scholarly journals Draft Whole Genome Sequence Analyses on Pseudomonas syringae pv. actinidiae Hypersensitive Response Negative Strains Detected from Kiwifruit Bleeding Sap Samples

2018 ◽  
Vol 108 (5) ◽  
pp. 552-560 ◽  
Author(s):  
Enrico Biondi ◽  
Alan Zamorano ◽  
Ernesto Vega ◽  
Stefano Ardizzi ◽  
Davide Sitta ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Genome Sequence ◽  
Hypersensitive Response ◽  
Time Window ◽  
Gene Clusters ◽  
Whole Genome Sequence ◽  
Optimal Time ◽  
Whole Genome ◽  
Isolation And Identification ◽  
The Difference

Kiwifruit bleeding sap samples, collected in Italian and Chilean orchards from symptomatic and asymptomatic plants, were evaluated for the presence of Pseudomonas syringae pv. actinidiae, the causal agent of bacterial canker. The saps were sampled during the spring in both hemispheres, before the bud sprouting, during the optimal time window for the collection of an adequate volume of sample for the early detection of the pathogen, preliminarily by molecular assays, and then through its direct isolation and identification. The results of molecular analyses showed more effectiveness in the P. syringae pv. actinidiae detection when compared with those of microbiological analyses through the pathogen isolation on the nutritive and semiselective media selected. The bleeding sap analyses allowed the isolation and identification of two hypersensitive response (HR) negative and hypovirulent P. syringae pv. actinidiae strains from different regions in Italy. Moreover, multilocus sequence analysis (MLSA) and whole genome sequence (WGS) were carried out on selected Italian and Chilean P. syringae pv. actinidiae virulent strains to verify the presence of genetic variability compared with the HR negative strains and to compare the variability of selected gene clusters between strains isolated in both countries. All the strains showed the lack of argK and coronatine gene clusters as reported for the biovar 3 P. syringae pv. actinidiae strains. Despite the biologic differences obtained in the tobacco bioassays and in pathogenicity assays, the MLSA and WGS analyses did not show significant differences between the WGS of the HR negative and HR positive strains; the difference, on the other hand, between PAC_ICE sequences of Italian and Chilean P. syringae pv. actinidiae strains was confirmed. The inability of the hypovirulent strains IPV-BO 8893 and IPV-BO 9286 to provoke HR in tobacco and the low virulence shown in this host could not be associated with mutations or recombinations in T3SS island.

scholarly journals Whole Genome Sequence of Dermacoccus abyssi MT1.1 Isolated from the Challenger Deep of the Mariana Trench Reveals Phenazine Biosynthesis Locus and Environmental Adaptation Factors

Marine Drugs ◽  
2020 ◽  
Vol 18 (3) ◽  
pp. 131 ◽  
Author(s):  
Wael M. Abdel-Mageed ◽  
Bertalan Juhasz ◽  
Burhan Lehri ◽  
Ali S. Alqahtani ◽  
Imen Nouioui ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Biological Activities ◽  
Radical Scavenging ◽  
Gene Clusters ◽  
2D Nmr ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Isolation And Identification ◽  
Mariana Trench ◽  
Stress Related Genes

Dermacoccus abyssi strain MT1.1T is a piezotolerant actinobacterium that was isolated from Mariana Trench sediment collected at a depth of 10898 m. The organism was found to produce ten dermacozines (A‒J) that belonged to a new phenazine family and which displayed various biological activities such as radical scavenging and cytotoxicity. Here, we report on the isolation and identification of a new dermacozine compound, dermacozine M, the chemical structure of which was determined using 1D and 2D-NMR, and high resolution MS. A whole genome sequence of the strain contained six secondary metabolite-biosynthetic gene clusters (BGCs), including one responsible for the biosynthesis of a family of phenazine compounds. A pathway leading to the biosynthesis of dermacozines is proposed. Bioinformatic analyses of key stress-related genes provide an insight into how the organism adapted to the environmental conditions that prevail in the deep-sea.

scholarly journals Analysis of Draft Genome Resources of Thirty-Three Canadian Strains of Pseudomonas syringae pv. tomato isolated between 1992 and 2008 Reveals achromobactin virulence cluster that is absent in the reference strain DC3000

2021 ◽  
Author(s):  
James Tambong ◽  
Renlin Xu ◽  
Diane Cuppels ◽  
Julie T Chapados ◽  
suzanne Gerdis ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Draft Genome ◽  
Genome Mining ◽  
Gene Clusters ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequences ◽  
Protein Coding ◽  
Genome Data ◽  
Bacterial Speck Disease

Pseudomonas syringae pv. tomato is the causal agent of bacterial speck disease of field and greenhouse tomato plants. Only one Canadian whole genome sequence of this economically important pathogen is publicly available in NCBI GenBank. Here, we report 33 whole genome sequences of Canadian strains of P. syringae pv. tomato isolated in Ontario, Canada, between 1992 and 2008. The genome sequences exhibited average nucleotide identity values of 98.64-98.72 % with P. syringae pv. tomato ICMP 2844PT and DC3000, validating the taxonomic standing of these Canadian strains. The genome sizes ranged from 6.20-6.39 Mbp with G+C content of 58.6% and comprised 5,889-6,166 protein-coding sequences (CDSs). The strains had pan- and core-genomes of 6808 and 4,993 gene clusters, respectively. Genome mining of the strains for virulence factors identified typical adherence genes, proteins related to antiphagocytosis, secretion system apparatuses and effectors. Also, partial or complete achromobactin biosynthetic cluster and iron transport genes were identified in all the Canadian strains but absent in P. syringae pv. tomato DC3000 or ICMP 2844 (pathotype). These new whole genome data of Canadian strains of P. syringae pv. tomato could be useful resources in understanding the evolution of this pathogen.

scholarly journals Whole genome sequence of Streptomyces colonosanans strain MUSC 93JT isolated from mangrove forest in Malaysia

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Hooi-Leng Ser ◽  
Jodi Woan-Fei Law ◽  
Wen-Si Tan ◽  
Wai-Fong Yin ◽  
Kok-Gan Chan
Keyword(s):  
Bioactive Compounds ◽  
Genome Sequence ◽  
Antioxidant Activities ◽  
Human Cancer ◽  
Wide Spectrum ◽  
Gene Clusters ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Selective Toxicity ◽  
Human Cancer Cell Lines

Under the family Actinobacteria, streptomycetes are ubiquitous in nature, producing a wide spectrum of bioactive compounds including antibacterial, antioxidant, anticancer and immunomodulatory properties. During a screening programme in Malaysia, Streptomyces colonosanans MUSC 93JT was isolated as a novel Streptomyces sp. from the mangrove soil in Sarawak. The strain exhibited potent antioxidant activities and cytotoxic activity against several human cancer cell lines. Due to these data, the strain was subjected to whole genome sequencing to uncover its genomic potential and further improve the understanding of the strain. The genome of MUSC 93JT consists of 7,015,076 bp (G + C content of 69.90%), carrying a total of 5,859 protein coding genes. Analysis using a bioinformatics tool, antiSMASH predicted a total of four biosynthetic gene clusters which displayed similarity of more than 70% to known gene clusters and one of which was associated with the production of a natural protectant, ectoine. Displaying selective toxicity that kills only cancer cells, ectoine has showed its potential to be developed as therapeutic agents for humans. Altogether, the current project clearly highlights the importance of under-explored environment like mangrove in natural product discovery. The availability of whole genome sequence MUSC 93JT warrants subsequent in-depth investigation and optimization for the production of bioactive compounds which can be exploited for the health and wellbeing of mankind.

scholarly journals Biotechnological and Ecological Potential of Micromonospora provocatoris sp. nov., a Gifted Strain Isolated from the Challenger Deep of the Mariana Trench

Marine Drugs ◽  
2021 ◽  
Vol 19 (5) ◽  
pp. 243
Author(s):  
Wael M. Abdel-Mageed ◽  
Lamya H. Al-Wahaibi ◽  
Burhan Lehri ◽  
Muneera S. M. Al-Saleem ◽  
Michael Goodfellow ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Gene Clusters ◽  
2D Nmr ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Whole Genome ◽  
Mariana Trench ◽  
Chemical Structures ◽  
Desferrioxamine B ◽  
Challenger Deep

A Micromonospora strain, isolate MT25T, was recovered from a sediment collected from the Challenger Deep of the Mariana Trench using a selective isolation procedure. The isolate produced two major metabolites, n-acetylglutaminyl glutamine amide and desferrioxamine B, the chemical structures of which were determined using 1D and 2D-NMR, including 1H-15N HSQC and 1H-15N HMBC 2D-NMR, as well as high resolution MS. A whole genome sequence of the strain showed the presence of ten natural product-biosynthetic gene clusters, including one responsible for the biosynthesis of desferrioxamine B. Whilst 16S rRNA gene sequence analyses showed that the isolate was most closely related to the type strain of Micromonospora chalcea, a whole genome sequence analysis revealed it to be most closely related to Micromonospora tulbaghiae 45142T. The two strains were distinguished using a combination of genomic and phenotypic features. Based on these data, it is proposed that strain MT25T (NCIMB 15245T, TISTR 2834T) be classified as Micromonospora provocatoris sp. nov. Analysis of the genome sequence of strain MT25T (genome size 6.1 Mbp) revealed genes predicted to responsible for its adaptation to extreme environmental conditions that prevail in deep-sea sediments.

scholarly journals Whole-genome sequence of a novel, mangrove-derived streptomycete, Streptomyces malaysiense strain MUSC 136T

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Hooi-Leng Ser ◽  
Wen-Si Tan ◽  
Wai-Fong Yin ◽  
Kok-Gan Chan ◽  
Learn-Han Lee
Keyword(s):  
Genome Sequence ◽  
Mangrove Forest ◽  
Streptomyces Griseus ◽  
Prediction Method ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters

Since the discovery of streptomycin from Streptomyces griseus in the early 1940s, streptomycetes from various environments have been studied thoroughly for the ability to produce bioactive compounds including antibacterial, antioxidant, anticancer, antifungal as well as immunomodulatory properties. Previously identified as a novel strain from a mangrove forest in Malaysia, Streptomyces malaysiense MUSC 136T was selected for genome sequencing to explore its genomic potential. The genomic size comprises of 7,963,326 bp with a G+C content of 72.2% and a total of 6,614 proteincoding genes. As an attempt to investigate the types of biosynthetic gene cluster present in the MUSC 136T, the whole genome sequence was analyzed with a bioinformatics tool, antibiotics & Secondary Metabolite Analysis Shell (antiSMASH). Using the “strict” prediction method, a total of seven biosynthetic gene clusters which displayed similarity of more than 80% to known gene clusters including ectoine, geosmin as well as desferrioxamine. Apart from emphasizing the importance of streptomycetes from unique environments like mangrove forest, the current study serves as a foundation for future studies on the role of specific genes present in biosynthetic gene clusters which enables the exploitation of MUSC 136T to synthesize important and valuable compounds.

scholarly journals Whole genome sequence of Desulfovibrio magneticus strain RS-1 revealed common gene clusters in magnetotactic bacteria

2009 ◽  
Vol 19 (10) ◽  
pp. 1801-1808 ◽  
Author(s):  
H. Nakazawa ◽  
A. Arakaki ◽  
S. Narita-Yamada ◽  
I. Yashiro ◽  
K. Jinno ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Gene Clusters ◽  
Magnetotactic Bacteria ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Common Gene

scholarly journals Draft Genome Sequence of Streptomyces albidoflavus 09MW18-IS, Cultivated from the Atlantic Ocean off the Coast of Virginia

2022 ◽  
Author(s):  
Indu Sharma ◽  
Masuud Washington ◽  
Jeremy Chen See ◽  
Rola Suleiman ◽  
Regina Lamendella
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Gene Clusters ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Content Type ◽  
Streptomyces Albidoflavus

We report a draft genome sequence for Streptomyces albidoflavus strain 09MW18-IS, isolated from the Atlantic slope off the coast of Virginia. The whole-genome sequence will provide novel insights into biosynthetic gene clusters and ecological adaptation in an oligotrophic environment.

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