High-throughput sequencing of virus-infected Cucurbita pepo samples revealed the presence of Zucchini shoestring virus in Zimbabwe

Karavina, Charles; Ibaba, Jacques Davy; Gubba, Augustine

doi:10.1186/s13104-020-4927-3

Cited by 6 publications

(2 citation statements)

References 34 publications

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“…This showed that DNA signatures belonged to 52 geminivuruses infecting crop hosts 35 geminiviruses infecting noncultivated plants, identified in different plant species. Their study demonstrated that HTS analyses can increase knowledge of virus diversity, and assist identification and detection of novel emerging known and unknown viruses without requirement for disease etiological information (Karavina et al, 2020).…”

Section: High-throughput Sequencing Tools In Viral Diagnosismentioning

confidence: 99%

Viruses of cucurbit crops: current status in the Mediterranean Region

Radouane

Ezrari

Belabess

et al. 2021

Phytopathol. Mediterr.

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Cucurbits are among the most cultivated crops, and the most economically important species are melon (Cucumis melo L.), cucumber (Cucumis sativus L.), watermelon (Citrullus lanatus Thumb.), squash (Cucurbita pepo L.), and pumpkin (Cucurbita spp.). These crops have become important income sources providing export and local consumption commodities in many Mediterranean countries. Increased area of cucurbits has led to the emergence of several viral diseases, which can have impacts on crop production and threaten agricultural sustainability. An overview of the most damaging cucurbit viruses in the Mediterranean area is provided to improve understanding of the diseases they cause and to emphasize effective disease management strategies. An updating of the geographical distribution of these viruses, the symptoms they cause and their means of transmission is also provided. Disease management methods and measures by farmers and phytosanitary authorities to address the virus outbreaks are outlined, including diagnostics, use of tolerant cultivars, and chemical and biological vector control. Mediterranean region farmers have learned many lessons from the damaging pandemics caused by cucurbit viruses, through the extensive published research, and this review provides a basis for managing future outbreaks of newly emerging virus infections.

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Section: High-throughput Sequencing Tools In Viral Diagnosismentioning

confidence: 99%

Viruses of cucurbit crops: current status in the Mediterranean Region

Radouane

Ezrari

Belabess

et al. 2021

Phytopathol. Mediterr.

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“…Because of its broad detection spectrum and novel pathogen detection ability, it has recently become an increasingly popular tool for pathogen detection. It has been used in many crops, such as wheat [ 34 ], grapevine [ 35 ], citrus [ 36 ], fruit trees [ 37 ], cucurbit [ 38 ], sugarcane [ 10 ], grasses [ 7 , 38 ] etc. for viral pathogen detection.…”

Section: Introductionmentioning

confidence: 99%

PhytoPipe: a phytosanitary pipeline for plant pathogen detection and diagnosis using RNA-seq data

Hu,

Hurtado-Gonzales,

Adhikari

et al. 2023

BMC Bioinformatics

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Background Detection of exotic plant pathogens and preventing their entry and establishment are critical for the protection of agricultural systems while securing the global trading of agricultural commodities. High-throughput sequencing (HTS) has been applied successfully for plant pathogen discovery, leading to its current application in routine pathogen detection. However, the analysis of massive amounts of HTS data has become one of the major challenges for the use of HTS more broadly as a rapid diagnostics tool. Several bioinformatics pipelines have been developed to handle HTS data with a focus on plant virus and viroid detection. However, there is a need for an integrative tool that can simultaneously detect a wider range of other plant pathogens in HTS data, such as bacteria (including phytoplasmas), fungi, and oomycetes, and this tool should also be capable of generating a comprehensive report on the phytosanitary status of the diagnosed specimen. Results We have developed an open-source bioinformatics pipeline called PhytoPipe (Phytosanitary Pipeline) to provide the plant pathology diagnostician community with a user-friendly tool that integrates analysis and visualization of HTS RNA-seq data. PhytoPipe includes quality control of reads, read classification, assembly-based annotation, and reference-based mapping. The final product of the analysis is a comprehensive report for easy interpretation of not only viruses and viroids but also bacteria (including phytoplasma), fungi, and oomycetes. PhytoPipe is implemented in Snakemake workflow with Python 3 and bash scripts in a Linux environment. The source code for PhytoPipe is freely available and distributed under a BSD-3 license. Conclusions PhytoPipe provides an integrative bioinformatics pipeline that can be used for the analysis of HTS RNA-seq data. PhytoPipe is easily installed on a Linux or Mac system and can be conveniently used with a Docker image, which includes all dependent packages and software related to analyses. It is publicly available on GitHub at https://github.com/healthyPlant/PhytoPipe and on Docker Hub at https://hub.docker.com/r/healthyplant/phytopipe.

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Cucurbitaceous vegetables-I

Chinnadurai

2024

Viral Diseases of Field and Horticultural Crops

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High-throughput sequencing of virus-infected Cucurbita pepo samples revealed the presence of Zucchini shoestring virus in Zimbabwe

Cited by 6 publications

References 34 publications

Viruses of cucurbit crops: current status in the Mediterranean Region

Viruses of cucurbit crops: current status in the Mediterranean Region

PhytoPipe: a phytosanitary pipeline for plant pathogen detection and diagnosis using RNA-seq data

Cucurbitaceous vegetables-I

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