Next Generation Sequencing, and Development of a Pipeline as a Tool for the Detection and Discovery of Citrus Pathogens to Facilitate Safer Germplasm Exchange

Plants, Journal Year: 2024, Volume and Issue: 13(3), P. 411 - 411

Published: Jan. 30, 2024

Citrus is affected by many diseases, and hence, the movement of citrus propagative materials highly regulated in USA. Currently used regulatory pathogen detection methods include biological laboratory-based technologies, which are time-consuming, expensive, have limitations. There an urgent need to develop alternate, rapid, economical, reliable testing for safe germplasm exchange. huanglongbing (HLB) has devastated industries leading increased exchanges between growing regions evaluating potentially valuable hybrids both HLB resistance multilocational performance. In present study, Next-Generation Sequencing (NGS) were sequence transcriptomes 21 test samples, including 15 well-characterized pathogen-positive plants. A workflow was designed CLC Genomics Workbench software, v 21.0.5 bioinformatics analysis data pathogens. NGS rapid found be a technique viral bacterial pathogens, discovery new viruses, complementary existing array laboratory assays. Using methods, we detected beet western yellows virus, newly reported variant yellow vein-associated virus associated with “fatal yellows” disease.

Language: Английский

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A Survey on Sugarcane Mosaic Symptoms Leads to the First Report of Sugarcane Chlorotic Streak Virus in Cameroon

Sugar Tech, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 9, 2025

Language: Английский

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Deciphering mixed infections by plant RNA virus and reconstructing complete genomes simultaneously present within-host

PLoS ONE, Journal Year: 2025, Volume and Issue: 20(1), P. e0311555 - e0311555

Published: Jan. 14, 2025

Local co-circulation of multiple phylogenetic lineages is particularly likely for rapidly evolving pathogens in the current context globalisation. When different co-occur same fields, they may be simultaneously present host plant (i.e. mixed infection), with potentially important consequences disease outcome. This case Burkina Faso rice yellow mottle virus (RYMV), which endemic to Africa and a major constraint on production. We aimed decipher distinct RYMV isolates that infect single sequence their genomes. To this end, we tested sequencing strategies, finally combined direct cDNA ONT (Oxford Nanopore Technology) bioinformatics tool RVhaplo. method was validated by successful reconstruction two viral genomes were less than hundred nucleotides apart (out genome 4450nt length, i.e. 2–3%), artificial mixes at ratio up 99/1. then used subsequently analyze infections from field samples, revealing three within one sample Faso. In most cases, complete sequences obtained, better estimation diversity detection recombination events. The described thus allows identify various haplotypes infecting plant, obtaining full-length sequences, as well rough estimate relative frequencies sample. It efficient, cost-effective, portable, so it could further implemented where endemic. Prospects include unravelling other RNA viruses threaten crop production worldwide.

Language: Английский

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Investigation of Viral Agents in Walnut (Juglans spp.) Trees by High Throughput Sequencing from Niğde province, Türkiye

Kahramanmaraş Sütçü İmam Üniversitesi Tarım ve Doğa Dergisi, Journal Year: 2025, Volume and Issue: 28(3), P. 820 - 829

Published: May 1, 2025

In October 2023, virus-like symptomatic walnut trees in Niğde province were investigated using high-throughput sequencing (HTS) to investigate viral infections. Double-stranded RNA (dsRNA) extraction was conducted, followed by conversion of dsRNA into cDNA. PCR then performed barcoding with MID primers for metagenomic analyses. The products from samples B13, B22, B23, and B21 + B5 sequenced the Illumina NovaSeq 6000 platform. data underwent bioinformatics analysis Geneious Prime CLC Genomic Workbench. this comparison, more contigs constructed Workbench, resulting precise outcomes BLASTx analysis. According map, reference analyses B21+B5 HTS data, 29,574 reads matched cherry leaf roll virus RNA1 (CLRV) RefSeq NC_015414, 405 CLRV RNA2 NC_015415. However, 4 cucumber mosaic (CMV) NC_001440 B23 data. To confirm presence these viruses, virus-specific used test total extracted walnuts. detected sample but not B5. CMV B23. Improving nucleic acid methods is recommended enhance detection agents sequencing.

Language: Английский

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Benchmarking of virome metagenomic analysis approaches using a large, 60+ members, viral synthetic community

Journal of Virology, Journal Year: 2023, Volume and Issue: 97(11)

Published: Oct. 27, 2023

We report here efforts to benchmark performance of two widespread approaches for virome analysis, which target either virion-associated nucleic acids (VANA) or highly purified double-stranded RNAs (dsRNAs). This was achieved using synthetic communities varying complexity levels, up a complex community 72 viral agents (115 molecules) comprising isolates from 21 families and 61 genera plant viruses. The results obtained confirm that the dsRNA-based approach provides more complete representation RNA virome, in particular, high ones. However, viromes low medium complexity, VANA appears reasonable alternative would be preferred choice if analysis DNA viruses is importance. Several parameters impacting were identified as well direct relationship between completeness description sample sequencing depth. strategy, results, tools used should prove useful range efforts.

Language: Английский

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Old Foe, New Host: Epidemiology, Genetic Diversity, and Pathogenic Characterization of Maize Streak Virus in Rice Fields from Burkina Faso

Phytobiomes Journal, Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 2, 2024

Rice is of critical significance regarding food security worldwide, including in Africa. Only two viruses impacting rice production Africa have been deeply investigated for decades: the yellow mottle virus ( Solemoviridae) and stripe necrosis Benyviridae). Using viral metagenomics, we aimed at broadening knowledge on interacting communities associated with plants landscapes exploring diversity epidemiological status circulating fields from Burkina Faso. We performed an survey this country between 2016 2019 involving 57 small farmers’ under systems: rainfed lowlands irrigated areas. More than 2,700 samples were collected without regard to disease symptoms following a regular scheme. Wild cultivated Poaceae (maize sugarcane) growing nearby also collected. Unexpectedly, metagenomics detected maize streak (MSV) Geminiviridae) analyzed samples. Further molecular analyses using rolling circle amplification-polymerase chain reaction showed that MSV was widely distributed highly prevalent both MSV-A MSV-G strains identified. MSV-G, exclusively identified thus far wild grasses, most strain, whereas MSV-A, known cause severe maize, sporadically infectious clones experimental conditions, confirmed pathogenicity rice. Thus, addition contributing surveillance Africa, our results illuminate new pathogenic aspects one studied plant significant economic consequences [Formula: see text] Copyright © 2024 The Author(s). This open access article CC BY-NC-ND 4.0 International license .

Language: Английский

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Diagnosis of Plant Viruses Using NGS to Support Virus Management and Tomato Breeding

Published: April 28, 2024

Viral diseases pose a significant threat to tomato crops (Solanum lycopersicum L.), one of the world's most economically important vegetable crops. The limited genetic diversity cultivated tomatoes contributes their high susceptibility viral infections. To address this challenge, breeding programs must harness resources found in native populations and wild relatives. Breeding efforts may aim develop broad-spectrum resistance against virome. identify viruses naturally infecting 19 advanced lines, derived from tomatoes, high-throughput sequencing (HTS) small RNAs validation by PCR RT-PCR were used. Single mixed infections with Tomato mosaic virus (ToMV), golden (ToGMoV), Pepper huasteco yellow vein (PHYVV) detected. complete consensus genomes three variants Mexican ToMV isolates reconstructed, potentially forming new clade distinct 3' UTR. absence reported mutations associated resistance-breaking suggests that Tm-1, Tm-2, Tm-22 genes could theoretically be used confer resistance. However, mutation rates 63 nucleotide insertion UTR suggest need evaluate known these variants. precise identification characterization infect germplasm as strategy for selecting appropriate disease management guiding efforts.

Language: Английский

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Translating virome analyses to support biosecurity, on-farm management, and crop breeding

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: March 14, 2023

Virome analysis via high-throughput sequencing (HTS) allows rapid and massive virus identification diagnoses, expanding our focus from individual samples to the ecological distribution of viruses in agroecological landscapes. Decreases costs combined with technological advances, such as automation robotics, allow for efficient processing numerous plant disease clinics, tissue culture laboratories, breeding programs. There are many opportunities translating virome support health. For example, can be employed development biosecurity strategies policies, including implementation risk assessments regulation reduce movement infected material. A challenge is identify which new discovered through HTS require allowed move germplasm trade. On-farm management incorporate information surveillance, monitoring known across scales, rapidly important agricultural understand their abundance spread. indexing programs used generate clean seed, crucial maintenance seed system production health, particularly vegetatively propagated crops roots, tubers, bananas. provide insight into expression levels by generating relative data, aiding cultivars resistant, or at least tolerant, viruses. The integration network machine learning techniques facilitate designing implementing strategies, using novel forms a scalable, replicable, practical approach developing viromes. In long run, these will designed sequence databases building on foundation pre-existing knowledge about taxonomy, distribution, host range. conclusion, early adoption integrated control impacting global markets, reducing introducing viruses, limiting effective translation depends capacity make benefits available globally.

Language: Английский

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Historical Review of Sugarcane Streak Mosaic Virus that Has Recently Emerged in Africa

Phytopathology, Journal Year: 2023, Volume and Issue: 114(4), P. 668 - 680

Published: Nov. 15, 2023

Sugarcane streak mosaic virus (SCSMV), now assigned to the genus

Language: Английский

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African army ants at the forefront of virome surveillance in a remote tropical forest

Peer Community Journal, Journal Year: 2023, Volume and Issue: 3

Published: March 13, 2023

In this study, we used a predator-enabled metagenomics strategy to sample the virome of remote and difficult-to-access densely forested African tropical region. Specifically, focused our study on use army ants genus Dorylus that are obligate collective foragers group predators attack overwhelm broad array animal prey. Using 209 ant samples collected from 29 colonies virion-associated nucleic acid-based approach, showed diversity bacterial, plant, invertebrate vertebrate viral sequences were accumulated by ants: including 157 different genera in 56 families. This suggests using scavengers such as swathes forest viromes can shed light composition structure populations these complex inaccessible ecosystems.

Language: Английский

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