Ning Zhang

Chinese Academy of Agricultural Sciences

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Jing Luo

Rutgers, The State University of New Jersey

Emily Walsh

Rutgers, The State University of New Jersey

David M. Geiser

Pennsylvania State University

P.W. Crous

Westerdijk Fungal Biodiversity Institute

Andrew N. Miller

University of Illinois Urbana-Champaign

Conrad L. Schoch

National Center for Biotechnology Information

M. Catherine Aime

Purdue University West Lafayette

Kevin D. Hyde

Mae Fah Luang University

Takayuki Aoki

National Agriculture and Food Research Organization

Paul M. Kirk

Royal Botanic Gardens, Kew

Cooperative Institutions

Chinese Academy of Sciences

156

Cornell University

103

Rutgers, The State University of New Jersey

Agricultural Research Service

United States Department of Agriculture

University of Chinese Academy of Sciences

Harvard University

Plant (United States)

National Institutes of Health

Chinese Academy of Agricultural Sciences

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Phylogenomic Analysis of a 55.1-kb 19-Gene Dataset Resolves a MonophyleticFusariumthat Includes theFusarium solaniSpecies Complex

Phytopathology (2020)

David M. Geiser Abdullah M. S. Al‐Hatmi Takayuki Aoki Tsutomu Arie Virgilio Balmas

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option available.

Monophyly

Polyphyly

Fusarium solani

10.1094/phyto-08-20-0330-le

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Citations (156)

Impact of Complete Revascularization in the ISCHEMIA Trial

Journal of the American College of Cardiology (2023)

Gregg W. Stone Ziad A. Ali Sean M. O’Brien Grace L. Rhodes Philippe Généreux

10.1016/j.jacc.2023.06.015

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Citations (24)

Typification and phylogenetic study ofPhyllosticta ampelicidaandP. vaccinii

Mycologia (2013)

Ke Zhang Ning Zhang Lei Cai

Phyllosticta ampelicida, the causal agent of black rot of grape, and P. vaccinii, the pathogen of early rot of cranberry, are neotypified and epitypified respectively by strains from American Type Culture Collection (ATCC). Morphological characteristics of these cultures are described and compared with type specimens and the original descriptions. Based on phylogeny inferred from DNA sequences of internal transcribed spacer (ITS), actin (ACT), translation elongation factor 1-alpha (TEF1) and glyceraldehyde-3-phosphate dehydrogenase (GPDH), traditionally defined P. ampelicida (teleomorph Guignardia bidwellii) is revealed to be a species complex including P. ampelicida sensu stricto, typified in this study, and two additional species, one of which is described as new P. parthenocissi. Our results did not support an anamorph/teleomorph connection between P. vaccinii and G. vaccinii in that they represent different species. Multilocus sequence data from the neotype and epitype were generated and deposited in GenBank.

Typification

Species complex

10.3852/12-392

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Citations (23)

A patched1 gene homologue participates in female differentiation of Cynoglossus semilaevis

Gene Expression Patterns (2022)

Qi Qian Zhongdian Dong Ning Zhang Changwei Shao Wenteng Xu

Patched

Sexual Differentiation

10.1016/j.gep.2022.119265

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Citations (0)

Genome wide analysis of the transition to pathogenic lifestyles in Magnaporthales fungi

Scientific Reports (2018)

Ning Zhang Guohong Cai Dana C. Price Jo Anne Crouch Pierre Gladieux

The rice blast fungus Pyricularia oryzae (syn. Magnaporthe oryzae, Magnaporthe grisea), a member of the order Magnaporthales in the class Sordariomycetes, is an important plant pathogen and a model species for studying pathogen infection and plant-fungal interaction. In this study, we generated genome sequence data from five additional Magnaporthales fungi including non-pathogenic species, and performed comparative genome analysis of a total of 13 fungal species in the class Sordariomycetes to understand the evolutionary history of the Magnaporthales and of fungal pathogenesis. Our results suggest that the Magnaporthales diverged ca. 31 millon years ago from other Sordariomycetes, with the phytopathogenic blast clade diverging ca. 21 million years ago. Little evidence of inter-phylum horizontal gene transfer (HGT) was detected in Magnaporthales. In contrast, many genes underwent positive selection in this order and the majority of these sequences are clade-specific. The blast clade genomes contain more secretome and avirulence effector genes, which likely play key roles in the interaction between Pyricularia species and their plant hosts. Finally, analysis of transposable elements (TE) showed differing proportions of TE classes among Magnaporthales genomes, suggesting that species-specific patterns may hold clues to the history of host/environmental adaptation in these fungi.

Pyricularia

Horizontal Gene Transfer

Magnaporthe

Host adaptation

10.1038/s41598-018-24301-6

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Citations (31)

The Influence of Emerging Atmospheric Organophosphorus Flame Retardant from Land Source Emissions on the East China Sea

Haibo Ma He Jian Haoyue Fan Ning Zhang Shijie Song

Organophosphate flame retardants (OPFRs) as emerging POPs pose a new challenge to the marine environment due to their toxicity and persistence. Persistent Organic Pollutants (POPs) emitted from land sources can be loaded to adjacent seawaters via atmospheric transport and deposition, contaminating the marine ecological environment. This study explores the contributions of OPFR emissions from different land sources and sectors to its contamination of the East China Sea, a heavily polluted marine ecosystem by OPFR, using a novel atmospheric transport model(ChnMETOP)for POPs and a marine food web model. The results show that the major land sources causing OPFR pollution in the East China Sea were situated in the Yangtze River Delta (YRD) and the middle reach areas of China's Yangtze River, confirming that source proximity made most significant contributions to OPFR pollution in the East China Sea. We examined the significance of primary emission sectors in OPFR distribution in the East China Sea. We show that, among those OPFR emission sectors, industrial emissions accounted for the highest modeled OPFR levels in the seawaters, followed by the OPFR usage process in textile, plastic, and rubber products. We also assessed the bioaccumulation of OPFR in the marine food web of the East China Sea and the potential risk in commercial fish consumers. Our result reveals low-risk exposure based on the risk limit of OPFR via dietary fish ingestion. However, the risk might increase if OPFRs are continuously bioaccumulated in the biotic and released into the abiotic marine environment. This study simultaneously identified both the source locations and emission sectors, thereby bearing important policy implications in mitigating OPFR pollution in the East China Sea marine environment.

China sea

10.2139/ssrn.4471751

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Toward monophyletic generic concepts in Magnaporthales: species with Harpophora asexual states

Mycologia (2015)

Jing Luo Emily Walsh Ning Zhang

We investigated the phylogenetic relationships among Magnaporthales fungi with harpophora-like asexual states based on DNA sequences of ITS, MCM7, RPB1 and TEF1 genes. The results indicated that these species are polyphyletic. Based on the four-gene phylogeny, the type species of Harpophora, H. radicicola, belongs to Gaeumannomyces and thus Harpophora is treated as a synonym of Gaeumannomyces. In addition, a monotypic new genus, Falciphora, is established based on F. oryzae, previous referred as Harpophora oryzae.

Polyphyly

Monophyly

Synonym (taxonomy)

Dothideomycetes

10.3852/14-302

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Citations (21)

Design, Synthesis and Seed Germination Inhibition Activity of Quinoline-6-sulfonamide Compounds

Chinese Journal of Organic Chemistry (2022)

Zhi-You Huang Ning Zhang Han-Wen Zuo Xu-Qi Zeng Han Liu

Quinoline

Sulfonamide

10.6023/cjoc202206040

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Citations (3)

Mycobiome Analysis of Tall Fescue Grass under Drought Stress Using the Illumina MiSeq and Oxford Nanopore Technology MinION

Phytobiomes Journal (2023)

Glen Groben Bruce B. Clarke Lee J. Kerkhof Stacy A. Bonos William A. Meyer

The effects that mycobiomes have on physiological traits in turfgrasses are poorly understood. Drought tolerance, an economically and ecologically important trait, can be influenced by symbiotic fungi. In this two-year study, we evaluated the mycobiome associated with tall fescue exposed to prolonged periods of drought stress in a rainout shelter. Twelve plants, comprising six sets of half-sibs (progenies having one parent in common), one exhibiting a drought-tolerant phenotype and the other a drought-susceptible phenotype, were selected for analysis each year. The mycobiomes associated with the shoot, root, and rhizosphere soil were evaluated for each tall fescue half-sib pair using both short-read Illumina MiSeq and long-read Oxford Nanopore Technology (ONT) MinION sequencing pipelines. Both platforms sequenced portions of the fungal nuclear ribosomal RNA genes. The Illumina MiSeq sequenced the internal transcribed spacer region (ITS, 600 bp), while the ONT MinION covered the small subunit, ITS, and partial large subunit (4,600 bp). Both sequencing pipelines revealed that the mycobiomes associated with the roots, shoots, and soil were significantly different. The ONT MinION pipeline identified more diverse fungal lineages and had higher taxonomic resolution than the Illumina pipeline. Our results also indicated that root pathogens may play a more important role than endophytic or mycorrhizal symbionts in tall fescue drought stress tolerance.

Minion

Illumina dye sequencing

Drought stress

Drought Tolerance

10.1094/pbiomes-10-22-0071-r

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Citations (2)

In-vitro antibacterial effect of tea polyphenols combined with common antibiotics on multidrug-resistant Klebsiella pneumoniae

Minerva Medica (2020)

Ning Zhang Wugao Liu Kejian Qian

BACKGROUND: To investigate the bactericidal effect of tea polyphenols on multidrug resistant Klebsiella pneumoniae and its antibacterial efficacy in combination with common antibiotics, and to explore its mechanism.METHODS: The VITEK 2 Compact automatic microbial identification system was used to identify 20 strains of Klebsiella pneumoniae isolated from clinical isolates. The KB method was used to detect sensitivity of common drugs such as imipenem, piperacillin, piperacillin/tazobactam and cefepime, cefotaxime and ceftazidime; agar dilution method was used for detection of minimum inhibitory concentration (MIC) of tea polyphenols; the variation of the diameter of the antibacterial ring after different concentrations (0.25 MIC, 0.5 MIC) of tea polyphenols in combination with commonly used antibacterial drugs was detected to judge the feasibility of the inhibition of the multidrug-resistant Klebsiella pneumoniae by the combination of tea polyphenols and commonly used antibacterial drugs. Congo red and crystal violent staining was used to detect the impact on bacterial biofilm formation and extracellular mucus-like substance (slime).RESULTS: The K-B values of 20 strains of Klebsiella pneumoniae against common antibiotics were 6-14 mm; the MIC of tea polyphenols against 20 strains of multi-drug resistant Klebsiella pneumoniae was 1024 ug/mL; 0.5 MIC tea polyphenols can increase the diameter of the bacteriostatic ring of imipenem, piperacillin, piperacillin/tazobactam, cefepime, cefotaxime and ceftazidime by 3-28 mm. Tea polyphenols at sub-inhibitory concentrations significantly inhibited the production of Klebsiella pneumoniae biofilm and extracellular mucus (slime).CONCLUSIONS: Tea polyphenols could be used in combination with commonly used antibiotics (imipenem, piperacillin, piperacillin/tazobactam, cefepime, cefotaxime and ceftazidime) against multidrug-resistant Klebsiella pneumoniae. It has a synergistic bactericidal effect and affects the formation of bacterial outer membrane and the production of extracellular slime-like substances (slime).

Cefepime

Agar dilution

10.23736/s0026-4806.20.06459-9

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Citations (8)