scholarly journals Characterization of the Mycovirome of the Phytopathogenic Fungus, Neofusicoccum parvum

Viruses ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 375
Author(s):  
Armelle Marais ◽  
Chantal Faure ◽  
Gwenaëlle Comont ◽  
Thierry Candresse ◽  
Elodie Stempien ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Phytopathogenic Fungus ◽  
Sequencing Analysis ◽  
Single Strain ◽  
Neofusicoccum Parvum ◽  
The Family ◽  
Pcr Products ◽  
Botryosphaeria Dieback

Neofusicoccum parvum is a fungal plant-pathogen belonging to the family Botryosphaeriaceae, and is considered one of the most aggressive causal agents of the grapevine trunk disease (GTD) Botryosphaeria dieback. In this study, the mycovirome of a single strain of N. parvum (COLB) was characterized by high throughput sequencing analysis of total RNA and subsequent bioinformatic analyses. Contig annotations, genome completions, and phylogenetic analyses allowed us to describe six novel mycoviruses belonging to four different viral families. The virome is composed of two victoriviruses in the family Totiviridae, one alphaendornavirus in the family Endornaviridae, two mitoviruses in the family Mitoviridae, and one narnavirus belonging to the family Narnaviridae. The presence of the co-infecting viruses was confirmed by sequencing the RT-PCR products generated from total nucleic acids extracted from COLB. This study shows that the mycovirome of a single N. parvum strain is highly diverse and distinct from that previously described in N. parvum strains isolated from grapevines.

scholarly journals Identification and Characterization of a Novel Emaravirus From Grapevine Showing Chlorotic Mottling Symptoms

2021 ◽  
Vol 12 ◽  
Author(s):  
Xudong Fan ◽  
Chen Li ◽  
Zunping Zhang ◽  
Fang Ren ◽  
Guojun Hu ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
High Throughput Sequencing ◽  
Rna Virus ◽  
Reading Frame ◽  
A Genome ◽  
The Family ◽  
Pcr Products ◽  
Chlorotic Mottling

A novel negative-sense, single-stranded (ss) RNA virus was identified in a “Shennong Jinhuanghou” (SJ) grapevine showing severe chlorotic mottling symptoms by integrating high-throughput sequencing (HTS) and conventional Sanger sequencing of reverse transcription polymerase chain reaction (RT-PCR) products. The virus was provisionally named as “grapevine emaravirus A” (GEVA). GEVA had a genome comprising five genomic RNA segments, each containing a single open reading frame on the viral complementary strand and two untranslated regions with complementary 13- nt stretches at the 5′ and 3′ terminal ends. RNA1 (7,090 nt), RNA2 (2,097 nt), RNA3 (1,615 nt), and RNA4 (1,640 nt) encoded putative proteins P1–P4 that, based on their conserved motifs, were identified as the RNA-dependent RNA polymerase, glycoprotein, nucleocapsid protein, and movement protein, respectively. However, the functional role of protein P5 encoded by RNA5 (1,308 nt) could not be determined. Phylogenetic trees constructed based on amino acids of P1 to P4, allocated GEVA in clade I, together with other species-related emaraviruses. These data support the proposal that GEVA is a representative member of a novel species in the genus Emaravirus of the family Fimoviridae. Moreover, when GEVA was graft-transmitted to SJ and “Beta” grapevines, all grafted plants showed the same symptoms, similar to those observed in the source of the inoculum. This is the first report to our knowledge of an emaravirus infecting grapevine and its possible association with chlorotic mottling symptoms.

Characterization of microbial community in cold-chain hairtail fish by high-throughput sequencing technology

2021 ◽  
Author(s):  
Jiali Xing ◽  
Xiaorong Xu ◽  
Xiaohu Luo ◽  
Ruihang Zheng ◽  
Lingyan Mao ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Bacterial Flora ◽  
Diversity Indices ◽  
Cold Chain ◽  
Class Level ◽  
The Family ◽  
Dominant Bacteria

Abstract: High-throughput sequencing was used to analyze the microbial communities in the muscle samples of hairtail fish to study their diversity and dynamic changes during cold-chain circulation. The results showed that the richness and diversity of the microbial community in hairtail fish had a transient decline in 0–24 h and decreased after the first rise during 24–216 h. The diversity and richness of bacteria in cold-chain hairtail fish reached the maximum at 168 h. The Shannon and Simpson diversity indices of the bacteria were 2.96 and 0.16, respectively, and their ACE and Chao1 richness indices were 254.84 and 155.10, respectively. In addition, the dominant bacteria were Proteobacteria in the phylum level, Gammaproteobacteria in the class level, Pseudomonadales in the order level, Pseudomonadaceae in the family level, and Pseudomonas in the genus level, and their relative abundance were 80.52%, 72.11%, 76.68%, 23.25%, and 53.50%, respectively. In this study, the structure of bacterial flora and the dominant bacteria in cold-chain hairtail fish were analyzed by high-throughput sequencing to provide a basis for exploring how to maintain the freshness of hairtail fish and for predicting the shelf-life of hairtail fish.

Discovery and genome characterization of a new Nepovirus infecting grapevine

Plant Disease ◽  
2020 ◽  
Author(s):  
Maher Al Rwahnih ◽  
Olufemi Joseph Alabi ◽  
Min Sook Hwang ◽  
Tongyan Tian ◽  
Dimitre Mollov ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Virus Transmission ◽  
Amino Acid Sequences ◽  
Molecular Characteristics ◽  
Vitis Vinifera L ◽  
Sequencing Analysis ◽  
Biological Index ◽  
Chenopodium Amaranticolor ◽  
Sequence Contigs

In 2012, dormant canes of a proprietary wine grape (Vitis vinifera L.) accession were included in the collection of the University of California-Davis Foundation Plant Services. No virus-like symptoms were elicited when bud chips from propagated own-rooted canes of the accession were graft-inoculated onto a panel of biological index grape varieties. However, chlorotic ring symptoms were observed on sap inoculated Chenopodium amaranticolor Coste & A. Rein and C. quinoa Willd. plants, indicating the presence of a mechanically transmissible virus. Transmission electron microscopy of virus preps from symptomatic C. quinoa revealed spherical, non-enveloped virions of ~27 nm in diameter. And nepovirus-like haplotypes of sequence contigs were detected in both the source grape accession and recipient C. quinoa plants using high throughput sequencing analysis. A novel bipartite nepovirus-like genome was assembled from these contigs and the termini of each RNA segment were verified by RACE assays. The RNA1 (7,186-nt) of the virus encode a large polyprotein P1 of 231.1 kDa while the RNA2 (4,460-nt) also encode a large polyprotein P2 of 148.9 kDa. Each of the polyadenylated RNA segment is flanked by 5′- (RNA1=156-nt; RNA2=170-nt) and 3′- (RNA1=834-nt; RNA2=261-nt) untranslated region sequences that shared >90% identities between their corresponding sequences. Maximum-likelihood phylogenetic analyses of the conserved Pro-Pol amino acid sequences of Secoviridae species revealed the clustering of the new virus within the nepovirus clade. Considering its biological and molecular characteristics, and based on current criteria, we propose that the novel virus, named as grapevine nepovirus A (GNVA), be assigned as a member of the genus Nepovirus.

Phylogenetic position of Sphaerospora testicularis and Latyspora scomberomori n. gen. n. sp. (Myxozoa) within the marine urinary clade

Parasitology ◽  
2010 ◽  
Vol 138 (3) ◽  
pp. 381-393 ◽  
Author(s):  
PAVLA BARTOŠOVÁ ◽  
MARK A. FREEMAN ◽  
HIROSHI YOKOYAMA ◽  
MONICA CAFFARA ◽  
IVAN FIALA
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Dicentrarchus Labrax ◽  
Sensu Stricto ◽  
Phylogenetic Position ◽  
Species Cluster ◽  
The Family ◽  
Sutural Line ◽  
Taxonomic Changes

SUMMARYAn amendment of the family Sinuolineidae (Myxosporea) is proposed in order to include a newly described genus Latyspora n. gen. The type species Latyspora scomberomori n. gen. n. sp. is a coelozoic parasite in the kidney tubules of Scomberomorus guttatus. In addition to the morphological and molecular characterization of L. scomberomori n. gen. n. sp., we also present novel SSU rDNA data on Sphaerospora testicularis, a serious parasite of Dicentrarchus labrax. Performed phylogenetic analyses revealed that both species cluster within the marine urinary clade encompassing the representatives with a shared insertion within their V4 SSU rRNA region and grouping according to the shape of their spores’ sutural line and their similar tissue tropism in the host. Sphaerospora testicularis is the closest relative to Parvicapsula minibicornis within the Parvicapsula subclade and L. scomberomori n. gen. n. sp. is the basal species of the Zschokkella subclade. The phylogenetic position of S. testicularis, outwith the basal Sphaerospora sensu stricto clade, and its morphology suggest it being a non-typical Sphaerospora. The sequence data provided on S. testicularis can help in future revisions of the strongly polyphyletic genus Sphaerospora. We recommend re-sequencing of several sphaerosporids as an essential step before such taxonomic changes are accomplished.

scholarly journals Characterization of the complete genomes of Camelus dromedarius papillomavirus types 1 and 2

2011 ◽  
Vol 92 (8) ◽  
pp. 1769-1777 ◽  
Author(s):  
A. E. Ure ◽  
A. K. Elfadl ◽  
A. I. Khalafalla ◽  
A. A. R. Gameel ◽  
J. Dillner ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Diagnostic Methods ◽  
Camelus Dromedarius ◽  
Bovine Papillomavirus ◽  
Lower Jaw ◽  
The Family ◽  
Complete Genomes ◽  
First Time

Camel papillomatosis has been described previously, but the genome of the suspected papillomavirus (PV) has not been identified. An outbreak of papillomatosis occurred in a dromedary farm of 55 animals in Sudan during August 2009. The disease was only present in young animals aged about 3–7 months, of which 44 % (11/25) were affected with lesions, mainly on the lips and lower jaw. This study reports for the first time the complete genomes of Camelus dromedarius papillomavirus types 1 (CdPV1) and 2 (CdPV2), isolated from a cauliflower-like nodule and a round oval raised nodule, respectively. Pairwise comparisons of their L1 nucleotide sequences revealed 69.2 % identity, and phylogenetic analyses suggested that these two PV types are grouped within the genus Deltapapillomavirus. Both viruses were isolated from fibropapillomas, although no putative E5 proteins homologous to that of bovine papillomavirus type 1 were identified. The genetic information will be useful for evolutionary studies of the family Papillomaviridae, as well as for the development of diagnostic methods for surveillance of the disease in dromedaries.

scholarly journals Sequencing of the rpoB Gene inLegionella pneumophila and Characterization of Mutations Associated with Rifampin Resistance in theLegionellaceae

2000 ◽  
Vol 44 (10) ◽  
pp. 2679-2683 ◽  
Author(s):  
K. Nielsen ◽  
P. Hindersson ◽  
N. Høiby ◽  
J. M. Bangsborg
Keyword(s):  
Dna Sequence ◽  
Legionella Pneumophila ◽  
Resistance Mechanism ◽  
Rpob Gene ◽  
Single Strain ◽  
Reading Frame ◽  
Recommended Treatment ◽  
The Family ◽  
Rifampin Resistance

ABSTRACT Rifampin in combination with erythromycin is a recommended treatment for severe cases of legionellosis. Mutations in therpoB gene are known to cause rifampin resistance inEscherichia coli and Mycobacterium tuberculosis, and the purpose of the present study was to investigate a possible similar resistance mechanism within the members of the family Legionellaceae. Since the RNA polymerase genes of this genus have never been characterized, the DNA sequence of the Legionella pneumophila rpoB gene was determined by the Vectorette technique for genome walking. A 4,647-bp DNA sequence that contained the open reading frame (ORF) of the rpoB gene (4,104 bp) and an ORF of 384 bp representing part of therpoC gene was obtained. A 316-bp DNA fragment in the center of the L. pneumophila rpoB gene, corresponding to a previously described site for mutations leading to rifampin resistance in M. tuberculosis, was sequenced from 18 rifampin-resistant Legionella isolates representing four species (L. bozemanii, L. longbeachae, L. micdadei, and L. pneumophila), and the sequences were compared to the sequences of the fragments from the parent (rifampin-sensitive) strains. Six single-base mutations which led to amino acid substitutions at five different positions were identified. A single strain did not contain any mutations in the 316-bp fragment. This study represents the characterization of a hitherto undescribed resistance mechanism within the family Legionellaceae.

scholarly journals First Detection of Rotavirus C in Asymptomatic Pigs from India with Unexpected Dominance and Characterization of the Structural and Nonstructural Genes

2021 ◽  
Author(s):  
Madhuri S Joshi ◽  
Shalu A. Arya ◽  
Manohar S. Shinde ◽  
Varanasi Gopalkrishna
Keyword(s):  
Detection Rate ◽  
Phylogenetic Analyses ◽  
Viral Agent ◽  
Time Intervals ◽  
Detection Rates ◽  
Single Strain ◽  
Significant Difference ◽  
Large Outbreak ◽  
Asymptomatic Infections

Abstract Epidemiological and molecular investigation was conducted on Rotavirus C (RVC), the viral agent documented with rising prevalence rate, disease severity and cross species transmission and large outbreak potential. Fecal specimens of pigs collected from two cities of Maharashtra state, India tested for RVC showed 20.1% detection rate with majority below 3 months of age. No significant difference in detection rates was observed in the specimens collected in 2009 from Northern and in 2013 from Western parts of Maharashtra. The phylogenetic analyses showed presence of the I7 and I10 genotypes of the VP6 gene and representative strains with G1 and E5 genotypes of the VP7 and NSP4 gene respectively. Full genome characterization of a single strain showed presence of G1, P1, I7, R1, C1, M3, A1, N5, T5, E5, H1 genotypes of the VP7, VP4, VP6, VP1, VP2, VP3, NSP1, NSP2, NSP3, NSP4 and NSP5 genes respectively. This is the first evidence of detection of porcine RVC in asymptomatic pigs in India as well as with highest detection rate reported in asymptomatic pigs till date globally. Identification of porcine RVC at two time intervals and two different parts of Maharashtra state indicates the possibility of continuous circulation of RVC in pig population through asymptomatic infections.

scholarly journals Characterization of the virome of shallots affected by the shallot mild yellow stripe disease in France

2019 ◽  
Author(s):  
Armelle Marais ◽  
Chantal Faure ◽  
Sébastien Theil ◽  
Thierry Candresse
Keyword(s):  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
New Disease ◽  
Disease Symptoms ◽  
Link Type ◽  
Virus Complex ◽  
Shallot Latent Virus ◽  
Yellow Stripe ◽  
Complete Genomic

AbstractTo elucidate the etiology of a new disease on shallot in France, double-stranded RNAs from asymptomatic and symptomatic shallot plants were analyzed by high-throughput sequencing (HTS). Contigs annotation, molecular characterization and phylogenetic analyses revealed the presence in symptomatic plants of a virus complex consisting of shallot virus X (ShVX, Allexivirus), shallot latent virus (SLV, Carlavirus) and two novel viruses belonging to the genera Carlavirus and Potyvirus, for which the names of shallot virus S (ShVS) and shallot mild yellow stripe associated virus (SMYSaV), are proposed. Complete or near complete genomic sequences were obtained for all these agents, revealing divergent isolates of ShVX and SLV. Trials to fulfill Koch’s postulates were pursued but failed to reproduce the symptoms on inoculated shallots, even though the plants were proved to be infected by the four viruses detected by HTS. Replanting of bulbs from SMYSaV-inoculated shallot plants resulted in infected plants, showing that the virus can perpetuate the infection over seasons. A survey analyzing 351 shallot samples over a four years period strongly suggests an association of SMYSaV with the disease symptoms. An analysis of SMYSaV diversity indicates the existence of two clusters of isolates, one of which is largely predominant in the field over years.The sequences reported in the present manuscript have been deposited in the GenBank database under accession numbers MG571549, MH292861, MH389247 to MH389255, and MG910501 to MG910598.

scholarly journals Characterization of an Isolate of Citrus Concave Gum-Associated Virus from Apples in China and Development of an RT-RPA Assay for the Rapid Detection of the Virus

Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2239
Author(s):  
Zhen Liu ◽  
Zhenfei Dong ◽  
Binhui Zhan ◽  
Shifang Li
Keyword(s):  
Reverse Transcription ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
The United States ◽  
Polymerase Chain Reaction Method ◽  
Large Scale Testing ◽  
Bright Stripe ◽  
Full Length Genome

Apple (Malus domestica) fruits exhibiting bright stripe symptoms were identified in Weihai City, Shandong Province, China. To investigate the virome in the apple samples, the method of high throughput sequencing (HTS) was used to identify the viruses. It was found that the sequence of citrus concave gum-associated virus (CCGaV) was involved in the apple transcriptome dataset. The full-length genome of the CCGaV-Weihai isolate contained two segments, the RNA1 was 6674 nt in size containing a conserved RNA-dependent RNA polymerase (RdRp), and the RNA2 was ambisense, 2706 nt in length, encoding a movement protein (MP) and a coat protein (CP). Sequence alignment and phylogenetic analyses indicated that CCGaV-Weihai was more closely related to CCGaV-H2799 isolated from the apple host in the United States and distantly related to CCGaV-CGW2 from Citrus sinensis in Italy, indicating a possibly geographical and host differentiation of CCGaV isolates. This was the first identification and characterization of CCGaV infecting apples in China. Additionally, a rapid and sensitive reverse transcription recombinase polymerase amplification (RT-RPA) assay technique was established for CCGaV detection in apple plants. The RT-RPA of CCGaV was not affected by other common viruses in apple plants and is about 10-fold more sensitive than the conventional reverse transcription polymerase chain reaction method, which can be used in large-scale testing.

scholarly journals Identification and Full Characterisation of Two Novel Crustacean Infecting Members of the Family Nudiviridae Provides Support for Two Subfamilies

Viruses ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1694
Author(s):  
Kelly S. Bateman ◽  
Rose Kerr ◽  
Grant D. Stentiford ◽  
Tim P. Bean ◽  
Chantelle Hooper ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Carcinus Maenas ◽  
International Committee ◽  
Shore Crab ◽  
Cell Nuclei ◽  
Crangon Crangon ◽  
The Family ◽  
Ultrastructural Characteristics ◽  
Core Genes

Multiple enveloped viruses with rod-shaped nucleocapsids have been described, infecting the epithelial cell nuclei within the hepatopancreas tubules of crustaceans. These bacilliform viruses share the ultrastructural characteristics of nudiviruses, a specific clade of viruses infecting arthropods. Using histology, electron microscopy and high throughput sequencing, we characterise two further bacilliform viruses from aquatic hosts, the brown shrimp (Crangon crangon) and the European shore crab (Carcinus maenas). We assembled the full double stranded, circular DNA genome sequences of these viruses (~113 and 132 kbp, respectively). Comparative genomics and phylogenetic analyses confirm that both belong within the family Nudiviridae but in separate clades representing nudiviruses found in freshwater and marine environments. We show that the three thymidine kinase (tk) genes present in all sequenced nudivirus genomes, thus far, were absent in the Crangon crangon nudivirus, suggesting there are twenty-eight core genes shared by all nudiviruses. Furthermore, the phylogenetic data no longer support the subdivision of the family Nudiviridae into four genera (Alphanudivirus to Deltanudivirus), as recently adopted by the International Committee on Taxonomy of Viruses (ICTV), but rather shows two main branches of the family that are further subdivided. Our data support a recent proposal to create two subfamilies within the family Nudiviridae, each subdivided into several genera.

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