Article
Entomology
Marika Rossi, Luciana Galetto, Nicola Bodino, Jessica Beltramo, Silvia Gamalero, Mattia Pegoraro, Domenico Bosco, Cristina Marzachi
Summary: Flavescence doree (FD) is a serious grapevine disease caused by uncultivable bacteria transmitted by hemipteran insects. Two different strains, FD-C and FD-D, are associated with the disease, with FD-C outcompeting FD-D during infection. In the laboratory insect vector Euscelidius variegatus, single infection with either strain was more common than mixed infection, suggesting competition among strains. Understanding the mechanisms regulating the epidemiology of FD strains is important for disease management.
Article
Multidisciplinary Sciences
Nami Lee, Mira Choi, Woori Kim, Soonkyu Hwang, Yongjae Lee, Ji Hun Kim, Gahyeon Kim, Hyeseong Kim, Suhyung Cho, Sun Chang Kim, Bernhard Palsson, Kyoung-Soon Jang, Byung-Kwan Cho
Summary: Streptomyces species have been studied for their medically important secondary metabolites, with considerable diversity between strains. This study reevaluated ten strains of Streptomyces venezuelae, revealing misclassification in seven of the strains. By mining secondary metabolite biosynthetic gene clusters and screening metabolites, a total of 59 secondary metabolites were identified.
Article
Infectious Diseases
Benjamin Youenou, Patricia Martins Simoes, Anne Tristan, Eric Farfour, Clemence Beauruelle, Camille Kolenda, Anne-Gaelle Ranc, Francois Vandenesch, Frederic Laurent, Celine Dupieux
Summary: This study describes the presence of linezolid-resistant MRSA strains carrying the cfr(B) gene in the French National Reference Centre for staphylococci. The strains showed resistance to linezolid but susceptibility to tedizolid, and carried the cfr(B) gene on the same chromosomal transposon. This finding highlights the risk of horizontal transfer of oxazolidinone resistance genes in Staphylococcus aureus.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Biochemical Research Methods
Hao Wu, Dan Wang, Feng Gao
Summary: Pan-genome analysis is widely used to study species evolution and genetic diversity, particularly in bacteria. However, the influence of strain selection on the accuracy and reliability of pan-genome results is not well understood. This study found that including confounding strains in pan-genome analyses of Bacillus subtilis can significantly affect the quality and accuracy of the results, emphasizing the importance of removing biases from such strains in the data processing stage to achieve a closer representation of the true pan-genome landscape.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biotechnology & Applied Microbiology
Amila S. N. W. Pahalagedara, Ruy Jauregui, Paul Maclean, Eric Altermann, Steve Flint, Jon Palmer, Gale Brightwell, Tanushree Barua Gupta
Summary: This study identified the potential of soil Clostridium spp. to produce novel antimicrobial compounds with unknown structures, laying the foundation for the discovery and characterization of potent antimicrobials. The findings expand the current knowledge base and encourage further research into bioactive compound production in members of the genus Clostridium.
Article
Multidisciplinary Sciences
Mahtab Moghaddam, Martin F. Wojciechowski, Shahrokh Kazempour-Osaloo
Summary: In this study, the plastid genomes of four Astragalus species were analyzed, including genome organization, codon usage, nucleotide diversity, prediction of RNA editing, and more. Comparative analysis revealed hypervariable regions and potential molecular markers. Positive selection signatures were found in several genes. These findings contribute to our understanding of chloroplast genome structure, evolutionary dynamics, and phylogenetic relationships in the Astragalus genus.
Article
Agriculture, Multidisciplinary
Jacson Ferreira, Claudia Alves Almeida, Thays Benites Camargo Pereira, Gabriel Favara, Ivan Paulo Bedendo
Summary: A study was conducted to detect and classify a phytoplasma strain causing disease in acerola bushes, identifying it as a member of the 'Candidatus Phytoplasma pruni' - related strain (subgroup 16SrIII-F). The phytoplasma induced similar symptoms in healthy plants and this is the first report of the presence of the 16SrIII-F subgroup in the Brazilian agroecosystem.
Article
Microbiology
Raquel P. Miranda, Paula C. G. Turrini, Dora T. Bonadio, Marcelo M. Zerillo, Arthur P. Berselli, Silvana Creste, Marie-Anne Van Sluys
Summary: An integrative approach combining genomics, transcriptomics, and cell biology was used to study leaf scald disease in sugarcane. Genome sequences of four Brazilian Xanthomonas albilineans strains with different virulence capabilities were compared, revealing variations in aggressiveness index and genome structure. This study reveals that leaf scald disease is not caused by a single determinant factor.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biology
Christophe Debonneville, Lea Mandelli, Justine Brodard, Raphael Groux, David Roquis, Olivier Schumpp
Summary: This research describes the genome sequencing of a phytoplasma causing grapevine Flavescence doree and reveals its specific characteristics compared to other phytoplasmas. The availability of this genome provides a basis for studying the pathogenicity mechanisms and evolution of the Flavescence doree phytoplasma.
Article
Biochemistry & Molecular Biology
Mikang Sim, Jongin Lee, Daehong Kwon, Daehwan Lee, Nayoung Park, Suyeon Wy, Younhee Ko, Jaebum Kim
Summary: RBRC is a new read-clustering algorithm that improves de novo microbial genome assembly by accurately estimating read proximity. It has shown excellent performance in simulation-based evaluation and application to real genomes, improving assembly quality without additional sequencing data. RBRC can be used to generate high-quality microbial strain genome assemblies when genome assemblies of related strains are available, and to upgrade existing microbial genome assemblies when additional sequencing data, such as long reads, are difficult to obtain.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Plant Sciences
Xue-Min Xu, Zhen Wei, Jun-Zhe Sun, Qing-Fei Zhao, Yang Lu, Zhen-Long Wang, Shi-Xin Zhu
Summary: This study analyzed the chloroplast genomes of 43 Leontopodium and closely related genera. It found that the chloroplast genomes of Filago, Gamochaeta, and Leontopodium were well-conserved, but differed in terms of length and certain regions. The molecular phylogenetic results were inconsistent with the previous taxonomic system based on morphology.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biology
Jing Chen, Jinbiao Jiao, Xuemei Yuan, Xiaohong Huang, Lei Huang, Lingyun Lin, Wenlin Yin, Jiayun Yao, Haiqi Zhang
Summary: In this study, the complete mitochondrial genomes of four Pelodiscus sinensis strains were reported, and the nucleotide composition and variable sites were analyzed. The genetic variations among the four strains were described through comparative analysis. Phylogenetic analysis determined the evolutionary relationship of P. sinensis strains with other Trionychidae species. Overall, this study provides genetic information for understanding the genetic variations and evolutionary relationship of P. sinensis strains, which is important for bioprospecting and conservation.
Article
Microbiology
Nicoletta Contaldo, Jelena Stepanovic, Francesco Pacini, Assunta Bertaccini, Bojan Duduk
Summary: By studying the genetic variability of 'Ca. P. solani' strains in different host species and geographic areas, 25 molecular variants were identified, showing a correlation with their distribution and year of infection. The crucial question in 'Ca. P. solani' epidemiology is to trace back the epidemic cycle of the infections.
Article
Plant Sciences
Peng Chen, Lichuan Chen, Xia Ye, Bin Tan, Xianbo Zheng, Jun Cheng, Wei Wang, Qiqi Yang, Yu Zhang, Jidong Li, Jiancan Feng
Summary: In this study, eight putative effector proteins of the jujube witches' broom (JWB) phytoplasma were identified, and one of them, Zaofeng6, was found to induce witches' broom symptoms and shoot proliferation. Zaofeng6 was also shown to interact with ZjTCP7 and decrease its expression, which in turn affected the expression of genes in the strigolactone signaling pathway. These findings contribute to our understanding of the jujube witches' broom disease.
HORTICULTURE RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Daria D. Nikolaeva, Mikhail S. Gelfand, Sofya K. Garushyants
Summary: The ribosome, responsible for protein biosynthesis, is highly conserved in structure and composition across species. However, some bacteria may lack certain ribosomal proteins, especially in organisms with significantly reduced genomes. The large subunit of the ribosome shows less conservation in protein composition compared to the small subunit.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Agronomy
Milena Petriccione, Anna Magri, Maria Gaudiano, Marco Scortichini
Summary: This study evaluated the expression levels of candidate reference genes in Xaj under three abiotic stresses and identified two reference genes sufficient for effective normalization of RT-qPCR data in all tested conditions. Results showed the importance of validating reference genes in each experimental condition to avoid misinterpretation of target gene expression levels.
Article
Biochemistry & Molecular Biology
Giulia Tarquini, Laura Pagliari, Paolo Ermacora, Rita Musetti, Giuseppe Firrao
Summary: The GPGV virus triggers the PTGS pathway in plants as a defense mechanism, while the coat protein of GPGV has the ability to suppress RNA silencing.
MOLECULAR PLANT-MICROBE INTERACTIONS
(2021)
Article
Plant Sciences
F. Savian, S. Prencipe, N. Filippini, L. Nari, M. Martini, P. Ermacora, D. Spadaro
Summary: Research has shown that Kiwifruit vine decline syndrome may be caused by an interaction between multiple soil-borne pathogens, mainly oomycetes, and waterlogging. Experiment results demonstrate that P. chamaehyphon is pathogenic to KVDS, raising questions about the role of waterlogging in the etiology of KVDS.
Article
Agronomy
Amanda C. Saville, Federico La Spada, Roberto Faedda, Quirico Migheli, Bruno Scanu, Paolo Ermacora, Giovanna Gilardi, Giorgia Fedele, Vitorrio Rossi, Nicolo Lenzi, Antonino Testa, Mohamed Bechir Allagui, Marwa Moumni, Enza Dongiovanni, Fatma Zohra Rekad, David E. L. Cooke, Antonella Pane, Santa O. Cacciola, Jean B. Ristaino
Summary: This genetic study of Phytophthora infestans samples collected from Italy, Algeria, and Tunisia identified four clonal lineages and highlighted potential new sources of introduction into Italy.
Article
Virology
Giulia Tarquini, Paolo Ermacora, Giuseppe Firrao
Summary: The severity of GLMD disease symptoms is associated with sequence variation in the GPGV genome, particularly at the 3'-end of the movement protein gene. Experimental results confirmed the critical role of the GPGV-MP C-terminus in determining the fate of the infection, as suggested by comparative sequence analysis.
Article
Microbiology
Gaia Carminati, Vittorio Brusa, Alberto Loschi, Paolo Ermacora, Marta Martini
Summary: In this study, the distribution and multiplication dynamics of a specific phytoplasma strain in tomato plants were investigated. Significant differences were found in phytoplasma concentration among different plant tissues, with the roots showing the highest concentration. This suggests that roots are the ideal tissue for early, sensitive, and robust phytoplasma diagnosis.
Article
Plant Sciences
Giulia Tarquini, Marta Martini, Simone Maestri, Giuseppe Firrao, Paolo Ermacora
Summary: This study reveals the cause of severe diseases affecting the 'Lamon bean' through sequencing analysis, showing that mixed infections of cucumber mosaic virus, bean yellow mosaic virus, and other viruses are responsible.
Review
Agronomy
Giulia Tarquini, Paolo Ermacora, Marta Martini, Giuseppe Firrao
Summary: Since its discovery in 2012, the grapevine Pinot gris virus (GPGV) has been discussed as the causative agent of grapevine leaf mottling and deformation (GMLD) syndrome. Over the past 10 years, evidence has emerged regarding the role of genetic and varietal diversity in the virus and host, as well as their interaction in antiviral defense and virus-mediated defense suppression. However, there is still a challenge in fully understanding the molecular events and environmental conditions that can affect viral infection severity and symptom display. The widespread spread of GPGV raises concerns about its potential as an emerging threat to the grapevine industry.
Article
Plant Sciences
Erica Cesari, Silverio Pachioli, Alessia L'Aurora, Valeria Scala, Nicoletta Pucci, Stefania Loreti, Marco Scortichini
Summary: In May 2019, a pomegranate orchard in Central Italy showed severe symptoms of black pitting, cankers, and leaf wilting. Through various tests, it was identified that the cause of the disease was Pseudomonas syringae. Artificial inoculations confirmed that the isolates caused similar symptoms in pomegranate, lemon, and pear. The study also showed the effectiveness of a formulation containing zinc, copper, manganese, chitosan, and garlic powder in reducing the severity of the disease in the field.
JOURNAL OF PHYTOPATHOLOGY
(2023)
Review
Virology
Giulia Tarquini, Mattia Dall'Ara, Paolo Ermacora, Claudio Ratti
Summary: Environmental changes and global warming can lead to the emergence of unknown viruses, which are spread through trade in plant products. Viruses pose a major threat to viticulture and the wine industry. Current management strategies focus on preventing virus introduction through the use of virus-free planting material and agrochemicals, but there is a need for alternative sustainable control methods.
Article
Plant Sciences
Erica Cesari, Fabio Marocchi, Alessia L'Aurora, Nicoletta Pucci, Valeria Scala, Stefania Loreti, Marco Scortichini
Summary: Copper-resistant strains of Pseudomonas syringae pv. actinidiae, the causal agent of kiwifruit bacterial canker, have been isolated for the first time in Italy and Europe.
JOURNAL OF PHYTOPATHOLOGY
(2023)
Proceedings Paper
Agricultural Engineering
G. Mian, G. Cipriani, S. Saro, M. Martini, P. Ermacora
Summary: Kiwifruit vine decline syndrome (KVDS) has been affecting Italian kiwifruit cultivation for nearly 10 years, causing symptoms like root rot and plant decline. Testing different kiwifruit species can help identify genotypes resistant to KVDS.
X INTERNATIONAL SYMPOSIUM ON KIWIFRUIT
(2022)
Article
Management
Giovanni Mian, Luca Iseppi, Giacomo Traversari, Paolo Ermacora, Guido Cipriani, Federico Nassivera
Summary: This study aims to examine the motivations behind the purchase intentions of kiwifruits and found that neophobia, consumer attitude, and quality attributes influence behavioral intention. This has important managerial implications for developing new marketing strategies for kiwifruit companies.
QUALITY-ACCESS TO SUCCESS
(2022)
Article
Horticulture
Giovanni Mian, Guido Cipriani, Simone Saro, Marta Martini, Paolo Ermacora
Summary: Kiwifruit Vine Decline Syndrome (KVDS) is causing significant losses in Italian kiwifruit cultivation. The syndrome is caused by soil-borne pathogens and waterlogging, resulting in root decay and canopy decline. Tolerant rootstocks have been identified as a promising tool for controlling the disease. Three potentially resistant genotypes have been identified after a two-year study.
Article
Plant Sciences
Laura Pagliari, Giulia Tarquini, Alberto Loschi, Sara Buoso, Gregor Kapun, Paolo Ermacora, Rita Musetti
Summary: The study revealed that the grapevine Pinot gris virus (GPGV) induces deformities in the endoplasmic reticulum of infected plants, which are exploited by the virus for replication. The upregulation of endoplasmic reticulum stress-related genes further confirms the significance of the ER in the interaction between grapevine and GPGV.
FUNCTIONAL PLANT BIOLOGY
(2021)