Dickeya dianthicola emerged from a potato culture area exhibiting a wide diversity of pectinolytic pathogens in northern Morocco

2020 ◽  
Author(s):  
Said Oulghazi ◽  
Mohieddine Moumni ◽  
Slimane Khayi ◽  
Kevin Robic ◽  
Sohaib Sarfraz ◽  
...  
Keyword(s):  
Species Diversity ◽  
Complete Genome ◽  
Draft Genome ◽  
Potential Threat ◽  
Circular Chromosome ◽  
Population Sampling ◽  
Potato Culture ◽  
Oxford Nanopore ◽  
Genome Analyses ◽  
Oxford Nanopore Technologies

Abstract Background: Dickeya and Pectobacterium are pectinolytic pathogens that cause damage to many plants including major crops. Emergence of D. solani and re-emergence D. dianthicola were recently observed in potato fields in several continents. The purpose of this work was to describe the species diversity of Dickeya and Pectobacterium collected from potato fields in Northern Morocco, where Dickeya potato pathogens have not been isolated until recently. Results: Along three years, 119 pathogens belonging to Pectobacterium and Dickeya genera were isolated from three potato culture areas and characterized using selective PCR and gapA gene sequencing. Out of them, 19% belonged to P. versatile, 3% to P. carotovorum, 5% to P. polaris, 56% to P. brasiliense, while 17% to D. dianthicola. The taxonomic assignations were confirmed by draft genome analyses of representative isolates belonging to the collected species. D. dianthicola were isolated from a unique area where a wide species diversity of pectinolytic pathogens was also observed. In potato maceration assay, D. dianthicola isolates were more aggressive than Pectobacterium isolates, a feature that should alert stakeholders of a potential threat linked to the emergence of D. dianthicola in this country. By combining Oxford Nanopore Technologies (ONT) and Illumina technologies, the sequence of the complete genome of D. dianthicola LAR.16.03.LID was obtained. A unique circular chromosome of 4,976,211 bp codes for 4,223 predicted proteins. Comparison of the three complete genomes of D. dianthicola strains RNS049, ME23 and LAR.16.03.LID revealed a highly conserved synteny and the occurrence of strain-specific regions associated with the presence of mobile elements. Conclusion: By combining population sampling and genomics, this study highlighted the ecological context from which D. dianthicola emerged in Morocco. Furthermore, the first complete genome of a D. dianthicola strain isolated in Northern Morocco will constitute a reference genome for investigating the dynamics of the emerging D. dianthicola pathogens in this country.

scholarly journals Diversity of Pectobacteriaceae Species in Potato Growing Regions in Northern Morocco

2020 ◽  
Vol 8 (6) ◽  
pp. 895 ◽  
Author(s):  
Saïd Oulghazi ◽  
Mohieddine Moumni ◽  
Slimane Khayi ◽  
Kévin Robic ◽  
Sohaib Sarfraz ◽  
...  
Keyword(s):  
Species Diversity ◽  
Complete Genome ◽  
Draft Genome ◽  
Epidemiological Studies ◽  
Gene Marker ◽  
Oxford Nanopore ◽  
Causative Agents ◽  
Genome Analyses ◽  
Oxford Nanopore Technologies

Dickeya and Pectobacterium pathogens are causative agents of several diseases that affect many crops worldwide. This work investigated the species diversity of these pathogens in Morocco, where Dickeya pathogens have only been isolated from potato fields recently. To this end, samplings were conducted in three major potato growing areas over a three-year period (2015–2017). Pathogens were characterized by sequence determination of both the gapA gene marker and genomes using Illumina and Oxford Nanopore technologies. We isolated 119 pathogens belonging to P. versatile (19%), P. carotovorum (3%), P. polaris (5%), P. brasiliense (56%) and D. dianthicola (17%). Their taxonomic assignation was confirmed by draft genome analyses of 10 representative strains of the collected species. D. dianthicola were isolated from a unique area where a wide species diversity of pectinolytic pathogens was observed. In tuber rotting assays, D. dianthicola isolates were more aggressive than Pectobacterium isolates. The complete genome sequence of D. dianthicola LAR.16.03.LID was obtained and compared with other D. dianthicola genomes from public databases. Overall, this study highlighted the ecological context from which some Dickeya and Pectobacterium species emerged in Morocco, and reported the first complete genome of a D. dianthicola strain isolated in Morocco that will be suitable for further epidemiological studies.

scholarly journals Complete Genome Sequence of the Type Strain Pectobacterium punjabense SS95, Isolated from a Potato Plant with Blackleg Symptoms

2020 ◽  
Vol 9 (32) ◽  
Author(s):  
Sohaib Sarfraz ◽  
Saïd Oulghazi ◽  
Jérémy Cigna ◽  
Shahbaz Talib Sahi ◽  
Kashif Riaz ◽  
...  
Keyword(s):  
Complete Genome ◽  
Type Strain ◽  
Gc Content ◽  
Illumina Miseq ◽  
Blackleg Disease ◽  
Circular Chromosome ◽  
Content Type ◽  
Potato Plants ◽  
Oxford Nanopore ◽  
Oxford Nanopore Technologies

ABSTRACT Pectobacterium punjabense is a newly described species causing blackleg disease in potato plants. Therefore, by the combination of long (Oxford Nanopore Technologies, MinION) and short (Illumina MiSeq) reads, we sequenced the complete genome of P. punjabense SS95T, which contains a circular chromosome of 4.793 Mb with a GC content of 50.7%.

scholarly journals Complete Genome Sequence of Pasteurella multocida HuN001, a Capsular Type A Strain from a Human

2021 ◽  
Vol 10 (26) ◽  
Author(s):  
Lin Lin ◽  
Chunhui Li ◽  
Fei Wang ◽  
Xueying Wang ◽  
Yue Zhang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Pasteurella Multocida ◽  
Sputum Sample ◽  
Capsular Type ◽  
Circular Chromosome ◽  
Content Type ◽  
Oxford Nanopore ◽  
Oxford Nanopore Technologies

Here, we report the complete genome sequence of clinical Pasteurella multocida strain HuN001, which was cultured from a sputum sample from a patient with pneumonia. Oxford Nanopore Technologies sequencing provided a complete genome sequence of P. multocida HuN001, which contains a 2,287,216-bp circular chromosome with an average G+C content of 40.33%.

scholarly journals Complete Genome Sequence of Neisseria gonorrhoeae Multilocus Sequence Type ST7363 Isolated from Thailand

2021 ◽  
Vol 10 (41) ◽  
Author(s):  
Thitima Cherdtrakulkiat ◽  
Thidathip Wongsurawat ◽  
Piroon Jenjaroenpun ◽  
Sawannee Sutheeworapong ◽  
Wanna Leelawiwat ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Sequence Type ◽  
Circular Chromosome ◽  
Content Type ◽  
Oxford Nanopore ◽  
Siriraj Hospital ◽  
Oxford Nanopore Technologies

A Neisseria gonorrhoeae multilocus sequence type (MLST) ST7363 strain was isolated from a patient at the Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand, in 2010 and completely sequenced. This strain is susceptible to ceftriaxone and cefixime. A complete circular chromosome and circular plasmids were assembled from combined Oxford Nanopore Technologies (ONT) and Illumina sequencing.

scholarly journals Complete Closed Genome Sequence of the Inulin-Utilizing Lactiplantibacillus plantarum Strain Lp900, Obtained Using a Hybrid Nanopore and Illumina Assembly

2021 ◽  
Vol 10 (17) ◽  
Author(s):  
Jori Fuhren ◽  
Reindert Nijland ◽  
Michiel Wels ◽  
Jos Boekhorst ◽  
Michiel Kleerebezem
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Dna Sequence ◽  
Genome Sequence ◽  
De Novo ◽  
Circular Chromosome ◽  
Content Type ◽  
Diverse Species ◽  
Oxford Nanopore ◽  
Oxford Nanopore Technologies

Lactiplantibacillus plantarum is a genetically and phenotypically diverse species of lactic acid bacteria. We announce the hybrid de novo assembly of Oxford Nanopore Technologies and Illumina DNA sequence reads, producing a closed circular chromosome of 3,206,992 bp and six plasmids of the inulin-utilizing L. plantarum strain Lp900.

scholarly journals Complete Genome Sequence of Pseudomonas otitidis Strain MrB4, Isolated from Lake Biwa in Japan

2020 ◽  
Vol 9 (16) ◽  
Author(s):  
Kentaro Miyazaki ◽  
Erina Hase ◽  
Tomomasa Maruya
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Type Strain ◽  
Lake Biwa ◽  
Draft Genome ◽  
Circular Chromosome ◽  
Content Type ◽  
Near Shore ◽  
Single Circular Chromosome

We isolated Pseudomonas otitidis strain MrB4 from the near-shore area of Lake Biwa in Japan and generated its complete genome sequence. MrB4 possesses a single circular chromosome of 6,089,454 bp, with ∼97% average nucleotide identity to the P. otitidis type strain MCC10330 (draft genome).

scholarly journals Draft Genome Sequence of Pandrug-Resistant Pseudomonas aeruginosa SPA03, Isolated from a Patient with Benign Prostatic Hyperplasia

2021 ◽  
Vol 10 (22) ◽  
Author(s):  
Chanakya Pachi Pulusu ◽  
Balaram Khamari ◽  
Manmath Lama ◽  
Arun Sai Kumar Peketi ◽  
Prakash Kumar ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Benign Prostatic Hyperplasia ◽  
Sequence Data ◽  
Draft Genome ◽  
Prostatic Hyperplasia ◽  
Illumina Hiseq ◽  
Content Type ◽  
Oxford Nanopore ◽  
Long Read ◽  
Oxford Nanopore Technologies

The draft genome of pandrug-resistant Pseudomonas aeruginosa strain SPA03, which belongs to global high-risk sequence type 357 (ST357) and was isolated from a patient with benign prostatic hyperplasia, is presented in this report. The genome assembly was generated by combining short-read Illumina HiSeq-X Ten and long-read Oxford Nanopore Technologies MinION sequence data using the Unicycler assembler.

scholarly journals Complete Genome Sequence of Campylobacter armoricus CA639, Which Carries Two Plasmids, Compiled Using Oxford Nanopore and Illumina Sequencing Technologies

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Amine M. Boukerb ◽  
Julien Schaeffer ◽  
Joëlle Serghine ◽  
Gregory Carrier ◽  
Françoise S. Le Guyader ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Illumina Sequencing ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Sequence Data ◽  
Hybrid Approach ◽  
Circular Chromosome ◽  
Sequencing Technologies ◽  
Oxford Nanopore

As determined by a hybrid approach combining Oxford Nanopore MinION and Illumina MiniSeq sequence data, Campylobacter armoricus strain CA639 harbored a circular chromosome of 1,688,169 bp with a G+C content of 28.47% and two plasmids named pCA639-1 and pCA639-2, with lengths of 51,123 and 28,139 bp, and G+C contents of 26.5% and 28.45%, respectively.

scholarly journals Draft Genome Sequence of an Environmental Vibrio cholerae Strain, 2012Env-25, Obtained Using Nanopore Sequencing Technology

2020 ◽  
Vol 9 (32) ◽  
Author(s):  
V Lyju Jose ◽  
Matthew T. Pileggi ◽  
Meer Taifur Alam ◽  
Afsar Ali ◽  
Adam C. N. Wong
Keyword(s):  
Vibrio Cholerae ◽  
Genome Sequence ◽  
Bacterial Species ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Cholerae Strain ◽  
Pathogenic Potential ◽  
Content Type ◽  
Oxford Nanopore ◽  
Oxford Nanopore Technologies

ABSTRACT Vibrio cholerae is a halophilic Gram-negative bacterial species and the etiological agent of cholera. Here, we report the draft genome sequence of an environmental V. cholerae strain, 2012Env-25, obtained using Oxford Nanopore Technologies (ONT) to provide insights into the ecology, evolution, and pathogenic potential of this bacterium.

scholarly journals Complete Genome Sequence of Tetracycline-Resistant Serratia liquefaciens S1, Isolated from Mixed Greens, Obtained Using Illumina MiSeq and Oxford Nanopore MinION Sequencing

2020 ◽  
Vol 9 (19) ◽  
Author(s):  
Maria Stein ◽  
Erik Brinks ◽  
Jana Rathje ◽  
Gyu-Sung Cho ◽  
Charles M. A. P. Franz
Keyword(s):  
Complete Genome Sequence ◽  
Complete Genome ◽  
Illumina Miseq ◽  
Circular Chromosome ◽  
Short Read ◽  
Content Type ◽  
Serratia Liquefaciens ◽  
Oxford Nanopore ◽  
Long Read ◽  
Single Circular Chromosome

Serratia liquefaciens strain S1 was isolated from mixed greens and sequenced with short-read Illumina MiSeq technology and long-read MinION technology. Hybrid sequence assembly generated a complete single circular chromosome and two extrachromosomal contigs, which together encoded 5,098 proteins, 85 tRNAs, and 22 rRNAs.

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