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Keywords = post-entry quarantine

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27 pages, 5135 KiB  
Review
Status and Distribution of Diseases Caused by Phytoplasmas in Africa
by Shakiru Adewale Kazeem, Agnieszka Zwolińska, Joseph Mulema, Akindele Oluwole Ogunfunmilayo, Shina Salihu, Joy Oluchi Nwogwugwu, Inusa Jacob Ajene, Justina Folasayo Ogunsola, Adedapo Olutola Adediji, Olubusola Fehintola Oduwaye, Kouamé Daniel Kra, Mustafa Ojonuba Jibrin and Wei Wei
Microorganisms 2025, 13(6), 1229; https://doi.org/10.3390/microorganisms13061229 - 27 May 2025
Viewed by 922
Abstract
Phytoplasma (“Candidatus Phytoplasma” species) diseases have been reported globally to severely limit the productivity of a wide range of economically important crops and wild plants causing different yellows-type diseases. With new molecular detection techniques, several unknown and known diseases with uncertain etiologies [...] Read more.
Phytoplasma (“Candidatus Phytoplasma” species) diseases have been reported globally to severely limit the productivity of a wide range of economically important crops and wild plants causing different yellows-type diseases. With new molecular detection techniques, several unknown and known diseases with uncertain etiologies or attributed to other pathogens have been identified as being caused by Phytoplasmas. In Africa, Phytoplasmas have been reported in association with diseases in a broad range of host plant species. However, the few reports of Phytoplasma occurrence in Africa have not been collated together to determine the status in different countries of the continent. Thus, this paper discusses the geographical distribution, detection techniques, insect vectors, alternative hosts and socio-economic impacts of Phytoplasma diseases in Africa. This is to create research perspectives on the disease’s etiology in Africa for further studies towards identifying and limiting their negative effects on the continent’s agricultural economy. In Africa, Phytoplasmas recorded in different countries affecting different crops belong to eight groups (16SrI, 16SrII, 16SrIII, 16SrIV, 16SrVI, 16SrXI, 16SrXIV and 16SrXXII) out of the 37 groups and over 150 subgroups reported worldwide on the basis of their 16S rRNA RFLP profile. Lethal yellow disease was the most destructive Phytoplasma reported in Africa and has a high socio-economic impact. Full article
(This article belongs to the Special Issue Phytoplasmas and Phytoplasma Diseases)
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17 pages, 5522 KiB  
Article
Comparative and Phylogenetic Analysis of Anthurium andraeanum Hybridization Based on Molecular and Morphological Traits
by Yingwen Pan, Jiatong Li and Chaozu He
Horticulturae 2024, 10(11), 1146; https://doi.org/10.3390/horticulturae10111146 - 28 Oct 2024
Viewed by 1432
Abstract
Hybridization is considered an important mode of species evolution, but the genetic evolutionary process of Anthurium andraeanum hybridization is still poorly characterized. In order to provide the molecular and morphological basis for phylogenetic analysis in A. andraeanum hybridization, we analyzed the morphological, nuclear [...] Read more.
Hybridization is considered an important mode of species evolution, but the genetic evolutionary process of Anthurium andraeanum hybridization is still poorly characterized. In order to provide the molecular and morphological basis for phylogenetic analysis in A. andraeanum hybridization, we analyzed the morphological, nuclear genomic, and chloroplast genomic data of five A. andraeanum cultivars and explored the correlations between different traits and nuclear and chloroplast genome characteristics. A. andraeanum hybrid 1 is an A. andraeanum ‘Baron’ (♀) × A. andraeanum ‘Spice’ (♂) cross, and A. andraeanum hybrid 2 is an A. andraeanum ‘Cheers’ (♀) × A. andraeanum hybrid 1 (♂) cross. The A. andraeanum hybrids reflected their parents’ heterozygous features in their morphologies, nuclear genomes, and chloroplast genomes. The morphological traits in the F1 generation were widely separated, showing continuous variation. Based on cluster analysis, the five A. andraeanum cultivars could be divided into two groups. The ISSR analysis results were highly correlated with the spathe color. Among the five A. andraeanum cultivars, the composition and structure features of chloroplast genomes were completely the same or highly similar, respectively. Phylogenetic analysis based on complete chloroplast genome data showed that the genetic stability of the chloroplast is high in A. andraeanum, manifested as uniparental maternal inheritance, where the chloroplast genome composition and structural features of hybrids are highly similar to those of the maternal parent. Full article
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21 pages, 5897 KiB  
Article
High-Throughput Sequencing Methods for the Detection of Two Strawberry Viruses in Post-Entry Quarantine
by Luciano Nunes-Leite, Lia W. Liefting, David W. Waite, Subuhi Khan and Jeremy R. Thompson
Viruses 2024, 16(10), 1550; https://doi.org/10.3390/v16101550 - 30 Sep 2024
Viewed by 1986
Abstract
High-throughput sequencing (HTS) technologies may be a useful tool for testing imported plant germplasm for multiple pathogens present in a sample, offering strain-generic detection not offered by most PCR-based assays. Metatranscriptomics (RNAseq) and tiled amplicon PCR (TA-PCR) were tested as HTS-based techniques to [...] Read more.
High-throughput sequencing (HTS) technologies may be a useful tool for testing imported plant germplasm for multiple pathogens present in a sample, offering strain-generic detection not offered by most PCR-based assays. Metatranscriptomics (RNAseq) and tiled amplicon PCR (TA-PCR) were tested as HTS-based techniques to detect viruses present in low titres. Strawberry mottle virus (SMoV), an RNA virus, and strawberry vein banding virus (SVBV), a DNA virus, were selected for comparison of RNAseq and TA-PCR with quantitative PCR assays. RNAseq of plant ribosomal RNA-depleted samples of low viral titre was used to obtain datasets from 3 M to 120 M paired-end (PE) reads. RNAseq demonstrated PCR-like sensitivity, able to detect as few as 10 viral copies/µL when 60 million (M) PE reads were generated. The custom TA-PCR primer panels designed for each virus were successfully used to recover most of the reference genomes for each virus. Single- and multiple-target TA-PCR allowed the detection of viruses in samples with around 10 viral copies/µL with a minimum continuous sequence length recovery of 500 bp. The limit of detection of the HTS-based protocols described here is comparable to that of quantitative PCR assays. This work lays the groundwork for an increased flexibility in HTS detection of plant viruses. Full article
(This article belongs to the Special Issue Advances in Plant Virus/Viroid Detection and Identification Methods)
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25 pages, 5303 KiB  
Article
Status of Cassava Witches’ Broom Disease in the Philippines and Identification of Potential Pathogens by Metagenomic Analysis
by Darwin Magsino Landicho, Ray Jerome Mojica Montañez, Maurizio Camagna, Sokty Neang, Abriel Salaria Bulasag, Peter Magan Magdaraog, Ikuo Sato, Daigo Takemoto, Kensaku Maejima, Marita Sanfuego Pinili and Sotaro Chiba
Biology 2024, 13(7), 522; https://doi.org/10.3390/biology13070522 - 15 Jul 2024
Cited by 3 | Viewed by 3759
Abstract
Cassava witches’ broom disease (CWBD) is one of the most devastating diseases of cassava (Manihot esculenta Crantz), and it threatens global production of the crop. In 2017, a phytoplasma, Candidatus Phytoplasma luffae (Ca. P. luffae), was reported in the Philippines, and [...] Read more.
Cassava witches’ broom disease (CWBD) is one of the most devastating diseases of cassava (Manihot esculenta Crantz), and it threatens global production of the crop. In 2017, a phytoplasma, Candidatus Phytoplasma luffae (Ca. P. luffae), was reported in the Philippines, and it has been considered as the causal agent, despite unknown etiology and transmission of CWBD. In this study, the nationwide occurrence of CWBD was assessed, and detection of CWBD’s pathogen was attempted using polymerase chain reaction (PCR) and next-generation sequencing (NGS) techniques. The results showed that CWBD has spread and become severe, exhibiting symptoms such as small leaf proliferation, shortened internodes, and vascular necrosis. PCR analysis revealed a low phytoplasma detection rate, possibly due to low titer, uneven distribution, or absence in the CWBD-symptomatic cassava. In addition, NGS techniques confirm the PCR results, revealing the absence or extremely low phytoplasma read counts, but a surprisingly high abundance of fastidious and xylem-limited fungus, Ceratobasidium sp. in CWBD-symptomatic plants. These findings cast doubt over the involvement of phytoplasma in CWBD and instead highlight the potential association of Ceratobasidium sp., strongly supporting the recent findings in mainland Southeast Asia. Further investigations are needed to verify the etiology of CWBD and identify infection mechanisms of Ceratobasidium sp. to develop effective diagnostic and control methods for disease management. Full article
(This article belongs to the Section Microbiology)
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14 pages, 3442 KiB  
Article
Global Potential Distribution of Invasive Species Pseudococcus viburni (Hemiptera: Pseudococcidae) under Climate Change
by Jiufeng Wei, Minmin Niu, Hanxi Zhang, Bo Cai and Wei Ji
Insects 2024, 15(3), 195; https://doi.org/10.3390/insects15030195 - 14 Mar 2024
Cited by 6 | Viewed by 2417
Abstract
The potential distribution range and management strategies for P. viburni are poorly understood. Based on historical distribution data and environmental factors, the present study predicted the potentially suitable areas for P. viburni spread under different climate change scenarios using MaxEnt (maximum entropy). The [...] Read more.
The potential distribution range and management strategies for P. viburni are poorly understood. Based on historical distribution data and environmental factors, the present study predicted the potentially suitable areas for P. viburni spread under different climate change scenarios using MaxEnt (maximum entropy). The results showed that precipitation of the coldest quarter (Bio19), precipitation seasonality (Bio15), and mean temperature of the wettest quarter (Bio8) were the most important environmental factors determining the distribution of P. viburni. Under the current climate conditions, its potential suitable areas are southern China, the whole of Japan, North America (especially the eastern part of the United States), the southwestern part of South America, the Mediterranean coast and most of Europe, the central part of Africa, i.e., the south of the Sahara Desert, and most of the southern coast of Australia. The total area of habitats suitable for this insect pest is predicted to be increased in the future. In order to prevent P. viburni transmission and spread, there is a need to strengthen the monitoring and quarantine measures against this pest at the Southern ports. Full article
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15 pages, 1110 KiB  
Review
New Virus Diagnostic Approaches to Ensuring the Ongoing Plant Biosecurity of Aotearoa New Zealand
by Catia Delmiglio, David W. Waite, Sonia T. Lilly, Juncong Yan, Candace E. Elliott, Julie Pattemore, Paul L. Guy and Jeremy R. Thompson
Viruses 2023, 15(2), 418; https://doi.org/10.3390/v15020418 - 1 Feb 2023
Cited by 5 | Viewed by 3478
Abstract
To protect New Zealand’s unique ecosystems and primary industries, imported plant materials must be constantly monitored at the border for high-threat pathogens. Techniques adopted for this purpose must be robust, accurate, rapid, and sufficiently agile to respond to new and emerging threats. Polymerase [...] Read more.
To protect New Zealand’s unique ecosystems and primary industries, imported plant materials must be constantly monitored at the border for high-threat pathogens. Techniques adopted for this purpose must be robust, accurate, rapid, and sufficiently agile to respond to new and emerging threats. Polymerase chain reaction (PCR), especially real-time PCR, remains an essential diagnostic tool but it is now being complemented by high-throughput sequencing using both Oxford Nanopore and Illumina technologies, allowing unbiased screening of whole populations. The demand for and value of Point-of-Use (PoU) technologies, which allow for in situ screening, are also increasing. Isothermal PoU molecular diagnostics based on recombinase polymerase amplification (RPA) and loop-mediated amplification (LAMP) do not require expensive equipment and can reach PCR-comparable levels of sensitivity. Recent advances in PoU technologies offer opportunities for increased specificity, accuracy, and sensitivities which makes them suitable for wider utilization by frontline or border staff. National and international activities and initiatives are adopted to improve both the plant virus biosecurity infrastructure and the integration, development, and harmonization of new virus diagnostic technologies. Full article
(This article belongs to the Special Issue State-of-the-Art Plant Virus Research in Australasia)
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9 pages, 222 KiB  
Entry
The Post-Pandemic Transformation of Art and Architecture Libraries
by Rose Orcutt, Lucy Campbell, Maya Gervits and Barbara Opar
Encyclopedia 2022, 2(4), 1893-1901; https://doi.org/10.3390/encyclopedia2040131 - 30 Nov 2022
Viewed by 2933
Definition
This entry paper considers the impact of the COVID-19 pandemic on the processes and functions of art and architecture libraries in North America and distinguishes between temporary changes and those that will endure and are here to stay. COVID-19 impacted all aspects of [...] Read more.
This entry paper considers the impact of the COVID-19 pandemic on the processes and functions of art and architecture libraries in North America and distinguishes between temporary changes and those that will endure and are here to stay. COVID-19 impacted all aspects of human life, placing tremendous stress on institutions and individuals globally. Academic libraries responded to the crisis by bringing resources to communities remotely and keeping constituents engaged to maintain a sense of normalcy. While libraries in schools of architecture, art, and design, responded similarly to other academic libraries, they also had unique needs. This entry paper is informed by two surveys of art and architecture library staff and faculty, alongside a preliminary literature review. The results of the first survey were published in Art Documentation and the results and analysis of the second survey are forthcoming. Both temporary and long-standing changes were implemented to ensure uninterrupted service in academic institutions. Temporary solutions included extending loan periods, quarantining materials, enforcing social distancing, and expanding document delivery. Changes that will endure post-pandemic include the increased acquisition of digital materials, remote instruction and reference consultations, increased resource access, and the utilization of a vast array of technologies. Full article
(This article belongs to the Collection Encyclopedia of COVID-19)
21 pages, 14165 KiB  
Article
Implementation of GA-VirReport, a Web-Based Bioinformatics Toolkit for Post-Entry Quarantine Screening of Virus and Viroids in Plants
by Ruvini V. Lelwala, Zacharie LeBlanc, Marie-Emilie A. Gauthier, Candace E. Elliott, Fiona E. Constable, Greg Murphy, Callum Tyle, Adrian Dinsdale, Mark Whattam, Julie Pattemore and Roberto A. Barrero
Viruses 2022, 14(7), 1480; https://doi.org/10.3390/v14071480 - 5 Jul 2022
Cited by 6 | Viewed by 3543
Abstract
High-throughput sequencing (HTS) of host plant small RNA (sRNA) is a popular approach for plant virus and viroid detection. The major bottlenecks for implementing this approach in routine virus screening of plants in quarantine include lack of computational resources and/or expertise in command-line [...] Read more.
High-throughput sequencing (HTS) of host plant small RNA (sRNA) is a popular approach for plant virus and viroid detection. The major bottlenecks for implementing this approach in routine virus screening of plants in quarantine include lack of computational resources and/or expertise in command-line environments and limited availability of curated plant virus and viroid databases. We developed: (1) virus and viroid report web-based bioinformatics workflows on Galaxy Australia called GA-VirReport and GA-VirReport-Stats for detecting viruses and viroids from host plant sRNA extracts and (2) a curated higher plant virus and viroid database (PVirDB). We implemented sRNA sequencing with unique dual indexing on a set of plants with known viruses. Sequencing data were analyzed using GA-VirReport and PVirDB to validate these resources. We detected all known viruses in this pilot study with no cross-sample contamination. We then conducted a large-scale diagnosis of 105 imported plants processed at the post-entry quarantine facility (PEQ), Australia. We detected various pathogens in 14 imported plants and discovered that de novo assembly using 21–22 nt sRNA fraction and the megablast algorithm yielded better sensitivity and specificity. This study reports the successful, large-scale implementation of HTS and a user-friendly bioinformatics workflow for virus and viroid screening of imported plants at the PEQ. Full article
(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)
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20 pages, 1801 KiB  
Article
Side-by-Side Comparison of Post-Entry Quarantine and High Throughput Sequencing Methods for Virus and Viroid Diagnosis
by Marie-Emilie A. Gauthier, Ruvini V. Lelwala, Candace E. Elliott, Craig Windell, Sonia Fiorito, Adrian Dinsdale, Mark Whattam, Julie Pattemore and Roberto A. Barrero
Biology 2022, 11(2), 263; https://doi.org/10.3390/biology11020263 - 8 Feb 2022
Cited by 18 | Viewed by 4334
Abstract
Rapid and safe access to new plant genetic stocks is crucial for primary plant industries to remain profitable, sustainable, and internationally competitive. Imported plant species may spend several years in Post Entry Quarantine (PEQ) facilities, undergoing pathogen testing which can impact the ability [...] Read more.
Rapid and safe access to new plant genetic stocks is crucial for primary plant industries to remain profitable, sustainable, and internationally competitive. Imported plant species may spend several years in Post Entry Quarantine (PEQ) facilities, undergoing pathogen testing which can impact the ability of plant industries to quickly adapt to new global market opportunities by accessing new varieties. Advances in high throughput sequencing (HTS) technologies provide new opportunities for a broad range of fields, including phytosanitary diagnostics. In this study, we compare the performance of two HTS methods (RNA-Seq and sRNA-Seq) with that of existing PEQ molecular assays in detecting and identifying viruses and viroids from various plant commodities. To analyze the data, we tested several bioinformatics tools which rely on different approaches, including direct-read, de novo, and reference-guided assembly. We implemented VirusReport, a new portable, scalable, and reproducible nextflow pipeline that analyses sRNA datasets to detect and identify viruses and viroids. We raise awareness of the need to evaluate cross-sample contamination when analyzing HTS data routinely and of using methods to mitigate index cross-talk. Overall, our results suggest that sRNA analyzed using VirReport provides opportunities to improve quarantine testing at PEQ by detecting all regulated exotic viruses from imported plants in a single assay. Full article
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17 pages, 1350 KiB  
Protocol
Application of Oxford Nanopore Technology to Plant Virus Detection
by Lia W. Liefting, David W. Waite and Jeremy R. Thompson
Viruses 2021, 13(8), 1424; https://doi.org/10.3390/v13081424 - 22 Jul 2021
Cited by 45 | Viewed by 8081
Abstract
The adoption of Oxford Nanopore Technologies (ONT) sequencing as a tool in plant virology has been relatively slow despite its promise in more recent years to yield large quantities of long nucleotide sequences in real time without the need for prior amplification. The [...] Read more.
The adoption of Oxford Nanopore Technologies (ONT) sequencing as a tool in plant virology has been relatively slow despite its promise in more recent years to yield large quantities of long nucleotide sequences in real time without the need for prior amplification. The portability of the MinION and Flongle platforms combined with lowering costs and continued improvements in read accuracy make ONT an attractive method for both low- and high-scale virus diagnostics. Here, we provide a detailed step-by-step protocol using the ONT Flongle platform that we have developed for the routine application on a range of symptomatic post-entry quarantine and domestic surveillance plant samples. The aim of this methods paper is to highlight ONT’s feasibility as a valuable component to the diagnostician’s toolkit and to hopefully stimulate other laboratories towards the eventual goal of integrating high-throughput sequencing technologies as validated plant virus diagnostic methods in their own right. Full article
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8 pages, 212 KiB  
Review
Evolution of Plant Virus Diagnostics Used in Australian Post Entry Quarantine
by Mark Whattam, Adrian Dinsdale and Candace E. Elliott
Plants 2021, 10(7), 1430; https://doi.org/10.3390/plants10071430 - 13 Jul 2021
Cited by 15 | Viewed by 4092
Abstract
As part of a special edition for MDPI on plant virology in Australia, this review provides a brief high-level overview on the evolution of diagnostic techniques used in Australian government Post-Entry Quarantine (PEQ) facilities for testing imported plants for viruses. A comprehensive range [...] Read more.
As part of a special edition for MDPI on plant virology in Australia, this review provides a brief high-level overview on the evolution of diagnostic techniques used in Australian government Post-Entry Quarantine (PEQ) facilities for testing imported plants for viruses. A comprehensive range of traditional and modern diagnostic approaches have historically been employed in PEQ facilities using bioassays, serological, and molecular techniques. Whilst these techniques have been effective, they are time consuming, resource intensive and expensive. The review highlights the importance of ensuring the best available science and diagnostic developments are constantly tested, evaluated, and implemented by regulators to ensure primary producers have rapid and safe access to new genetics to remain productive, sustainable and competitive. Full article
(This article belongs to the Collection Plant Virology in Australia)
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