scholarly journals Molecular Characterization of the Complete Coding Sequence of Olive Leaf Yellowing-Associated Virus

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1272
Author(s):  
Ana Belén Ruiz-García ◽  
Thierry Candresse ◽  
Celia Canales ◽  
Félix Morán ◽  
Carlos Machado de Oliveira ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Genomic Sequence ◽  
Olive Tree ◽  
Open Reading Frames ◽  
Olive Leaf ◽  
Coding Sequence ◽  
The Family ◽  
Leaf Yellowing ◽  
Yellowing Disease

Genome organization and phylogenetic relationships of olive leaf yellowing-associated virus (OLYaV) with other members of the Closteroviridae family were determined. The complete coding sequence of OLYaV was obtained by high throughput sequencing of total RNA from a 35-year-old olive tree (cv. Zarzaleña) from Brazil, showing olive leaf yellowing disease and deformations in the wood. This represents the first report of OLYaV in this country. A genomic sequence of 16,700 nt containing 11 open reading frames (ORFs) was recovered, representing the complete virus coding capacity. The knowledge of the nucleotide sequence of the genome including the gene that codes the coat protein will facilitate the development of diagnostic tests, which are limited so far to PCR-based methods targeting the HSP70h gene. Interestingly, a thaumatin-like protein (ORF2), previously reported in other unassigned viruses in the Closteroviridae family, persimmon virus B and actidinia virus 1, was identified in the OLYaV genome. Phylogenetic analysis of shared proteins (ORF1a, ORF1b, HSP70h, HSP90h and CP) with all members of the Closteroviridae family provides new insight into the taxonomic position of these three closteroviruses and suggests they could represent a new genus in the family.

scholarly journals Molecular Characterization of A Novel Victorivirus Infecting Corynespora Cassiicola

2021 ◽  
Author(s):  
Mingming Liu ◽  
Yunxia Ni ◽  
Hui Zhao ◽  
Xintao Liu ◽  
Min Jia ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Open Reading Frames ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Corynespora Cassiicola ◽  
Rna Dependent Rna Polymerase ◽  
The Family ◽  
Fungal Viruses ◽  
Reading Frames

Abstract One victorivirus was detected in the isolate of Corynespora cassiicola strains 20180909-03, which was named Corynespora cassiicola victorivirus 1 (CcVV1). The whole-genome sequence of the virus was sequenced and identified. The CcVV1 genome is 5140 nt and contains 56.87%GC with two large open reading frames (ORFs) overlapping at the tetranucleotide AUGA. The two ORFs were predicted to encode coat protein (CP) and RNA-dependent RNA polymerase (RdRp) respectively, which were conservative in dsRNA fungal viruses of the family Totiviridae. Conservative domains comparison and phylogenetic analysis of the deduced amino acid sequence of RdRp and CP showed that CcVV1 was a new virus of the Victorivirus genus. As far as we know, it is the first report of a genomic sequence of the genus Victorivirus infecting Corynespora cassiicola.

Molecular characterization of a novel mycovirus isolated from Rhizoctonia solani AG-1 IA 9-11

2021 ◽  
Author(s):  
Yang Sun ◽  
Yan qiong Li ◽  
Wen han Dong ◽  
Ai li Sun ◽  
Ning wei Chen ◽  
...  
Keyword(s):  
Rhizoctonia Solani ◽  
Rna Virus ◽  
Dsrna Virus ◽  
Open Reading Frames ◽  
The Family ◽  
Significant Amino Acid Sequence ◽  
Overlapping Open Reading Frames ◽  
Significant Amino Acid ◽  
Reading Frames

Abstract The complete genome of the dsRNA virus isolated from Rhizoctonia solani AG-1 IA 9–11 (designated as Rhizoctonia solani dsRNA virus 11, RsRV11 ) were determined. The RsRV11 genome was 9,555 bp in length, contained three conserved domains, SMC, PRK and RT-like super family, and encoded two non-overlapping open reading frames (ORFs). ORF1 potentially coded for a 204.12 kDa predicted protein, which shared low but significant amino acid sequence identities with the putative protein encoded by Rhizoctonia solani RNA virus HN008 (RsRV-HN008) ORF1. ORF2 potentially coded for a 132.41 kDa protein which contained the conserved motifs of the RNA-dependent RNA polymerase (RdRp). Phylogenetic analysis indicated that RsRV11 was clustered with RsRV-HN008 in a separate clade independent of other virus families. It implies that RsRV11, along with RsRV-HN008 possibly a new fungal virus taxa closed to the family Megabirnaviridae, and RsRV11 is a new member of mycoviruses.

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.

scholarly journals Identification and Characterization of a Novel Robigovirus Species from Sweet Cherry in Turkey

Pathogens ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 57 ◽  
Author(s):  
Kadriye Çağlayan ◽  
Vahid Roumi ◽  
Mona Gazel ◽  
Eminur Elçi ◽  
Mehtap Acioğlu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Sweet Cherry ◽  
Prunus Avium ◽  
Open Reading Frames ◽  
Cherry Tree ◽  
Coding Regions ◽  
Sweet Cherries ◽  
Identification And Characterization ◽  
Reading Frames

High throughput sequencing of total RNA isolated from symptomatic leaves of a sweet cherry tree (Prunus avium cv. 0900 Ziraat) from Turkey identified a new member of the genus Robigovirus designated cherry virus Turkey (CVTR). The presence of the virus was confirmed by electron microscopy and overlapping RT-PCR for sequencing its whole-genome. The virus has a ssRNA genome of 8464 nucleotides which encodes five open reading frames (ORFs) and comprises two non-coding regions, 5′ UTR and 3′ UTR of 97 and 296 nt, respectively. Compared to the five most closely related robigoviruses, RdRp, TGB1, TGB2, TGB3 and CP share amino acid identities ranging from 43–53%, 44–60%, 39–43%, 38–44% and 45–50%, respectively. Unlike the four cherry robigoviruses, CVTR lacks ORFs 2a and 5a. Its genome organization is therefore more similar to African oil palm ringspot virus (AOPRV). Using specific primers, the presence of CVTR was confirmed in 15 sweet cherries and two sour cherries out of 156 tested samples collected from three regions in Turkey. Among them, five samples were showing slight chlorotic symptoms on the leaves. It seems that CVTR infects cherry trees with or without eliciting obvious symptoms, but these data should be confirmed by bioassays in woody and possible herbaceous hosts in future studies.

scholarly journals Molecular and Evolutionary Characterization of the cp32/18 Family of Supercoiled Plasmids in Borrelia burgdorferi297

2000 ◽  
Vol 68 (3) ◽  
pp. 1574-1586 ◽  
Author(s):  
Melissa J. Caimano ◽  
Xiaofeng Yang ◽  
Taissia G. Popova ◽  
Michael L. Clawson ◽  
Darrin R. Akins ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Genomic Sequence ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Exogenous Dna ◽  
Variable Regions ◽  
Different Types ◽  
Sequence Relatedness ◽  
Reading Frames

ABSTRACT In this study, we characterized seven members of the cp32/18 family of supercoiled plasmids in Borrelia burgdorferi297. Complete sequence analysis of a 21-kb plasmid (cp18-2) confirmed that the strain 297 plasmids are similar in overall content and organization to their B31 counterparts. Of the 31 open reading frames (ORFs) in cp18-2, only three showed sequence relatedness to proteins with known functions, and only one, a ParA/SopA ortholog, was related to nonborrelial polypeptides. Besides the lipoproteins, none of the ORFs appeared likely to encode a surface-exposed protein. Comparison with the B31 genomic sequence indicated that paralogs for most of the ORFs in cp18-2 can be identified on other genetic elements. cp18-2 was found to lack a 9- to 10-kb fragment present in the 32-kb homologs which, by extrapolation from the B31 cp32 sequences, contains at least 15 genes presumed to be unnecessary for plasmid maintenance. Sequence analysis of the lipoprotein-encoding variable loci provided evidence that recombinatorial processes within these regions may result in the acquisition of exogenous DNA. Pairwise analysis with random shuffling revealed that the multiple lipoproteins (Mlp; formerly designated 2.9 LPs) fall into two distinct homology groups which appear to have arisen by gene fusion events similar to those recently proposed to have generated the three OspE, OspF, and Elp lipoprotein families (D. R. Akins, M. J. Caimano, X. Yang, F. Cerna, M. V. Norgard, and J. D. Radolf, Infect. Immun. 67:1526–1532, 1999). Comparative analysis of the variable regions also indicated that recombination within the loci of each plasmid may occur independently. Last, comparison of variable loci revealed that the cp32/18 plasmid complements of the B31 and 297 isolates differ substantially, indicating that the two strains have been subject to divergent adaptive pressures. In addition to providing evidence for two different types of recombinatorial events involving cp32/18 plasmids, these findings underscore the need for genetic analysis of diverse borrelial isolates in order to elucidate the Lyme disease spirochete's complex parasitic strategies.

scholarly journals Isolation and Characterization of a Bacteriophage Infecting Pseudomonas Aeruginosa and Its Application as a Potential Decontaminating Agent

2021 ◽  
Author(s):  
Sonika Sharma ◽  
Sibnarayan Datta ◽  
Soumya Chatterjee ◽  
Moumita Dutta ◽  
Jhuma Samanta ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Burst Size ◽  
Gc Content ◽  
Alginate Beads ◽  
Open Reading Frames ◽  
Isolation And Characterization ◽  
The Family ◽  
Infected Cells

Abstract To treat antibiotic resistance bacteria, bacteriophage (also called 'phage') application has recently drawn considerable attention from researchers globally. Bacteria like Pseudomonas aeruginosa are known to be associated with nosocomial infections especially in patients with compromised immune systems. In the present work, phage against P. aeruginosa (named 'DRLP1') was isolated from wastewater, enriched and characterized. Morphologically DRLP1 belongs to the family Myoviridae with a high lytic ability. DRLP1 has a burst size of approximately 100 PFU/infected cells, a rapid adsorption time when supplemented with MgCl2, and has viability in a wide temperature range and pH. Genomic sequencing and bioinformatics analysis showed that the phage genome is linear double-stranded, 66,243 bp in length and have a GC content of 54.9%. the genome encodes 93 phage related ORFs open reading frames (ORFs). Phage stability in lyophilized state, adsorption study on sodium alginate beads, and in-vitro pathogen reduction assays were also investigated. Study carried out with artificially contaminated fomites suggests that this phage has the potential for application as a biological decontaminant agent against P. aeruginosa in different conditions.

scholarly journals Characterization and complete genome sequences of two novel variants of the family Closteroviridae from Chinese kiwifruit

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242362
Author(s):  
Xin Feng ◽  
Rui-lian Lai ◽  
Min-xia Gao ◽  
Wen-guang Chen ◽  
Ru-jian Wu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Genomic Organization ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Genome Sequences ◽  
Viral Genomes ◽  
Relationship Analysis ◽  
The Family ◽  
Novel Variants ◽  
Rapid Amplification

Two distinct closterovirus-like genome sequences (termed AdV-1 v1 and v2) were identified in Actinidia chinensis var. deliciosa ‘Miliang-1’ that had no disease symptoms using high-throughput sequencing. Using overlapping reverse transcription-polymerase chain reaction and rapid amplification of cDNA ends, the genomic sequences of AdV-1 v1 and v2 were confirmed as 17,646 and 18,578 nucleotides in length, respectively. The two complete genomes contained 9 and 15 open reading frames, respectively, coding for proteins having domains typical of Closteroviridae, such as RNA-dependent RNA polymerase (RdRp), heat shock protein 70 homolog (HSP70h) and coat protein (CP). Sequence analysis showed that the amino acid sequences of RdRp, HSP70h, and CP of the two variants exhibited high similarity (> 80%), while their genomic organization was somewhat different. This suggested that the two viral genomes identified here are variants of the family Closteroviridae in a single kiwifruit host. Furthermore, phylogenetic relationship analysis revealed that the two variants had a closer relationship with the unclassified virus Persimmon virus B (PeVB) and Actinidia virus 1 (AcV-1) than with other members of the family Closteroviridae, as did their genomic organization. It is speculated that the two variants, together with PeVB and AcV-1 belong to a new subfamily of Closteroviridae.

scholarly journals Complete Genome Sequence of Macrobrachium rosenbergii Golda Virus (MrGV) from China

Animals ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 27
Author(s):  
Fanzeng Meng ◽  
Yiting Wang ◽  
Guohao Wang ◽  
Tao Hu ◽  
La Xu ◽  
...  
Keyword(s):  
Nucleocapsid Protein ◽  
Genomic Sequence ◽  
Clinical Signs ◽  
Macrobrachium Rosenbergii ◽  
Open Reading Frames ◽  
Freshwater Prawn ◽  
Ribosomal Frameshift ◽  
Giant Freshwater Prawn ◽  
The Family ◽  
Reading Frames

In a meta-transcriptome study of the giant freshwater prawn Macrobrachium rosenbergii sampled in 2018 from a hatchery, we identified a variant of Macrobrachium rosenbergii golda virus (MrGV) in postlarvae without clinical signs. The virus belongs to the family Roniviridae, and the genome of this MrGV variant, Mr-18, consisted of 28,957 nucleotides, including 4 open reading frames (ORFs): (1) ORF1a, encoding a 3C-like protein (3CLP) (4933 aa); (2) ORF1b, encoding a replicase polyprotein (2877 aa); (3) ORF2, encoding a hypothetical nucleocapsid protein (125 aa); and (4) ORF3, encoding a glycoprotein (1503 aa). ORF1a overlaps with ORF1b with 40 nucleotides, where a −1 ribosomal frameshift with slippage sequence 5′-G14925GGUUUU14931-3′ produces the pp1ab polyprotein. The genomic sequence of Mr-18 shared 97.80% identity with MrGV LH1-2018 discovered in Bangladesh. The amino acid sequence identities between them were 99.30% (ORF1a), 99.60% (ORF1b), 100.00% (ORF2), and 99.80% (ORF3), respectively. Phylogenetic analysis of the RNA-dependent RNA polymerase (RdRp) proteins revealed that they clustered together and formed a separate cluster from the genus Okavirus. The finding of MrGV in China warrants further studies to determine its pathogenicity and prevalence within the region.

scholarly journals Characterization of a Novel Mitovirus Infecting Melanconiella theae Isolated From Tea Plants

2021 ◽  
Vol 12 ◽  
Author(s):  
Karim Shafik ◽  
Muhammad Umer ◽  
Huafeng You ◽  
Hamdy Aboushedida ◽  
Zhenhua Wang ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Dsrna Segment ◽  
Rna Dependent Rna Polymerase ◽  
Stem Loop ◽  
Transmission Electron ◽  
The Family ◽  
Dsrna Genome ◽  
Tea Plants ◽  
Rich Content

A dsRNA segment was identified in the fungus Melanconiella theae isolated from tea plants. The complete dsRNA sequence, determined by random cloning together with RACE protocol, is 2,461 bp in length with an AU-rich content (62.37%) and comprises a single ORF of 2,265-nucleotides encoding an RNA-dependent RNA-polymerase (RdRp, 754 amino acids in size). The terminus sequences can fold into predicted stable stem-loop structures. A BLASTX and phylogenetic analysis revealed the dsRNA genome shows similarities with the RdRp sequences of mitoviruses, with the highest identity of 48% with those of grapevine-associated mitovirus 20 and Colletotrichum fructicola mitovirus 1. Our results reveal a novel member, tentatively named Melanconiella theae mitovirus 1 (MtMV1), belongs to the family Mitoviridae. MtMV1 is capsidless as examined by transmission electron microscope, efficiently transmitted through conidia as 100 conidium-generated colonies were analyzed, and easily eliminated by hyphal tipping method combined with green-leaf tea powder. MtMV1 has a genomic sequence obviously divergent from those of most members in the family Mitoviridae and some unique characteristics unreported in known members. This is the first report of a mycovirus infecting Melanconiella fungi to date.

scholarly journals Characterization of an Enteropathogenic Bovine Calicivirus Representing a Potentially New Calicivirus Genus

2002 ◽  
Vol 76 (20) ◽  
pp. 10089-10098 ◽  
Author(s):  
J. R. Smiley ◽  
K. O. Chang ◽  
J. Hayes ◽  
J. Vinjé ◽  
L. J. Saif
Keyword(s):  
Amino Acids ◽  
Nonstructural Protein ◽  
The United States ◽  
Open Reading Frames ◽  
Nonstructural Proteins ◽  
Intestinal Lesions ◽  
The Family ◽  
Histological Data ◽  
Capsid Protein Vp1

ABSTRACT Bovine enteric caliciviruses (BEC) are associated with diarrhea in young calves. The BEC strains detected in Europe form a third genogroup within the genus “Norwalk-like viruses” (NLV) of the family Caliciviridae. In this report, we present sequence, clinical, and histological data characterizing a novel enteropathogenic BEC strain, NB, detected in fecal specimens from calves in the United States. The complete RNA genome of the NB virus is 7,453 bases long and is organized into two open reading frames (ORFs). ORF-1 is 2,210 amino acids long and encodes a large nonstructural polyprotein contiguous with the major capsid protein (VP1), similar to the lagoviruses and “Sapporo-like viruses” (SLV). The conserved calicivirus motifs were identified in the nonstructural proteins. ORF-2 is located at the 3′ end of the genome and encodes a small basic protein (VP2) of 225 amino acids. The 5′ and 3′ untranslated regions are 74 and 67 bases long, respectively. Among caliciviruses, NB virus shows amino acid identities of 14.1 to 22.6% over the entire ORF-1 nonstructural-protein sequence with NLV, SLV, vesivirus, and lagovirus strains, while the overall sequence identity of the complete NB VP-1 with other caliciviruses is low, varying between 14.6 and 26.7%. Phylogenetic analysis of the complete VP1 protein, including strains from all four calicivirus genera, showed the closest grouping of NB virus to be with viruses in the genus Lagovirus, which cause liver infections and systemic hemorrhage in rabbits. In gnotobiotic calves, however, NB virus elicited only diarrhea and intestinal lesions that were most severe in the upper small intestine (duodenum and jejunum), similar to the NLV BEC strains. The tissues of major organs, including the lung, liver, kidney, and spleen, had no visible microscopic lesions.

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