scholarly journals A Complete Genome Sequence of the Wood Stem Endophyte Bacillus velezensis BY6 Strain Possessing Plant Growth-Promoting and Antifungal Activities

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Ping Zhang ◽  
Jian Diao ◽  
Guangqiang Xie ◽  
Ling Ma ◽  
Lihai Wang
Keyword(s):  
Secondary Metabolite ◽  
Single Molecule ◽  
Complete Genome ◽  
Pathogenic Fungus ◽  
Gc Content ◽  
Endophytic Bacterium ◽  
Gene Clusters ◽  
Bacillus Velezensis ◽  
Sequencing Platform ◽  
Plant Growth Promoting

An endophytic bacterium Bacillus velezensis BY6 was isolated from the wood stems of healthy Populus davidiana × P. alba var. pyramidalis (PdPap). The BY6 strain can inhibit pathogenic fungus Alternaria alternate in PdPap and promote growth of PdPap seedlings. In the present study, we used the Pacific Biosciences long-read sequencing platform, a single-molecule real-time (SMRT) technology for strain BY6, to perform complete genome sequencing. The genome size was 3,898,273 bp, the number of genes was 4,045, and the average GC content was 47.33%. A complete genome of strain BY6 contained 110 secondary metabolite gene clusters. Nine of the secondary metabolite gene clusters exhibited antifungal activity and promoted growth functions primarily involved in the synthesis of surfactin, bacteriocins, accumulated iron ions, and related antibiotics. Gene clusters provide genetic resources for biotechnology and genetic engineering, and enhance understanding of the relationship between microorganisms and plants.

scholarly journals Complete Genome Sequence of Bacillus velezensis GQJK49, a Plant Growth-Promoting Rhizobacterium with Antifungal Activity

2017 ◽  
Vol 5 (35) ◽  
Author(s):  
Jinjin Ma ◽  
Hu Liu ◽  
Kai Liu ◽  
Chengqiang Wang ◽  
Yuhuan Li ◽  
...  
Keyword(s):  
Antifungal Activity ◽  
Plant Growth ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gene Clusters ◽  
Bacillus Velezensis ◽  
Lycium Barbarum ◽  
Plant Growth Promoting ◽  
Growth Promoting

ABSTRACT Bacillus velezensis GQJK49 is a plant growth-promoting rhizobacterium with antifungal activity, which was isolated from Lycium barbarum L. rhizosphere. Here, we report the complete genome sequence of B. velezensis GQJK49. Twelve gene clusters related to its biosynthesis of secondary metabolites, including antifungal and antibacterial antibiotics, were predicted.

scholarly journals Complete Genome Sequence of Pandoraea pnomenusa TF-18, a Multidrug-Resistant Organism Isolated from the Rhizosphere of Rice (Oryza sativa L. subsp. japonica)

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Mihnea R. Mangalea ◽  
Emily K. Luna ◽  
Janet Ziegle ◽  
Christine Chang ◽  
Angela M. Bosco-Lauth ◽  
...  
Keyword(s):  
Single Molecule ◽  
Complete Genome ◽  
Oryza Sativa L ◽  
Gc Content ◽  
Multidrug Resistant ◽  
Selective Medium ◽  
Resistant Organism ◽  
Smrt Sequencing ◽  
Sequencing Technology ◽  
Content Type

Pandoraea pnomenusa strain TF-18 was isolated from the roots of rice seedlings on selective medium containing four classes of antibiotics for isolation of Burkholderia pseudomallei. Using Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing technology, we report here a complete genome of 5,499,432 bases, a GC content of 64.8%, and 4,849 coding sequences.

scholarly journals Complete Genome Sequence of Bacillus paralicheniformis MDJK30, a Plant Growth-Promoting Rhizobacterium with Antifungal Activity

2017 ◽  
Vol 5 (25) ◽  
Author(s):  
Yun Wang ◽  
Hu Liu ◽  
Kai Liu ◽  
Chengqiang Wang ◽  
Hailin Ma ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Root Rot ◽  
Complete Genome ◽  
Gene Clusters ◽  
Content Type ◽  
Bacillus Paralicheniformis ◽  
Plant Growth Promoting ◽  
Growth Promoting ◽  
Metabolism Gene

ABSTRACT Bacillus paralicheniformis MDJK30 was isolated from the rhizosphere of a peony. It could control the pathogen of peony root rot. Here, we report the complete genome sequence of B. paralicheniformis MDJK30. Eleven secondary metabolism gene clusters were predicted.

scholarly journals A Rare Thioquinolobactin Siderophore Present in a Bioactive Pseudomonas sp. DTU12.1

2019 ◽  
Vol 11 (12) ◽  
pp. 3529-3533
Author(s):  
Pavelas Sazinas ◽  
Morten Lindqvist Hansen ◽  
May Iren Aune ◽  
Marie Højmark Fischer ◽  
Lars Jelsbak
Keyword(s):  
Gene Cluster ◽  
Secondary Metabolite ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Plant Pathogens ◽  
Gene Clusters ◽  
Fungal Species ◽  
Antagonistic Activity ◽  
Evolutionary Origins

Abstract Many of the soil-dwelling Pseudomonas species are known to produce secondary metabolite compounds, which can have antagonistic activity against other microorganisms, including important plant pathogens. It is thus of importance to isolate new strains of Pseudomonas and discover novel or rare gene clusters encoding bioactive products. In an effort to accomplish this, we have isolated a bioactive Pseudomonas strain DTU12.1 from leaf-covered soil in Denmark. Following genome sequencing with Illumina and Oxford Nanopore technologies, we generated a complete genome sequence with the length of 5,943,629 base pairs. The DTU12.1 strain contained a complete gene cluster for a rare thioquinolobactin siderophore, which was previously described as possessing bioactivity against oomycetes and several fungal species. We placed the DTU12.1 strain within Pseudomonas gessardii subgroup of fluorescent pseudomonads, where it formed a distinct clade with other Pseudomonas strains, most of which also contained a complete thioquinolobactin gene cluster. Only two other Pseudomonas strains were found to contain the gene cluster, though they were present in a different phylogenetic clade and were missing a transcriptional regulator of the whole cluster. We show that having the complete genome sequence and establishing phylogenetic relationships with other strains can enable us to start evaluating the distribution and evolutionary origins of secondary metabolite clusters.

scholarly journals Complete Genome Sequence of Pseudomonas syringae pv. lapsa Strain ATCC 10859, Isolated from Infected Wheat

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Jun Kong ◽  
Hongshan Jiang ◽  
Baiyun Li ◽  
Wenjun Zhao ◽  
Zhihong Li ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gc Content ◽  
Gene Clusters ◽  
Strain Atcc ◽  
Circular Chromosome ◽  
Coding Sequences

Pseudomonas syringae pv. lapsa is a pathovar of Pseudomonas syringae that can infect wheat. The complete genome of P. syringae pv. lapsa strain ATCC 10859 contains a 5,918,899-bp circular chromosome with 4,973 coding sequences, 16 rRNAs, 69 tRNAs, and an average GC content of 59.13%. The analysis of this genome revealed several gene clusters that are related to pathogenesis and virulence.

scholarly journals Complete Genome Sequence of Streptomyces sp. Sge12, Which Produces Antibacterial and Fungicidal Activities

2017 ◽  
Vol 5 (21) ◽  
Author(s):  
Jianguo Xu ◽  
Min Xu ◽  
Kai Liu ◽  
Qinyin Peng ◽  
Meifeng Tao
Keyword(s):  
Forest Soil ◽  
Secondary Metabolite ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gene Clusters ◽  
Antimicrobial Activities ◽  
Gram Positive ◽  
Streptomyces Sp ◽  
Gram Positive Bacteria

ABSTRACT Streptomyces sp. Sge12 was isolated from forest soil and exhibited remarkable antimicrobial activities against selected fungi and Gram-positive bacteria. Here, we report the complete genome sequence of this strain, which contains 37 putative secondary metabolite gene clusters.

scholarly journals Complete Genome Sequence of the Cytokinin-Producing Biocontrol Strain Pseudomonas fluorescens G20-18

2021 ◽  
Vol 10 (30) ◽  
Author(s):  
Tue K. Nielsen ◽  
Mengistu F. Mekureyaw ◽  
Lars H. Hansen ◽  
Mette H. Nicolaisen ◽  
Thomas G. Roitsch ◽  
...  
Keyword(s):  
Plant Growth ◽  
Pseudomonas Fluorescens ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Gene Clusters ◽  
Circular Chromosome ◽  
Content Type ◽  
Plant Growth Promoting ◽  
Growth Promoting

Here, we report the complete genome sequence of the cytokinin-producing plant growth-promoting strain Pseudomonas fluorescens G20-18. The complete genome assembly resulted in a single, circular chromosome of 6.48 Mbp and harbors several secondary metabolite biosynthesis gene clusters that are potentially involved in its plant growth-promoting function.

scholarly journals Genomic, Antimicrobial, and Aphicidal Traits of Bacillus velezensis ATR2, and Its Biocontrol Potential against Ginger Rhizome Rot Disease Caused by Bacillus pumilus

2021 ◽  
Vol 10 (1) ◽  
pp. 63
Author(s):  
Leiqin Liang ◽  
Yajuan Fu ◽  
Sangsang Deng ◽  
Yan Wu ◽  
Meiying Gao
Keyword(s):  
Pathogenic Bacteria ◽  
Plant Immunity ◽  
Pathogenic Fungus ◽  
Pathogenic Fungi ◽  
Gene Clusters ◽  
Bacillus Velezensis ◽  
Ginger Rhizome ◽  
Biocontrol Potential ◽  
Rot Disease ◽  
Rhizome Rot

Ginger rhizome rot disease, caused by the pathogen Bacilluspumilus GR8, could result in severe rot of ginger rhizomes and heavily threaten ginger production. In this study, we identified and characterized a new Bacillus velezensis strain, designated ATR2. Genome analysis revealed B. velezensis ATR2 harbored a series of genes closely related to promoting plant growth and triggering plant immunity. Meanwhile, ten gene clusters involved in the biosynthesis of various secondary metabolites (surfactin, bacillomycin, fengycin, bacillibactin, bacilysin, difficidin, macrolactin, bacillaene, plantazolicin, and amylocyclicin) and two clusters encoding a putative lipopeptide and a putative phosphonate which might be explored as novel bioactive compounds were also present in the ATR2 genome. Moreover, B. velezensis ATR2 showed excellent antagonistic activities against multiple plant pathogenic bacteria, plant pathogenic fungi, human pathogenic bacteria, and human pathogenic fungus. B. velezensis ATR2 was also efficacious in control of aphids. The antagonistic compound from B. velezensis ATR2 against B.pumilus GR8 was purified and identified as bacillomycin D. In addition, B. velezensis ATR2 exhibited excellent biocontrol efficacy against ginger rhizome rot disease on ginger slices. These findings showed the potential of further applications of B. velezensis ATR2 as a biocontrol agent in agricultural diseases and pests management.

scholarly journals A detailed in silico analysis of secondary metabolite biosynthesis clusters in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

2019 ◽  
Author(s):  
Carolyn Graham-Taylor ◽  
Lars G Kamphuis ◽  
Mark Derbyshire
Keyword(s):  
Secondary Metabolites ◽  
Host Range ◽  
Secondary Metabolite ◽  
Sclerotinia Sclerotiorum ◽  
Plant Pathogens ◽  
Pathogenic Fungus ◽  
Gene Clusters ◽  
Sequence Diversity ◽  
Broad Host Range ◽  
Data Set

Abstract Background The broad host range pathogen Sclerotinia sclerotiorum infects over 400 plant species and causes substantial yield losses in crops worldwide. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but little is known about the secondary metabolite repertoire of S. sclerotiorum. In this study, we predicted secondary metabolite biosynthetic gene clusters in the genome of S. sclerotiorum and analysed their expression during infection of Brassica napus using an existing transcriptome data set. We also investigated their sequence diversity among a panel of 25 previously published S. sclerotiorum isolate genomes.Results We identified 80 putative secondary metabolite clusters. Over half of the clusters contained at least three transcriptionally coregulated genes. Comparative genomics revealed clusters homologous to clusters in the closely related plant pathogen Botrytis cinerea for production of carotenoids, hydroxamate siderophores, DHN melanin and botcinic acid. We also identified putative phytotoxin clusters that can potentially produce the polyketide sclerin and an epipolythiodioxopiperazine. Secondary metabolite clusters were enriched in subtelomeric genomic regions, and those containing paralogues showed a particularly strong association with repeats. The positional bias we identified was borne out by intraspecific comparisons that revealed putative secondary metabolite genes suffered more presence / absence polymorphisms and exhibited a significantly higher sequence diversity than other genes.Conclusions These data suggest that S. sclerotiorum produces numerous secondary metabolites during plant infection and that their gene clusters undergo enhanced rates of mutation, duplication and recombination in subtelomeric regions. The microevolutionary regimes leading to S. sclerotiorum secondary metabolite diversity have yet to be elucidated. Several potential phytotoxins documented in this study provide the basis for future functional analyses.

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