Genomic characterization of silvergrass cryptic virus 1, a novel partitivirus infecting Miscanthus sinensis

Costa, L. C.; Hu, Xiaojun; Malapi‐Wight, Martha; O’Connell, Mary J.; Hendrickson, Leticia; Turner, Roy S.; McFarland, Clint; Foster, Joseph; Hurtado‐Gonzales, Oscar P.

doi:10.1007/s00705-021-05294-6

Cited by 4 publications

(3 citation statements)

References 23 publications

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“…Miscanthus spp. are host to several viruses including sugarcane mosaic virus (3), switchgrass mosaic virus (4), sorghum mosaic virus (5), Miscanthus yellow eck virus (6), silvergrass cryptic virus 1 (7), Miscanthus sinensis mosaic virus (8), and Miscanthus streak virus (9). Some of these viruses also infect sugarcane.…”

Section: Main Textmentioning

confidence: 99%

Complete sequence and genome characterization of miscanthus virus M, a new betaflexivirus from Miscanthus sp.

Abrahamian,

Grinstead,

Kinard

et al. 2024

Arch Virol

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Section: Main Textmentioning

confidence: 99%

Complete sequence and genome characterization of miscanthus virus M, a new betaflexivirus from Miscanthus sp.

Abrahamian,

Grinstead,

Kinard

et al. 2024

Arch Virol

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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%

“…), enzyme-linked immunosorbent assay (ELISA), polymerase chain reaction (PCR), and loop-mediated isothermal amplification (LAMP) [5,6]. More recently, high-throughput sequencing (HTS), also known as next-generation sequencing (NGS) or deep sequencing has been used by diagnosticians and researchers for detecting and identifying plant pathogens, which has resulted in a steady increase in the identification of plant pathogens affecting various crops [2,[7][8][9][10][11][12][13]. Since it does not require a priori phytosanitary status knowledge of the sample, HTS offers certain advantages when compared to targeted-diagnostic techniques such as ELISA or PCR [10,11,[14][15][16][17][18].…”

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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Identification and characterization of the complete genome sequence of a tripartite cryptic virus from mulberry (Morus alba)

Yang,

Ling,

Peng

et al. 2023

Eur J Plant Pathol

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Genomic characterization of silvergrass cryptic virus 1, a novel partitivirus infecting Miscanthus sinensis

Cited by 4 publications

References 23 publications

Complete sequence and genome characterization of miscanthus virus M, a new betaflexivirus from Miscanthus sp.

Complete sequence and genome characterization of miscanthus virus M, a new betaflexivirus from Miscanthus sp.

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

Identification and characterization of the complete genome sequence of a tripartite cryptic virus from mulberry (Morus alba)

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