Virome analysis of lily plants reveals a new potyvirus

Li, Yongqiang; Jia, Anning; Qiao, Yan; Xiang, Jun; Zhang, Yongjiang; Wang, Wenhe

doi:10.1007/s00705-017-3690-9

Cited by 21 publications

(13 citation statements)

References 22 publications

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“…It has many advantages over serological and molecular detection methods that require specific antisera or prior knowledge of nucleotide sequences [19]. Metagenomic HTS has significantly influenced the diagnosis of known and unknown plant viruses as well as genome diversity and evolutionary investigations at different taxonomic levels [14][15][16][17][18][19][20][21][22][23][24][25][26]. Recent advances in HTS technology and improved bioinformatics pipelines have appreciably reduced sequencing costs and time.…”

Section: Introductionmentioning

confidence: 99%

Viromes of Ten Alfalfa Plants in Australia Reveal Diverse Known Viruses and a Novel RNA Virus

Samarfard

McTaggart

Sharman³

et al. 2020

Pathogens

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Alfalfa plants in the field can display a range of virus-like symptoms, especially when grown over many years for seed production. Most known alfalfa viruses have RNA genomes, some of which can be detected using diagnostic assays, but many viruses of alfalfa are not well characterized. This study aims to identify the RNA and DNA virus complexes associated with alfalfa plants in Australia. To maximize the detection of RNA viruses, we purified double-stranded RNA (dsRNA) for high throughput sequencing and characterized the viromes of ten alfalfa samples that showed diverse virus-like symptoms. Using Illumina sequencing of tagged cDNA libraries from immune-captured dsRNA, we identified sequences of the single-stranded RNA viruses, alfalfa mosaic virus (AMV), bean leafroll virus, a new emaravirus tentatively named alfalfa ringspot-associated virus, and persistent dsRNA viruses belonging to the families Amalgaviridae and Partitiviridae. Furthermore, rolling circle amplification and restriction enzyme digestion revealed the complete genome of chickpea chlorosis Australia virus, a mastrevirus (family Geminiviridae) previously reported only from chickpea and French bean that was 97% identical to the chickpea isolate. The sequence data also enabled the assembly of the first complete genome (RNAs 1–3) of an Australian AMV isolate from alfalfa.

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Section: Introductionmentioning

confidence: 99%

Viromes of Ten Alfalfa Plants in Australia Reveal Diverse Known Viruses and a Novel RNA Virus

Samarfard

McTaggart

Sharman³

et al. 2020

Pathogens

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“…Due to the rapid advances in next-generation sequencing (NGS), co-infected known and novel viruses can be easily identified with full genomes [ 19 – 21 ]. For example, NGS of a small RNA library revealed co-infection of CMV, LSV, and a novel virus referred to as Lily yellow mosaic virus (LYMV) in the genus Potyvirus [ 22 ]. However, the NGS technique is not widely applied in the study of viruses infecting lilies.…”

Section: Introductionmentioning

confidence: 99%

RNA viromes of the oriental hybrid lily cultivar “Sorbonne”

Cho

2018

BMC Genomics

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BackgroundThe lily is a perennial flowering plant belonging to the genus Lilium in the family Liliaceae. Most cultivated lily plants are propagated by bulbs. Therefore, numerous lily bulbs are frequently infected by diverse viruses causing viral diseases. To date, no study has examined the viromes of plants of one type with identical genetic backgrounds collected from different geographical regions.ResultsHere, we examined different viromes of the lily cultivar “Sorbonne” using 172 gigabytes of transcriptome data composed of 23 libraries from four different projects for the cultivar “Sorbonne.” We identified 396 virus-associated contigs from all but one library. We identified six different viruses, including Plantago asiatica mosaic virus (PlAMV), Cucumber mosaic virus (CMV), Lily symptomless virus (LSV), Tulip virus X (TVX), Lily mottle virus (LMoV), and Tobacco rattle virus (TRV). Of them, PlAMV was the most common virus infecting the lily. Scale and flower samples possessed a high number of virus-associated reads. We assembled 32 nearly complete genomes for the six identified viruses possessing the polyadenylate tails. Genomes of all six viruses were highly conserved in the lily cultivar “Sorbonne” based on mutation analysis. We identified defective RNAs from LSV, TVX, and PlAMV localized in the triple gene block region. Phylogenetic analyses showed that virus genomes are highly correlated with geographical regions and host plants.ConclusionsWe conducted comprehensive virome analyses of a single lily cultivar, “Sorbonne,” using transcriptome data. Our results shed light on an array of lily virome-associated topics, including virus identification, the dominant virus, virus accumulation in different plant tissues, virus genome assembly, virus mutation, identification of defective RNAs, and phylogenetic relationships of identified viruses. Taken together, we provide very useful methods and valuable results that can be applied in other virome-associated studies.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5138-3) contains supplementary material, which is available to authorized users.

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“…At pharmacological doses, ATRA binds PML-RARα through the RARα ligand-binding domain, changing the conformation, releasing transcriptional co-repressor and recruiting transcriptional co-activators. This allows PML-RARα to activate transcription of its target genes, re-establishing cellular differentiation [28-30]. …”

Section: Introductionmentioning

confidence: 99%

Effects of Fifty-Hertz Electromagnetic Fields on Granulocytic Differentiation of ATRA-Treated Acute Promyelocytic Leukemia NB4 Cells

Provenzano

Amatori

Nasoni

et al. 2018

Cell Physiol Biochem

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Background/Aims: Life on Earth is constantly exposed to electromagnetic fields (EMFs) and the effects induced by EMFs on biological systems have been extensively studied producing different and sometimes contradictory results. Extremely low-frequency electromagnetic fields (ELF-EMFs) have shown to play a role in regulating cell proliferation and differentiation, although how EMFs influence these processes remains unclear. Human acute promyelocytic leukemia (APL) cells are characterized by the arrest of differentiation at the promyelocytic stage due to epigenetic perturbations induced by PML/RARα fusion protein (Promyelocytic Leukemia protein - PML/Retinoic Acid Receptor alpha - RARα). Therapeutic administration of all-trans retinoic acid (ATRA) re-establishes the leukemogenic mechanism re-inducing the normal differentiation processes. Methods: We studied the effects of ELF-EMFs (50 Hz, 2 mT) on the ATRA-mediated granulocytic differentiation process of APL NB4 cells (a cell line established from the bone marrow of a patient affected by the acute promyelocytic leukemia) by monitoring cellular proliferation and morphology, nitrob lue tetrazolium (NBT) reduction and the expression of differentiation surface markers. Finally, we investigated mechanisms focusing on reactive oxygen species (ROS) generation and related molecular pathways. Results: ELF-EMF exposure decreases cellular proliferation potential and helps ATRA-treated NB4 cells to mature. Furthermore, the analysis of ROS production and the consequent extracellular signal regulated kinases (ERK1/2) phosphorylation suggest that a changed intracellular oxidative balance may influence the biological effects of ELF-EMFs. Conclusions: These results indicate that the exposure to ELF-EMF promotes ATRA-induced granulocytic differentiation of APL cells.

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Virome analysis of lily plants reveals a new potyvirus

Cited by 21 publications

References 22 publications

Viromes of Ten Alfalfa Plants in Australia Reveal Diverse Known Viruses and a Novel RNA Virus

Viromes of Ten Alfalfa Plants in Australia Reveal Diverse Known Viruses and a Novel RNA Virus

RNA viromes of the oriental hybrid lily cultivar “Sorbonne”

Effects of Fifty-Hertz Electromagnetic Fields on Granulocytic Differentiation of ATRA-Treated Acute Promyelocytic Leukemia NB4 Cells

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