2022 ◽

Author(s):

Fateh Singh ◽

Katherukamem Rajukumar ◽

Dhanapal Senthilkumar ◽

Govindarajulu Venkatesh ◽

Deepali Srivast ◽

...

Keyword(s):

Amino Acid ◽

Genetic Analysis ◽

Amino Acid Sequences ◽

Nucleotide Identity ◽

Domestic Pigs ◽

S1 Gene ◽

Mammalian Orthoreovirus ◽

Genomic Characterization ◽

Type 3

Abstract During a surveillance study to monitor porcine epidemic diarrohoea virus and transmissible gastroenteritis virus in India, a total of 1043 swine samples including faeces (n=264) and clotted blood (n=779) were collected and tested. Five samples (four faecal and one serum) showed cytopathic effects in Vero cells. Transmission electron microscopy of infective cell supernatant revealed the presence of two types of virions. Next generation sequencing (de novo) enabled complete genome assembly of Mammalian orthorubulavirus 5 (MRuV5; 15246 bp) and all 10 gene segments of Mammalian orthoreovirus (MRV; 22219 bp and 20512 bp). Genetic analysis of the MRuV5 revealed grouping of the Indian MRuV5 with those isolated from various mammalian species in South Korea and China, sharing more than 99% nucleotide identity. Deduced amino acid sequences of the HN, NP and F genes of MRuV5 isolates showed three (92L, 111R, 447H), two (86S, 121S) and two (139T, 246T) amino acid substitutions, respectively, compared to previously reported virus strains. The Indian MRV isolates were identified as MRV type-3 based on genetic analysis of S1 gene, showing the highest nucleotide identity (97.73%) with the MRV3 strain ZJ2013 isolated from pigs in China. Deduced amino acid sequences of MRV3 S1 gene revealed amino acid residues 198-204NLAIRLP, 249I, 340D, 419E known for sialic acid binding and neurotropism. We report the co-isolation and whole-genomic characterization of MRuV5 and MRV3 recorded incidentally for the first time from domestic pigs in India. It attracts attention to perform detailed surveillance studies and continuous monitoring of evolution and spread of emerging viruses, which may have pathogenic potential in animal and human hosts.

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Genomic characterization of γ-terpinene synthase from Thymus caespititius

Planta Medica ◽

10.1055/s-0031-1282602 ◽

2011 ◽

Vol 77 (12) ◽

Cited By ~ 2

Author(s):

AS Lima ◽

B Lukas ◽

J Novak ◽

AC Figueiredo ◽

LG Pedro ◽

...

Keyword(s):

Genomic Characterization

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Characterization of a cDNA for Rhesus Monkey Protein C Inhibitor – Evidence for N-Terminal Involvement in Heparin Stimulation

Thrombosis and Haemostasis ◽

10.1055/s-0038-1649885 ◽

1995 ◽

Vol 74 (04) ◽

pp. 1079-1087 ◽

Cited By ~ 8

Author(s):

Klaus-P Radtke ◽

José A Fernández ◽

Bruno O Villoutreix ◽

Judith S Greengard ◽

John H Griffin

Keyword(s):

Rhesus Monkey ◽

Protein C ◽

Activated Protein C ◽

Pcr Amplification ◽

Amino Acid Sequences ◽

Heparin Binding ◽

Reactive Center ◽

Protein C Inhibitor ◽

Polymerase Chain

SummarycDNAs for protein C inhibitor (PCI) were cloned from human and rhesus monkey 1 liver RNAs by reverse transcription and polymerase chain reaction (PCR) amplification. Sequencing showed that rhesus monkey and human PCI cDNAs were 93% identical. Predicted amino acid sequences differed at 26 of 387 residues. Pour of these differences (T352M, N359S, R362K, L3631) were in the reactive center loop that is important for inhibitory specificity, and two were in the N-terminal helix (M8T, E13K) that is implicated in glycosaminoglycan binding. PCI in human or rhesus monkey plasma showed comparable inhibitory activity towards human activated protein C in the presence of 10 U/ml heparin. However, maximal acceleration of the inhibition of activated protein C required 5-fold lower heparin concentration for rhesus monkey than for human plasma, consistent with the interpretation that the additional positive charge (E13K) in a putative-heparin binding region increased the affinity for heparin.

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