Characterization of viruses and viroids in <i>Vitis vinifera</i> ‘Kyoho’ in Hangzhou China by small RNA deep sequencing and molecular detection

Li, Hongmei; Wei, Lingzhu; Cheng, Qiqun; Cheng, Jianhui; Zhang, Xian; Chen, Weiwei; Lai, Tongfei; Yu, Zhiming; Zhang, Pengcheng; Wu, Jiang; Shi, Nongnong

doi:10.1080/14620316.2020.1845985

Cited by 3 publications

(2 citation statements)

References 25 publications

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“…During the process of viral infection small RNAs (sRNAs) accumulate abundantly in plants and can be detected by deep sequencing of infected plants. sRNA-seq provides a unique opportunity to easily detect and identify grapevine viruses and viroids due to the abundance of sRNAs ( Navarro et al, 2009 ; Giampetruzzi et al, 2012 ; Eichmeier et al, 2016 ; Czotter et al, 2018 ; Demian et al, 2020 ; Li et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Virome Status of Preclonal Candidates of Grapevine Varieties (Vitis vinifera L.) From the Slovenian Wine-Growing Region Primorska as Determined by High-Throughput Sequencing

et al. 2022

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Diseases caused by viruses and virus-like organisms are one of the major problems in viticulture and grapevine marketing worldwide. Therefore, rapid and accurate diagnosis and identification is crucial. In this study, we used HTS of virus- and viroid-derived small RNAs to determine the virome status of Slovenian preclonal candidates of autochthonous and local grapevine varieties (Vitis vinifera L.). The method applied to the studied vines revealed the presence of nine viruses and two viroids. All viral entities were validated and more than 160 Sanger sequences were generated and deposited in NCBI. In addition, a complete description into the co-infections in each plant studied was obtained. No vine was found to be virus- and viroid-free, and no vine was found to be infected with only one virus or viroid, while the highest number of viral entities in a plant was eight.

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Section: Introductionmentioning

confidence: 99%

Virome Status of Preclonal Candidates of Grapevine Varieties (Vitis vinifera L.) From the Slovenian Wine-Growing Region Primorska as Determined by High-Throughput Sequencing

et al. 2022

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“…It was hypothesized that it would be possible to identify viral species infecting different crops using deep sequencing of siRNAs [ 20 ]. Deep sequencing technologies facilitated the identification of numerous viruses and novel viruses, such as the Grapevine Pinot gris virus and rose leaf rosette-associated virus [ 21 , 22 , 23 ].…”

Section: Introductionmentioning

confidence: 99%

Pathological Features and Genetic Polymorphism Analysis of Tomato Spotted Wilt Virus in Infected Tomato Fruit

Lv,

Mo,

Deng

et al. 2023

Genes

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An in-house tomato inbred line, YNAU335, was planted in a greenhouse in spring from 2014 to 2017, and showed immunity to tomato spotted wilt virus (TSWV). YNAU335 was infected with TSWV in the spring from 2018 to 2020, and disease was observed on the leaves, sepals, and fruits. In 2021 and 2022, YNAU335 was planted in spring in the same greenhouse, which was suspected of being infected with TSWV, and visible disease symptoms were observed on the fruits. Transmission electron microscopy, deep sequencing of small RNAs, and molecular mutation diagnosis were used to analyze the pathological features and genetic polymorphism of TSWV infecting tomato fruit. Typical TSWV virions were observed in the infected fruits, but not leaves from YNAU335 grown between 2021 and 2022, and cross-infection was very rarely observed. The number of mitochondria and chloroplasts increased, but the damage to the mitochondria was greater than that seen in the chloroplasts. Small RNA deep sequencing revealed the presence of multiple viral species in TSWV-infected and non-infected tomato samples grown between 2014–2022. Many virus species, including TSWV, which accounted for the largest proportion, were detected in the TSWV-infected tomato leaves and fruit. However, a variety of viruses other than TSWV were also detected in the non-infected tissues. The amino acids of TSWV nucleocapsid proteins (NPs) and movement proteins (MPs) from diseased fruits of YNAU335 picked in 2021–2022 were found to be very diverse. Compared with previously identified NPs and MPs from TSWV isolates, those found in this study could be divided into three types: non-resistance-breaking, resistance-breaking, and other isolates. The number of positive clones and a comparison with previously identified amino acid mutations suggested that mutation F at AA118 of the MP (GenBank OL310707) is likely the key to breaking the resistance to TSWV, and this mutation developed only in the infected fruit of YNAU335 grown in 2021 and 2022.

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Investigation on Viral Pathogens in <i>Vitis vinifera</i> from Four Production Bases in Hangzhou Vicinity of China by sRNAseq and Molecular Validation

Li¹,

Wei²,

Wu³

et al. 2021

AJPS

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Characterization of viruses and viroids in Vitis vinifera ‘Kyoho’ in Hangzhou China by small RNA deep sequencing and molecular detection

Cited by 3 publications

References 25 publications

Virome Status of Preclonal Candidates of Grapevine Varieties (Vitis vinifera L.) From the Slovenian Wine-Growing Region Primorska as Determined by High-Throughput Sequencing

Virome Status of Preclonal Candidates of Grapevine Varieties (Vitis vinifera L.) From the Slovenian Wine-Growing Region Primorska as Determined by High-Throughput Sequencing

Pathological Features and Genetic Polymorphism Analysis of Tomato Spotted Wilt Virus in Infected Tomato Fruit

Investigation on Viral Pathogens in <i>Vitis vinifera</i> from Four Production Bases in Hangzhou Vicinity of China by sRNAseq and Molecular Validation

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Characterization of viruses and viroids in Vitis vinifera ‘Kyoho’ in Hangzhou China by small RNA deep sequencing and molecular detection

Cited by 3 publications

References 25 publications

Virome Status of Preclonal Candidates of Grapevine Varieties (Vitis vinifera L.) From the Slovenian Wine-Growing Region Primorska as Determined by High-Throughput Sequencing

Virome Status of Preclonal Candidates of Grapevine Varieties (Vitis vinifera L.) From the Slovenian Wine-Growing Region Primorska as Determined by High-Throughput Sequencing

Pathological Features and Genetic Polymorphism Analysis of Tomato Spotted Wilt Virus in Infected Tomato Fruit

Investigation on Viral Pathogens in &lt;i&gt;Vitis vinifera&lt;/i&gt; from Four Production Bases in Hangzhou Vicinity of China by sRNAseq and Molecular Validation

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Investigation on Viral Pathogens in <i>Vitis vinifera</i> from Four Production Bases in Hangzhou Vicinity of China by sRNAseq and Molecular Validation