Article
Virology
Solomon Maina, Linda Zheng, Brendan C. Rodoni
Summary: The study developed a targeted genome sequencing (TG-Seq) approach that can detect multiple plant viruses simultaneously with high sensitivity and potential. It successfully detected all expected viral amplicons in mPCR reactions, providing more accurate and detailed virus detection.
Review
Microbiology
Amy H. Fitzpatrick, Agnieszka Rupnik, Helen O'Shea, Fiona Crispie, Sinead Keaveney, Paul Cotter
Summary: This review assesses and recommends approaches for targeted and agnostic High Throughput Sequencing of RNA viruses, highlighting the challenges and biases that method choice can impart to sequencing results. Methodology choices from RNA extraction to library preparation have a significant impact on the detection or characterization of RNA viruses.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Peter Alaxin, Lukas Predajna, Adam Achs, Zdeno Subr, Michaela Mrkvova, Miroslav Glasa
Summary: Two genetic groups of HSVd (6A and 7A) were identified in Slovakia, with low intra-group divergence but higher inter-group divergence due to specific mutations. Mixed infection of these variants was also found within single grapevine plants.
Article
Plant Sciences
Eugene Koh, William Goh, Irene Julca, Erielle Villanueva, Marek Mutwil
Summary: The Plant Expression Omnibus (PEO) is a web application that provides biologists with access to gene expression insights across over 100 plant species. Users can explore the expression patterns of genes across different organs and discover functional annotations.
Article
Virology
Francesco Di Serio, Robert A. Owens, Beatriz Navarro, Pedro Serra, Angel Emilio Martinez de Alba, Sonia Delgado, Alberto Carbonell, Selma Gago-Zachert
Summary: Viroids, small non-protein coding circular RNAs, can infect host plants independently of helper viruses. This review focuses on the role of post-transcriptional RNA silencing in the interaction between viroids and plants, specifically in plant antiviroid defense and viroid pathogenesis. The review also pays tribute to Dr. Ricardo Flores, who made significant contributions to elucidate molecular mechanisms involved in plant-viroid interactions.
Article
Plant Sciences
John M. K. Roberts, Anna E. C. Jooste, Lara-Simone Pretorius, Andrew D. W. Geering
Summary: Avocado is a rapidly growing fruit industry, but avocado sunblotch viroid (ASBVd) poses a major threat to production and export markets. ASBVd can be transmitted through male pollen or female gametes. Surveillance for ASBVd is challenging due to the strict evidence requirements, but using honey bees to monitor the virus shows promise. In this study, ASBVd was detected in bees and pollen samples collected from orchards with known infection rates using real-time RT-PCR and high-throughput sequencing.
Article
Microbiology
Sandro L. Valenzuela, Tomas Norambuena, Veronica Morgante, Francisca Garcia, Juan C. Jimenez, Carlos Nunez, Ignacia Fuentes, Bernardo Pollak
Summary: This study proposes a method utilizing biological information to enhance diagnostic certainty. By using viral replicases to define genome coverage thresholds, the researchers have demonstrated the sensitivity and specificity of this approach in viral detection.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Vahid J. Javaran, Abdonaser Poursalavati, Pierre Lemoyne, Dave T. Ste-Croix, Peter Moffett, Mamadou L. Fall
Summary: There is a global need for identifying viral pathogens and providing clean plant materials to limit the spread of viral diseases. A reliable, cost-effective, and easy-to-use diagnostic tool is crucial for managing viral-like diseases. This study develops and validates a dsRNA-based nanopore sequencing protocol, which outperforms existing methods in detecting viruses and viroids in grapevines. The proposed data analysis workflows also demonstrate high accuracy in classifying viral reads.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Calla L. Telzrow, Paul J. Zwack, Shannon Esher Righi, Fred S. Dietrich, Cliburn Chan, Kouros Owzar, J. Andrew Alspaugh, Joshua A. Granek
Summary: The study compared three RNA enrichment methods on Cryptococcus neoformans RNA and found that the RNase H depletion method was more efficient in depleting rRNA than the Poly(A) isolation method, while the Ribo-Zero depletion method closely recapitulated non-coding RNA levels. The data was used to accurately map C. neoformans mitochondrial rRNA genes and explore novel long non-coding RNA genes.
G3-GENES GENOMES GENETICS
(2021)
Article
Biotechnology & Applied Microbiology
David W. McKellar, Iwijn De Vlaminck
Summary: Spatial total RNA-sequencing (STRS) combines in situ polyadenylation with existing spatial transcriptomics technologies, providing a comprehensive view of the transcriptome in tissues. This technique was used to spatially map coding, noncoding and nonhost RNAs in skeletal muscle regeneration and viral myocarditis models.
NATURE BIOTECHNOLOGY
(2023)
Article
Plant Sciences
Annelies Haegeman, Yoika Foucart, Kris De Jonghe, Thomas Goedefroit, Maher Al Rwahnih, Neil Boonham, Thierry Candresse, Yahya Z. A. Gaafar, Oscar P. Hurtado-Gonzales, Zala Kogej Zwitter, Denis Kutnjak, Janja Lamovsek, Marie Lefebvre, Martha Malapi, Irena Mavric Plesko, Serkan Onder, Jean-Sebastien Reynard, Ferran Salavert Pamblanco, Olivier Schumpp, Kristian Stevens, Chandan Pal, Lucie Tamisier, Cigdem Ulubas Serce, Inge van Duivenbode, David W. Waite, Xiaojun Hu, Heiko Ziebell, Sebastien Massart
Summary: High-throughput sequencing of plant tissues is a crucial tool for plant virologists to detect plant viruses. However, during the analysis of the data, researchers often neglect sequences without homologies to viruses, which may contain traces of other pathogens. In this study, we re-analyzed RNA-seq datasets and found non-viral plant pathogens, including fungi, insects, and mites. This highlights the potential of using total RNA-seq data for detecting various plant pathogens.
Review
Biochemistry & Molecular Biology
Zhiqi Deng, Liqun Ma, Peiyu Zhang, Hongliang Zhu
Summary: Small RNAs play significant roles in plant development, stress response, and antiviral immunity. This paper reviews the mechanisms by which small RNAs regulate viral defense in plants and the strategies employed by viruses to overcome host immune responses. Additionally, the current development status of new virus defense applications based on small RNA silencing is discussed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Virology
Liguo Zhang, Punam Bisht, Anthony Flamier, M. Inmaculada Barrasa, Max Friesen, Alexsia Richards, Stephen H. Hughes, Rudolf Jaenisch
Summary: SARS-CoV-2 sequences can be reverse-transcribed and integrated into the genomes of virus-infected cells by a LINE1-mediated retrotransposition mechanism. Whole-genome sequencing methods and an enrichment method called TagMap were used to detect retrotranspositions, with TagMap being able to identify rare viral retrotranspositions in non-overexpressing cells. LINE1 overexpression increased retrotranspositions about 1000-fold.
Article
Virology
Deborah Schoenegger, Oumaima Moubset, Paolo Margaria, Wulf Menzel, Stephan Winter, Philippe Roumagnac, Armelle Marais, Thierry Candresse
Summary: This study benchmarks the performance of two common virome analysis approaches and finds that the dsRNA-based method provides a more complete representation of the RNA virome, particularly for high complexity communities. However, for low to medium complexity viromes, the VANA method is a reasonable alternative, especially if the analysis of DNA viruses is important. The study also identifies important parameters and proposes a direct relationship between the completeness of virome description and sample sequencing depth.
JOURNAL OF VIROLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Aziz M. Al'Khafaji, Jonathan T. Smith, Kiran V. Garimella, Mehrtash Babadi, Victoria Popic, Moshe Sade-Feldman, Michael Gatzen, Siranush Sarkizova, Marc A. Schwartz, Emily M. Blaum, Allyson Day, Maura Costello, Tera Bowers, Stacey Gabriel, Eric Banks, Anthony A. Philippakis, Genevieve M. Boland, Paul C. Blainey, Nir Hacohen
Summary: Full-length RNA-sequencing methods using long-read technologies are limited in throughput. We introduce MAS-ISO-seq, a technique that programmably concatenates cDNAs for long-read sequencing, increasing throughput by >15-fold to nearly 40 million cDNA reads per run. Applied to single-cell RNA sequencing of tumor-infiltrating T cells, MAS-ISO-seq showed a 12- to 32-fold increase in the discovery of differentially spliced genes.
NATURE BIOTECHNOLOGY
(2023)
Article
Virology
Jeremy Di Mattia, Marie-Stephanie Vernerey, Michel Yvon, Elodie Pirolles, Mathilde Villegas, Yahya Gaafar, Heiko Ziebell, Yannis Michalakis, Jean-Louis Zeddam, Stephane Blanc
JOURNAL OF VIROLOGY
(2020)
Review
Biochemistry & Molecular Biology
Yahya Z. A. Gaafar, Heiko Ziebell
ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY
(2020)
Article
Microbiology
Yahya Z. A. Gaafar, Marcel Westenberg, Marleen Botermans, Krizbai Laszlo, Kris De Jonghe, Yoika Foucart, Luca Ferretti, Denis Kutnjak, Anja Pecman, Natasa Mehle, Jan Kreuze, Giovanna Muller, Nikolaos Vakirlis, Despoina Beris, Christina Varveri, Heiko Ziebell
Summary: High-throughput sequencing technologies and bioinformatic analyses are increasingly being used as routine diagnostic tools in plant virology. An interlaboratory comparison study showed high accuracy in virus detection with ribodepleted totRNA, but the bioinformatic pipeline used by each laboratory influenced the correct detection of viruses.
Article
Virology
Yahya Z. A. Gaafar, Frank Rabenstein, Amjad Zia, Abdel-Rhman Z. A. Gaafar, Heiko Ziebell
Summary: A novel virus named FSaV was identified in Germany, with a quadruple genome of negative-sense, single-stranded RNA. It shares high nucleotide identity with IWSV and RHBV, potentially representing a new species of the Tenuivirus genus, with Festuca being the likely original host.
Article
Plant Sciences
Coline Temple, Arnaud G. Blouin, Kris De Jonghe, Yoika Foucart, Marleen Botermans, Marcel Westenberg, Ruben Schoen, Pascal Gentit, Michele Visage, Eric Verdin, Catherine Wipf-Scheibel, Heiko Ziebell, Yahya Z. A. Gaafar, Amjad Zia, Xiao-Hua Yan, Katja R. Richert-Poeggeler, Roswitha Ulrich, Mark Paul S. Rivarez, Denis Kutnjak, Ana Vucurovic, Sebastien Massart
Summary: This study applied high throughput sequencing (HTS) technologies to identify Physostegia chlorotic mottle virus (PhCMoV) in Austria. Through international collaboration, the study characterized PhCMoV in multiple European countries and confirmed its association with severe fruit symptoms on economically important crops.
Article
Biotechnology & Applied Microbiology
Baiome Abdelmaguid Baiome, Xianfeng Ye, Zhongyuan Yuan, Yahya Z. A. Gaafar, Sherif Melak, Hui Cao
Summary: Xenorhabdus indica strain AB produces volatile organic compounds (VOCs) that have significant antifungal activity against Fusarium oxysporum. 85% of the identified volatile compounds were determined to be new compounds, opening up new research opportunities for their properties, effects, and potential applications in pharmaceutical and agricultural industries.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Agriculture, Multidisciplinary
Judith Nora Seeger, Heiko Ziebell, Helmut Saucke
Summary: The impact of Pea necrotic yellow dwarf virus (PNYDV) on faba bean was studied and found to have a more severe effect on nodulation, nitrogen fixation, and yield compared to Pea enation mosaic virus (PEMV). Although one variety showed milder symptoms in the field towards PNYDV, it exhibited similar susceptibility in artificially inoculated field experiments.
JOURNAL OF PLANT DISEASES AND PROTECTION
(2022)
Review
Plant Sciences
Rabia Ilyas, Mareike J. Rohde, Katja R. Richert-Poeggeler, Heiko Ziebell
Summary: Tobamoviruses are well-studied plant viruses, but there is still much to uncover about their interactions with host plants and the molecular mechanisms involved in latent infection.
Article
Plant Sciences
Annelies Haegeman, Yoika Foucart, Kris De Jonghe, Thomas Goedefroit, Maher Al Rwahnih, Neil Boonham, Thierry Candresse, Yahya Z. A. Gaafar, Oscar P. Hurtado-Gonzales, Zala Kogej Zwitter, Denis Kutnjak, Janja Lamovsek, Marie Lefebvre, Martha Malapi, Irena Mavric Plesko, Serkan Onder, Jean-Sebastien Reynard, Ferran Salavert Pamblanco, Olivier Schumpp, Kristian Stevens, Chandan Pal, Lucie Tamisier, Cigdem Ulubas Serce, Inge van Duivenbode, David W. Waite, Xiaojun Hu, Heiko Ziebell, Sebastien Massart
Summary: High-throughput sequencing of plant tissues is a crucial tool for plant virologists to detect plant viruses. However, during the analysis of the data, researchers often neglect sequences without homologies to viruses, which may contain traces of other pathogens. In this study, we re-analyzed RNA-seq datasets and found non-viral plant pathogens, including fungi, insects, and mites. This highlights the potential of using total RNA-seq data for detecting various plant pathogens.
Article
Microbiology
Yahya Z. A. Gaafar, Heiko Ziebell
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2020)