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5 pages, 147 KiB

Open AccessEditorial

Plant Viruses, Viroids and Phytoplasmas: Insight into Evolutionary, Pathogenicity, and Epidemiology Studies

by Luca Ferretti and Anna Taglienti

Plants 2025, 14(4), 551; https://doi.org/10.3390/plants14040551 - 11 Feb 2025

Viewed by 724

Abstract

Plant viruses, viroids, and phytoplasmas are systemic, unculturable pathogens that are increasingly endangering sustainable food security and environmental safety worldwide [...] Full article

(This article belongs to the Special Issue Plant Viruses, Viroids and Phytoplasmas: Insight into Evolutionary, Pathogenicity, and Epidemiology Studies)

Research

Jump to: Editorial

14 pages, 1608 KiB

Open AccessArticle

Phytoplasma DNA Enrichment from Sugarcane White Leaves for Shotgun Sequencing Improvement

by Karan Lohmaneeratana, Gabriel Gutiérrez, Arinthip Thamchaipenet and Ralf Erik Wellinger

Plants 2024, 13(21), 3006; https://doi.org/10.3390/plants13213006 - 28 Oct 2024

Cited by 1 | Viewed by 1212

Abstract

Sugarcane white leaf (SCWL) disease, caused by Candidatus Phytoplasma sacchari, poses a significant threat to sugarcane cultivation. An obligate parasite, phytoplasma is difficult to culture in laboratory conditions, making the isolation of its DNA from the massive amount of plant host DNA extremely [...] Read more.

Sugarcane white leaf (SCWL) disease, caused by Candidatus Phytoplasma sacchari, poses a significant threat to sugarcane cultivation. An obligate parasite, phytoplasma is difficult to culture in laboratory conditions, making the isolation of its DNA from the massive amount of plant host DNA extremely challenging. Yet, the appropriate amount and quality of plant microbiome-derived DNA are key for high-quality DNA sequencing data. Here, a simple, cost-effective, alternative method for DNA isolation was applied using a guanidine-HCl-hydroxylated silica (GuHCl-Silica)-based method and microbiome DNA enrichment based on size-selective low-molecular-weight (LMW) DNA by PEG/NaCl precipitation. qPCR analysis revealed a significant enrichment of phytoplasma DNA in the LMW fraction. Additionally, the NEBNext Microbiome DNA enrichment kit was utilized to further enrich microbial DNA, demonstrating a remarkable increase in the relative abundance of phytoplasma DNA to host DNA. Shotgun sequencing of the isolated DNA gave high-quality data on the metagenome assembly genome (MAG) of Ca. Phytoplasma sacchari SCWL with completeness at 95.85 and 215× coverage. The results indicate that this combined approach of PEG/NaCl size selection and microbiome enrichment is effective for obtaining high-quality genomic data from phytoplasma, surpassing previous methods in efficiency and resource utilization. This low-cost method not only enhances the recovery of microbiome DNA from plant hosts but also provides a robust framework for studying plant pathogens in complex plant models. Full article

(This article belongs to the Special Issue Plant Viruses, Viroids and Phytoplasmas: Insight into Evolutionary, Pathogenicity, and Epidemiology Studies)

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16 pages, 3843 KiB

Open AccessArticle

Biological and Molecular Characterization of a New Isolate of Tomato Mottle Mosaic Virus Causing Severe Shoestring and Fruit Deformities in Tomato Plants in India

by Prantik Mazumder, Firoz Mondal, Mehulee Sarkar, Anik Majumdar, Kajal Kumar Biswas, Susheel Kumar Sharma, Milan Kumar Lal, Rahul Kumar Tiwari, Ravinder Kumar and Anirban Roy

Plants 2024, 13(19), 2811; https://doi.org/10.3390/plants13192811 - 8 Oct 2024

Cited by 1 | Viewed by 1674

Abstract

Tomato (Solanum lycopersicum L.), the second most important vegetable crop globally, faces a significant threat from various viral diseases. A newly emerging disease, characterised by distinctive shoestring symptoms on leaves and the development of unripe, small, and hard fruit, poses a serious [...] Read more.

Tomato (Solanum lycopersicum L.), the second most important vegetable crop globally, faces a significant threat from various viral diseases. A newly emerging disease, characterised by distinctive shoestring symptoms on leaves and the development of unripe, small, and hard fruit, poses a serious challenge to tomato cultivation in India. An initial survey in an experimental field revealed more than 50% of the plants displayed symptoms of the shoestring disease, resulting in substantial reductions in fruit yield and quality. Transmission electron microscopy (TEM) and molecular analyses identified an isolate of the tomato mottle mosaic virus (ToMMV) in the affected plants. When the partially purified virus was mechanically inoculated into tomato cv. Pusa Ruby plants, it reproduced the characteristic shoestring symptoms, confirming its causal relationship with the disease. Notably, the present shoestring isolate of ToMMV (ToMMV-Tss) was found to induce similar shoestring symptoms in most of the major commercial tomato varieties when inoculated under controlled experimental conditions in the glasshouse, indicating its aggressive nature. Host range studies demonstrated that the ToMMV-Tss can infect several solanaceous species, while cucurbitaceous hosts remained unaffected. Moreover, the virus was found to be seed-transmissible, with a small percentage of seedlings from infected plants displaying symptoms. These findings underscore the significant impact of ToMMV on tomato production in India and emphasise the need for reliable diagnostic tools and effective management strategies to curb the spread and mitigate the impact of this virus on commercial tomato cultivation. Full article

(This article belongs to the Special Issue Plant Viruses, Viroids and Phytoplasmas: Insight into Evolutionary, Pathogenicity, and Epidemiology Studies)

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5 pages, 794 KiB

Open AccessCommunication

Genomic Sequence of a Czech Isolate of Erysimum Latent Virus from Sisymbrium altissimum

by Karima Ben Mansour, Josef Špak, Petr Komínek, Miloslav Zouhar, Pavel Ryšánek and Adrian J. Gibbs

Plants 2024, 13(18), 2554; https://doi.org/10.3390/plants13182554 - 11 Sep 2024

Cited by 1 | Viewed by 981

Abstract

The Erysimum latent virus (ELV), a tymovirus, was first isolated from several wild and cultivated brassicas in Germany. Its virions were shown to be serologically distinct from those of the turnip yellow mosaic virus (TYMV), which is also found in wild and cultivated [...] Read more.

The Erysimum latent virus (ELV), a tymovirus, was first isolated from several wild and cultivated brassicas in Germany. Its virions were shown to be serologically distinct from those of the turnip yellow mosaic virus (TYMV), which is also found in wild and cultivated plants in several European countries but also in other parts of the world. TYMV and ELV were among the first plant viruses to have had their genomes sequenced, and when other tymovirus genomes were sequenced, it was found that, in phylogenies, ELV is probably the basal outlier to all other tymoviruses. Here, we report the near-complete genomic sequence of another isolate of ELV from Czechia. This isolate was found in 1990 in Sisymbrium altissimum plants showing mosaic symptoms. It was detected using ELISA tests and electron microscopy. We have now sequenced the full coding sequence of this isolate using contemporary high throughput methods and found that the German and Czech isolates of ELV are closely related and are of the same virus species. Full article

(This article belongs to the Special Issue Plant Viruses, Viroids and Phytoplasmas: Insight into Evolutionary, Pathogenicity, and Epidemiology Studies)

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13 pages, 7159 KiB

Open AccessArticle

The N-Terminal Region of Cucumber Mosaic Virus 2a Protein Is Involved in the Systemic Infection in Brassica juncea

by Tae-Seon Park, Dong-Joo Min, Ji-Soo Park and Jin-Sung Hong

Plants 2024, 13(7), 1001; https://doi.org/10.3390/plants13071001 - 31 Mar 2024

Cited by 1 | Viewed by 1430

Abstract

Brassica juncea belongs to the Brassicaceae family and is used as both an oilseed and vegetable crop. As only a few studies have reported on the cucumber mosaic virus (CMV) in B. juncea, we conducted this study to provide a basic understanding [...] Read more.

Brassica juncea belongs to the Brassicaceae family and is used as both an oilseed and vegetable crop. As only a few studies have reported on the cucumber mosaic virus (CMV) in B. juncea, we conducted this study to provide a basic understanding of the B. juncea and CMV interactions. B. juncea-infecting CMV (CMV-Co6) and non-infecting CMV (CMV-Rs1) were used. To identify the determinants of systemic infection in B. juncea, we first constructed infectious clones of CMV-Co6 and CMV-Rs1 and used them as pseudo-recombinants. RNA2 of CMV was identified as an important determinant in B. juncea because B. juncea were systemically infected with RNA2-containing pseudo-recombinants; CMV-Co6, R/6/R, and R/6/6 were systemically infected B. juncea. Subsequently, the amino acids of the 2a and 2b proteins were compared, and a chimeric clone was constructed. The chimeric virus R/6Rns/R6cp, containing the C-terminal region of the 2a protein of CMV-Rs1, still infects B. juncea. It is the 2a protein that determines the systemic CMV infection in B. juncea, suggesting that conserved 160G and 214A may play a role in systemic CMV infection in B. juncea. Full article

(This article belongs to the Special Issue Plant Viruses, Viroids and Phytoplasmas: Insight into Evolutionary, Pathogenicity, and Epidemiology Studies)

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13 pages, 9883 KiB

Open AccessArticle

Adoption of the 2A Ribosomal Skip Principle to Track Assembled Virions of Pepper Mild Mottle Virus in Nicotiana benthamiana

by Mengting Jiao, Yueyan Yin, Yanzhen Tian, Jianing Lei, Lin Lin, Jian Wu, Yuwen Lu, Hongying Zheng, Fei Yan, Jianguang Wang and Jiejun Peng

Plants 2024, 13(7), 928; https://doi.org/10.3390/plants13070928 - 22 Mar 2024

Cited by 4 | Viewed by 1527

Abstract

The coat protein (CP) is an important structural protein that plays many functional roles during the viral cycle. In this study, the CP of pepper mild mottle virus (PMMoV) was genetically fused to GFP using the foot-and-mouth disease virus peptide 2A linker peptide [...] Read more.

The coat protein (CP) is an important structural protein that plays many functional roles during the viral cycle. In this study, the CP of pepper mild mottle virus (PMMoV) was genetically fused to GFP using the foot-and-mouth disease virus peptide 2A linker peptide and the construct (PMMoV-GFP^2A) was shown to be infectious. The systemic spread of the virus was monitored by its fluorescence in infected plants. Electron microscopy and immunocolloidal gold labelling confirmed that PMMoV-GFP^2A forms rod-shaped particles on which GFP is displayed. Studies of tissue ultrastructure and virion self-assembly confirmed that PMMoV-GFP^2A could be used to monitor the real-time dynamic changes of CP location during virus infection. Aggregations of GFP-tagged virions appeared as fluorescent plaques in confocal laser microscopy. Altogether, PMMoV-GFP^2A is a useful tool for studying the spatial and temporal changes of PMMoV CP during viral infection. Full article

(This article belongs to the Special Issue Plant Viruses, Viroids and Phytoplasmas: Insight into Evolutionary, Pathogenicity, and Epidemiology Studies)

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17 pages, 5713 KiB

Open AccessArticle

A Distinct Arabidopsis Latent Virus 1 Isolate Was Found in Wild Brassica hirta Plants and Bees, Suggesting the Potential Involvement of Pollinators in Virus Spread

by Victoria Reingold, Avi Eliyahu, Neta Luria, Diana Leibman, Noa Sela, Oded Lachman, Elisheva Smith, Yael Mandelik, Asaf Sadeh and Aviv Dombrovsky

Plants 2024, 13(5), 671; https://doi.org/10.3390/plants13050671 - 28 Feb 2024

Cited by 1 | Viewed by 1789

Abstract

During our search for aphid-pathogenic viruses, a comovirus was isolated from wild asymptomatic Brassica hirta (white mustard) plants harboring a dense population of Brevicoryne brassicae aphids. The transmission-electron-microscopy visualization of purified virions revealed icosahedral particles. The virus was mechanically transmitted to plants belonging [...] Read more.

During our search for aphid-pathogenic viruses, a comovirus was isolated from wild asymptomatic Brassica hirta (white mustard) plants harboring a dense population of Brevicoryne brassicae aphids. The transmission-electron-microscopy visualization of purified virions revealed icosahedral particles. The virus was mechanically transmitted to plants belonging to Brassicaceae, Solanaceae, Amaranthaceae, and Fabaceae families, showing unique ringspot symptoms only on B. rapa var. perviridis plants. The complete viral genome, comprised of two RNA segments, was sequenced. RNA1 and RNA2 contained 5921 and 3457 nucleotides, respectively, excluding the 3′ terminal poly-adenylated tails. RNA1 and RNA2 each had one open-reading frame encoding a polyprotein of 1850 and 1050 amino acids, respectively. The deduced amino acids at the Pro-Pol region, delineated between a conserved CG motif of 3C-like proteinase and a GDD motif of RNA-dependent RNA polymerase, shared a 96.5% and 90% identity with the newly identified Apis mellifera-associated comovirus and Arabidopsis latent virus 1 (ArLV1), respectively. Because ArLV1 was identified early in 2018, the B. hirta comovirus was designated as ArLV1-IL-Bh. A high-throughput-sequencing-analyses of the extracted RNA from managed honeybees and three abundant wild bee genera, mining bees, long-horned bees, and masked bees, sampled while co-foraging in a Mediterranean ecosystem, allowed the assembly of ArLV1-IL-Bh, suggesting pollinators’ involvement in comovirus spread in weeds. Full article

(This article belongs to the Special Issue Plant Viruses, Viroids and Phytoplasmas: Insight into Evolutionary, Pathogenicity, and Epidemiology Studies)

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13 pages, 1217 KiB

Open AccessArticle

Plants under Siege: Investigating the Relevance of ‘Ca. P. solani’ Cixiid Vectors through a Multi-Test Study

by Andrea Kosovac, Emil Rekanović, Živko Ćurčić, Jelena Stepanović and Bojan Duduk

Plants 2023, 12(24), 4157; https://doi.org/10.3390/plants12244157 - 14 Dec 2023

Cited by 1 | Viewed by 1466

Abstract

Crop losses caused by the plant pathogenic bacterium ‘Candidatus Phytoplasma solani’ (CaPsol) underscore the need to better understand its perplexing epidemiological pathways. Hyalesthes obsoletus (Hemiptera, Cixiidae) is a prominent CaPsol vector with three plant associations in Serbia (ex Urtica dioica/HobsUd; [...] Read more.

Crop losses caused by the plant pathogenic bacterium ‘Candidatus Phytoplasma solani’ (CaPsol) underscore the need to better understand its perplexing epidemiological pathways. Hyalesthes obsoletus (Hemiptera, Cixiidae) is a prominent CaPsol vector with three plant associations in Serbia (ex Urtica dioica/HobsUd; ex Convolvulus arvensis/HobsCa; ex Crepis foetida/HobsCf). Another cixiid planthopper, Reptalus quinquecostatus (Dufour), has been recently confirmed as a noteworthy CaPsol vector. A multi-test study assessed the relevance of H. obsoletus associations and R. quinquecostatus populations from Crataegus monogyna and Prunus spinosa in CaPsol occurrence in sugar beet, maize, and tobacco. Molecular typing of the CaPsol strains transmitted to test plants in experimental trials provided the first evidence of HobsUd transmitting CaPsol tuf-a type to sugar beet, HobsCa infecting maize and tobacco with tuf-b type, and HobsCf transmitting CaPsol tuf-b to maize. Affiliation of R. quinquecostatus with the specific CaPsol genotype, dSTOLg, was reaffirmed in this study. The possible involvement of R. quinquecostatus in maize redness disease and tobacco stolbur was suggested, given that this cixiid was identified as a vector of CaPsol to these crops. The obtained results indicate that the tested vectors pose a threat to cultivated plants in Serbia, underscoring the need to recognize their relevance in CaPsol disease occurrences. Full article

(This article belongs to the Special Issue Plant Viruses, Viroids and Phytoplasmas: Insight into Evolutionary, Pathogenicity, and Epidemiology Studies)

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14 pages, 1742 KiB

Open AccessArticle

Carlavirus Species Infecting Hop Plants in Italy: Molecular Identification and Phylogenetic Analyses of the Detected Isolates

by Marta Luigi, Livia Donati, Renato Sciarroni, Andrea Gentili, Anna Taglienti, Antonio Tiberini, Francesco Faggioli and Luca Ferretti

Plants 2023, 12(19), 3514; https://doi.org/10.3390/plants12193514 - 9 Oct 2023

Cited by 2 | Viewed by 1386

Abstract

Hop (Humulus lupulus L.) is a minor ingredient in the beer production but has a strong influence on the beer quality due to the high chemical complexity of the cones used in brewing. One of the major factors that can severely affect [...] Read more.

Hop (Humulus lupulus L.) is a minor ingredient in the beer production but has a strong influence on the beer quality due to the high chemical complexity of the cones used in brewing. One of the major factors that can severely affect the chemical composition of the hop cones and their marketability is the presence of viral infections in the plant. Amongst the five major hop viruses, three belong to the Carlavirus genus: hop mosaic virus (HpMV), hop latent virus (HpLV), and American hop latent virus (AHLV). The occurrence of carlaviruses on hop germplasm in Italy was firstly recorded in 2017 but, in that context, a generic detection was only performed and no information on the infecting Carlavirus species was provided. To fill this gap, 51 hop samples previously found infected by carlaviruses were analysed by RT-PCR employing primer pairs specific for the coat protein (CP) of HpMV, HpLV and AHLV, respectively. HpLV resulted largely prevalent as it was detected in 96.1% of tested samples whereas for HpMV and AHLV an infection rate of 5.9% and 3.9% was recorded, respectively. CP nucleotide sequences from 13 selected virus isolates were obtained and analysed; moreover, the complete genome sequence of 7 isolates was obtained by using high throughput sequencing (HTS). Phylogenetic analysis showed close relationships among isolates from different geographical origin, including European and non-European countries, according to the worldwide movement of hop germplasm due to global trade. This is the first report of HpMV, HpLV and AHLV on hop germplasm in Italy. Full article

(This article belongs to the Special Issue Plant Viruses, Viroids and Phytoplasmas: Insight into Evolutionary, Pathogenicity, and Epidemiology Studies)

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