scholarly journals Identification and characterization of a novel potyvirus infecting Paris yunnanensis

2021 ◽  
Author(s):  
Pingxiu Lan ◽  
Peng He ◽  
Mengji Cao ◽  
Guohua Zhou ◽  
Li Chenrong ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Genomic Sequence ◽  
Pairwise Comparison ◽  
Distinct Species ◽  
Reading Frame ◽  
Single Clade ◽  
Terminal Poly ◽  
Identification And Characterization ◽  
Complete Genomic

Abstract The complete genomic sequence of a novel potyvirus from Paris yunnanensis was determined by high-throughput sequencing then confirmed by Sanger sequencing. Its genomic RNA consists 9600 nucleotides (nt) excluding the 3’-terminal poly (A) tail, containing a typical large open reading frame (ORF) of potyviruses and encoding a putative polyprotein of 3098 amino acids (aa). Pairwise comparison analysis showed the virus shares sequence identity with other members of Potyvirus was 53.0–57.8% at genome sequence level, and 39.3–51.2% at polyprotein sequence level. Phylogenetic analysis indicated that the virus was clustered as a single clade within the genus Potyvirus both using nt and aa level. These results suggest that the virus should be considered as a distinct species within the genus Potyvirus, and it was tentatively named as “Paris mottle virus” (PaMoV).

scholarly journals Identification and Characterization of a Novel Potyvirus Infecting Paris Yunnanensis

2021 ◽  
Author(s):  
Pingxiu Lan ◽  
Peng He ◽  
Mengji Cao ◽  
Guohua Zhou ◽  
Chenrong Li ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Genomic Sequence ◽  
Pairwise Comparison ◽  
Distinct Species ◽  
Plum Pox Virus ◽  
Reading Frame ◽  
Terminal Poly ◽  
Chilli Veinal Mottle Virus ◽  
Identification And Characterization

Abstract The complete genomic sequence of a novel potyvirus from Paris yunnanensis was determined by high-throughput sequencing then confirmed by Sanger sequencing. Its genomic RNA consists 9600 nucleotides (nt) excluding the 3’-terminal poly (A) tail, containing a typical large open reading frame (ORF) of potyviruses and encoding a putative polyprotein of 3098 amino acids (aa). Pairwise comparison analysis showed the virus shares sequence identity with other members of Potyvirus was 53.0% to 57.8% at genome sequence level, and 39.3% to 51.2% at polyprotein sequence level. Phylogenetic analysis indicated that the virus was most closely related to the subgroup of plum pox virus and that of chilli veinal mottle virus within the genus Potyvirus. These results suggest that the virus should be considered as a distinct species within the genus Potyvirus and was tentatively named as “Paris mottle associated virus” (PMaV).

Cloning and characterization of an alternative splicing transcript of the gene coding for human cytidine deaminase

2007 ◽  
Vol 85 (1) ◽  
pp. 96-102 ◽  
Author(s):  
Bianca Cristina Garcia Lisboa ◽  
Tamara da Rocha Machado ◽  
Daniel Carvalho Pimenta ◽  
Sang Won Han
Keyword(s):  
Alternative Splicing ◽  
Dna Sequences ◽  
Genomic Sequence ◽  
Cytidine Deaminase ◽  
Alternative Form ◽  
Nih3t3 Cells ◽  
Reading Frame ◽  
Gene Coding ◽  
Identification And Characterization

Human cytidine deaminase (HCD) catalyzes the deamination of cytidine or deoxycytidine to uridine or deoxyuridine, respectively. The genomic sequence of HCD is formed by 31 kb with 4 exons and several alternative splicing signals, but an alternative form of HCD has yet to be reported. Here we describe the cloning and characterization of a small form of HCD, HSCD, and it is likely to be a product of alternative splicing of HCD. The alignment of DNA sequences shows that the HSCD matches HCD in 2 parts, except for a deletion of 170 bp. Based on the HCD genome organization, exons 1 and 4 should be joined and all sequences of introns and exons 2 and 3 should be deleted by splicing. This alternative splicing shifted the translation of the reading frame from the point of splicing. The estimated molecular mass is 9.8 kDa, and this value was confirmed by Western blot and mass spectroscopy after expressing the gene fused with glutathionine-S-transferase in the pGEX vector. The deletion and shift of the reading frame caused a loss of HCD activity, which was confirmed by enzyme assay and also with NIH3T3 cells modified to express HSCD and challenged against cytosine arabinoside. In this work we describe the identification and characterization of HSCD, which is the product of alternative splicing of the HCD gene.

scholarly journals The Banana Root Endophytome: Differences between Mother Plants and Suckers and Evaluation of Selected Bacteria to Control Fusarium oxysporum f.sp. cubense

2021 ◽  
Vol 7 (3) ◽  
pp. 194
Author(s):  
Carmen Gómez-Lama Cabanás ◽  
Antonio J. Fernández-González ◽  
Martina Cardoni ◽  
Antonio Valverde-Corredor ◽  
Javier López-Cepero ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Canary Islands ◽  
High Throughput Sequencing ◽  
Fungal Communities ◽  
Phenological Stage ◽  
Mother Plants ◽  
Fusarium Wilt Of Banana ◽  
Identification And Characterization

This study aimed to disentangle the structure, composition, and co-occurrence relationships of the banana (cv. Dwarf Cavendish) root endophytome comparing two phenological plant stages: mother plants and suckers. Moreover, a collection of culturable root endophytes (>1000) was also generated from Canary Islands. In vitro antagonism assays against Fusarium oxysporum f.sp. cubense (Foc) races STR4 and TR4 enabled the identification and characterization of potential biocontrol agents (BCA). Eventually, three of them were selected and evaluated against Fusarium wilt of banana (FWB) together with the well-known BCA Pseudomonas simiae PICF7 under controlled conditions. Culturable and non-culturable (high-throughput sequencing) approaches provided concordant information and showed low microbial diversity within the banana root endosphere. Pseudomonas appeared as the dominant genus and seemed to play an important role in the banana root endophytic microbiome according to co-occurrence networks. Fungal communities were dominated by the genera Ophioceras, Cyphellophora, Plecosphaerella, and Fusarium. Overall, significant differences were found between mother plants and suckers, suggesting that the phenological stage determines the recruitment and organization of the endophytic microbiome. While selected native banana endophytes showed clear antagonism against Foc strains, their biocontrol performance against FWB did not improve the outcome observed for a non-indigenous reference BCA (strain PICF7).

Identification and characterization of salt-responsive microRNAs in Populus tomentosa by high-throughput sequencing

Biochimie ◽  
2013 ◽  
Vol 95 (4) ◽  
pp. 743-750 ◽  
Author(s):  
Yuanyuan Ren ◽  
Lei Chen ◽  
Yiyun Zhang ◽  
Xiangyang Kang ◽  
Zhiyi Zhang ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Populus Tomentosa ◽  
Identification And Characterization

scholarly journals Recovery of Infectious Virus by Transfection of In Vitro-Generated RNA from Tulane Calicivirus cDNA

2008 ◽  
Vol 82 (22) ◽  
pp. 11429-11436 ◽  
Author(s):  
Chao Wei ◽  
Tibor Farkas ◽  
Karol Sestak ◽  
Xi Jiang
Keyword(s):  
Reverse Genetics ◽  
Genomic Sequence ◽  
Rhesus Macaques ◽  
Wild Type Virus ◽  
Primate Research ◽  
Complete Genomic Sequence ◽  
Subgenomic Rna ◽  
Reading Frame ◽  
Complete Genomic

ABSTRACT Tulane virus (TV) is a newly reported calicivirus that was isolated from stool samples of captive rhesus macaques from the Tulane National Primate Research Center (TNPRC). The virus has been cultivated successfully in LLC-MK2 rhesus monkey kidney cells. Its complete genomic sequence suggests that TV represents a new genus and is evolutionarily more closely related to Norovirus than to any other genus of Caliciviridae. In this study, we demonstrated that RNA transcripts made in vitro from the full-length genomic cDNA of TV were infectious upon transfection into permissive LLC-MK2 cells. The recombinant virus exhibited plaque morphologies and growth kinetics similar to those of the wild-type virus in this cell line. Capping was required for TV RNA infectivity. Although a subgenomic RNA has been detected in TV-transfected cells, a separate subgenomic RNA transcript was not required for the initial transfection to establish the replication. Transfection of truncated RNA lacking open reading frame 2 (ORF2) and ORF3 or TV-norovirus chimeric RNA resulted in abortive replication without the production of infectious progeny viruses, indicating that both ORFs are essential for the replication of TV. A heterologous insertion at the 5′ end of the genome also hampered viral replication, suggesting that an authentic 5′ end of the genome is critical for replication. The availability of the complete genomic sequence and the reverse genetics system described herein make TV a valuable model for studying calicivirus pathogenesis and replication.

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