Publications by authors named "Shanyue Zhou"

9 Publications

  • Page 1 of 1

Comparison of mitochondrial genomes from multi-, Bi-, and uninucleate .

Mitochondrial DNA B Resour 2021 Feb 9;6(2):472-474. Epub 2021 Feb 9.

Key Laboratory of Pest Monitoring and Green Management, MOA, Department of Plant Pathology, China Agricultural University, Beijing, China.

Six circular mitochondrial genomes of multi-, bi-, and uninucleate isolates were assembled and found that all the genomes contain 14 conserved protein-coding genes, one ribosomal protein (rps3), and 23 tRNA in the same order. The mitogenome sizes of uninucleate isolates were relatively smaller than binucleate and multinucleate stains. The size variations between uninucleate and multinucleate isolates were from both intergenic and intronic regions, whereas the differences between uninucleate and binucleate isolates were predominantly from intergenic regions. The phylogenetic analysis revealed that strains of the same nucleate types had a closer relationship.
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http://dx.doi.org/10.1080/23802359.2021.1872430DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7889275PMC
February 2021

Evolutionary and genomic comparisons of hybrid uninucleate and nonhybrid Rhizoctonia fungi.

Commun Biol 2021 Feb 15;4(1):201. Epub 2021 Feb 15.

Key Laboratory of Pest Monitoring and Green Management, MOA; Joint Laboratory for International Cooperation in Crop Molecular Breeding; Department of Plant Pathology, China Agricultural University, Beijing, China.

The basidiomycetous fungal genus, Rhizoctonia, can cause severe damage to many plants and is composed of multinucleate, binucleate, and uninucleate species differing in pathogenicity. Here we generated chromosome-scale genome assemblies of the three nuclear types of Rhizoctonia isolates. The genomic comparisons revealed that the uninucleate JN strain likely arose by somatic hybridization of two binucleate isolates, and maintained a diploid nucleus. Homeolog gene pairs in the JN genome have experienced both decelerated or accelerated evolution. Homeolog expression dominance occurred between JN subgenomes, in which differentially expressed genes show potentially less evolutionary constraint than the genes without. Analysis of mating-type genes suggested that Rhizoctonia maintains the ancestral tetrapolarity of the Basidiomycota. Long terminal repeat-retrotransposons displayed a reciprocal correlation with the chromosomal GC content in the three chromosome-scale genomes. The more aggressive multinucleate XN strain had more genes encoding enzymes for host cell wall decomposition. These findings demonstrate some evolutionary changes of a recently derived hybrid and in multiple nuclear types of Rhizoctonia.
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http://dx.doi.org/10.1038/s42003-021-01724-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7884421PMC
February 2021

Genome Sequence Resource of , a Fungal Pathogen Causing Grape White Rot Disease.

Mol Plant Microbe Interact 2020 Jun 29;33(6):787-789. Epub 2020 Apr 29.

College of Plant Health and Medicine, The Key Lab of Integrated Crop Pests Management of Shandong Province, Qingdao Agricultural University, Qingdao, Shandong 266109, China.

Several fungal pathogens cause grape white rot disease and is a predominant pathogen in Chinese vineyards. The disease occurs on leaves, vines, and fruit berries, leading to considerable yield losses and even to total destruction of vineyards. Here, we present the first Pacbio and Illumina-sequenced draft genome assembly of QNYT13637 and its annotation. This genome sequence provides a unique resource that will be a powerful foundation for future research on exploring virulence-related genes, investigating the pathogenicity mechanism of the pathogen, and, finally, improvement of white rot disease management strategies.
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http://dx.doi.org/10.1094/MPMI-02-20-0041-ADOI Listing
June 2020

FgEaf6 regulates virulence, asexual/sexual development and conidial septation in Fusarium graminearum.

Curr Genet 2020 Jun 14;66(3):517-529. Epub 2019 Nov 14.

College of Plant Health and Medicine, The Key Lab of Integrated Crop Pests Management of Shandong Province, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang, Qingdao, 266109, Shandong, China.

Fusarium graminearum is a destructive fungal pathogen and a major cause of Fusarium head blight (FHB) which results in severe grain yield losses and quality reduction. Additionally, the pathogen produces mycotoxins during plant infection, which are harmful to the health of humans and livestock. As it is well known that lysine acetyltransferase complexes play important roles in pathogenesis, the roles of the Eaf6 homolog-containing complex have not been reported in fungal pathogen. In this study, a Eaf6 homolog FgEaf6 was identified in F. graminearum. To investigate the functions of FgEaf6, the gene was deleted using the split-marker method. ΔFgEaf6 mutant exhibited manifold defects in hyphal growth, conidial septation, asexual and sexual reproduction. Moreover, the virulence of the ΔFgEaf6 mutant was drastically reduced in both wheat heads and wheat coleoptiles. However, the FgEaf6 gene deletion did not impact DON production. An FgEaf6-gfp fusion localized to the nucleus and a conserved coiled-coil (C-C) domain was predicted in the sequence. Mutants with deletions in the C-C domain displayed similar defects during development and virulence as observed in the ΔFgEaf6 mutant. Moreover, the truncated gene was cytoplasm localized. In conclusion, the FgEaf6 encodes a nuclear protein, which plays key regulatory roles in hyphal growth, conidial septation, asexual/sexual reproduction, and the virulence of F. graminearum. The C-C is an indispensable domain in the gene. This is the first report on Eaf6 homolog functioning in virulence of fungal pathogen.
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http://dx.doi.org/10.1007/s00294-019-01043-0DOI Listing
June 2020

Comparative acetylome analysis reveals the potential roles of lysine acetylation for DON biosynthesis in Fusarium graminearum.

BMC Genomics 2019 Nov 12;20(1):841. Epub 2019 Nov 12.

State Key Laboratory of Crop Stress Biology for Arid Aeras, Northwest A&F University, Yangling, 712100, Shaanxi, China.

Background: Fusarium graminearum is a destructive fungal pathogen of wheat, barley and other small grain cereals. During plant infection, the pathogen produces trichothecene mycotoxin deoxynivalenol (DON), which is harmful to human and livestock. FgGCN5 encodes a GCN5 acetyltransferase. The gene deletion mutant Fggcn5 failed to produce DON. We assumed that lysine acetylation might play a key regulatory role in DON biosynthesis in the fungus.

Results: In this study, the acetylome comparison between Fggcn5 mutant and wild-type strain PH-1 was performed by using affinity enrichment and high resolution LC-MS/MS analysis. Totally, 1875 acetylated proteins were identified in Fggcn5 mutant and PH-1. Among them, 224 and 267 acetylated proteins were identified exclusively in Fggcn5 mutant and PH-1, respectively. Moreover, 95 differentially acetylated proteins were detected at a significantly different level in the gene deletion mutant:43 were up-regulated and 52 were down-regulated. GO enrichment and KEGG-pathways enrichment analyses revealed that acetylation plays a key role in metabolism process in F. graminearum.

Conclusions: Seeing that the gens playing critical roles in DON biosynthesis either in Fggcn5 mutant or PH-1. Therefore, we can draw the conclusion that the regulatory roles of lysine acetylation in DON biosynthesis in F. graminearum results from the positive and negative regulation of the related genes. The study would be a foundation to insight into the regulatory mechanism of lysine acetylation on DON biosynthesis.
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http://dx.doi.org/10.1186/s12864-019-6227-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6852988PMC
November 2019

Inhibitory effect and possible mechanism of a Pseudomonas strain QBA5 against gray mold on tomato leaves and fruits caused by Botrytis cinerea.

PLoS One 2018 10;13(1):e0190932. Epub 2018 Jan 10.

College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China.

The fungal pathogen Botrytis cinerea causes gray mold disease on various hosts, which results in serious economic losses. Over the past several decades, many kinds of fungicides have been used to successfully control the disease. Meanwhile, the uses of fungicides lead to environmental pollution as well as a potential threat to the human health by the chemical residues in tomato fruit. Also, the gray mold disease is difficult to control with fungicides. Therefore, exploring alternative measures such as biological controls could be the best choice to control the disease and alleviate damages caused by fungicides. In this study, we isolated and identified a novel Pseudomonas strain termed as QBA5 from healthy tomato plant based on the morphological, biochemical characteristics and molecular detection. The antifungal activity assays revealed that, in the presence of QBA5, conidia germination, germ tube elongation and mycelial growth of B. cinerea were significantly inhibited. Most importantly, QBA5 exerted a significant preventive effectiveness against gray mold on tomato fruits and plants. The possible mechanism of QBA5 involved in the inhibition of B. cinerea was investigated. It revealed that the conidia plasma membrane of B. cinerea was severely damaged by QBA5. Further, four different antifungal compounds in the supernatant of QBA5 were separated by preparative high performance liquid chromatography (PHPLC). Overall, the data indicate that there is a considerable potential for QBA5 to reduce the damage caused by gray mold disease on tomato.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0190932PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5761960PMC
February 2018

Systematic analysis of the lysine acetylome in Fusarium graminearum.

BMC Genomics 2016 12 13;17(1):1019. Epub 2016 Dec 13.

College of Agronomy and Plant Protection, The Key Lab of Integrated Crop Pests Management of Shandong Province, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang, Qingdao, Shandong, 266109, China.

Background: Lysine acetylation in proteins is a ubiquitous and conserved post-translational modification, playing a critical regulatory role in almost every aspect of living cells. Although known for many years, its function remains elusive in Fusarium graminearum, one of the most important necrotrophic plant pathogens with huge economic impact.

Results: By the combination of affinity enrichment and high-resolution LC-MS/MS analysis, large-scale lysine acetylome analysis was performed. In total, 577 lysine acetylation sites matched to 364 different proteins were identified. Bioinformatics analysis of the acetylome showed that the acetylated proteins are involved in a wide range of cellular functions and exhibit diverse subcellular localizations. Remarkably, 10 proteins involved in the virulence or DON (deoxynivalenol) biosynthesis were found to be acetylated, including 4 transcription factors, 4 protein kinases and 2 phosphatases. Protein-protein interaction network analysis revealed that acetylated protein complexes are involved in diversified interactions.

Conclusions: This work provides the first comprehensive survey of a possible lysine acetylome in F. graminearum and reveals previously unappreciated roles of lysine acetylation in the regulation of diverse biological processes. This work provides a resource for functional analysis of acetylated proteins in filamentous fungi.
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http://dx.doi.org/10.1186/s12864-016-3361-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5153868PMC
December 2016

Molecular evolution and functional divergence of tubulin superfamily in the fungal tree of life.

Sci Rep 2014 Oct 23;4:6746. Epub 2014 Oct 23.

1] NWAFU-PU Joint Research Center, State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China [2] Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA.

Microtubules are essential for various cellular activities and β-tubulins are the target of benzimidazole fungicides. However, the evolution and molecular mechanisms driving functional diversification in fungal tubulins are not clear. In this study, we systematically identified tubulin genes from 59 representative fungi across the fungal kingdom. Phylogenetic analysis showed that α-/β-tubulin genes underwent multiple independent duplications and losses in different fungal lineages and formed distinct paralogous/orthologous clades. The last common ancestor of basidiomycetes and ascomycetes likely possessed two paralogs of α-tubulin (α1/α2) and β-tubulin (β1/β2) genes but α2-tubulin genes were lost in basidiomycetes and β2-tubulin genes were lost in most ascomycetes. Molecular evolutionary analysis indicated that α1, α2, and β2-tubulins have been under strong divergent selection and adaptive positive selection. Many positively selected sites are at or adjacent to important functional sites and likely contribute to functional diversification. We further experimentally confirmed functional divergence of two β-tubulins in Fusarium and identified type II variations in FgTub2 responsible for function shifts. In this study, we also identified δ-/ε-/η-tubulins in Chytridiomycetes. Overall, our results illustrated that different evolutionary mechanisms drive functional diversification of α-/β-tubulin genes in different fungal lineages, and residues under positive selection could provide targets for further experimental study.
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http://dx.doi.org/10.1038/srep06746DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5381371PMC
October 2014

Molecular cloning and differential expression of an gamma-aminobutyrate transaminase gene, OsGABA-T, in rice (Oryza sativa) leaves infected with blast fungus.

J Plant Res 2006 Nov 8;119(6):663-9. Epub 2006 Aug 8.

Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural University, Beijing, People's Republic of China.

gamma-Aminobutyrate transaminase (GABA-T) catalyzes the conversion of GABA to succinic semialdehyde. Using differential display PCR and cDNA library screening, a full-length GABA-T cDNA (OsGABA-T) was isolated from rice (Oryza sativa) leaves infected with an incompatible race of Magnaporthe grisea. The deduced amino acid sequence comprises 483 amino acid residues and shares 85-69% identity with GABA-T sequences from other plants. OsGABA-T expression is induced by blast fungus infection, mechanical wounding and ultraviolet radiation in rice leaves and is not detected in normal rice organs. This gene is also induced by defense signal molecules such as salicylic acid and abscisic acid, but not by jasmonic acid. Our data suggest that OsGABA-T (GABA shunt) may play a role in restricting the levels of cell death during the host-pathogen interaction.
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http://dx.doi.org/10.1007/s10265-006-0018-3DOI Listing
November 2006