Diversity of Pectobacteriaceae Species in Potato Growing Regions in Northern Morocco

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.

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

10.21203/rs.2.22648/v1 ◽

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.

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

Microbiology Resource Announcements ◽

10.1128/mra.00420-20 ◽

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%.

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

Microbiology Resource Announcements ◽

10.1128/mra.00395-21 ◽

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%.

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

Microbiology Resource Announcements ◽

10.1128/mra.00336-21 ◽

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.

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

Microbiology Resource Announcements ◽

10.1128/mra.00625-20 ◽

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.

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Complete Genome Sequence of a Canadian Klebsiella michiganensis Strain, Obtained Using Oxford Nanopore Technologies Sequencing

Microbiology Resource Announcements ◽

10.1128/mra.00960-20 ◽

2020 ◽

Vol 9 (46) ◽

Author(s):

Mingsong Kang ◽

John Chmara ◽

Marc-Olivier Duceppe ◽

Beverley Phipps-Todd ◽

Hongsheng Huang

Keyword(s):

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Opportunistic Pathogen ◽

Treatment Facility ◽

Content Type ◽

Hospital Acquired Infections ◽

Oxford Nanopore ◽

Hospital Acquired ◽

Oxford Nanopore Technologies

ABSTRACT Klebsiella michiganensis is a Gram-negative opportunistic pathogen that is associated with many hospital-acquired infections in humans. Here, we report the complete genome sequence of a K. michiganensis strain isolated from a Canadian wastewater treatment facility.

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Complete Genome Sequences of Bordetella pertussis Clinical Isolate FR5810 and Reference Strain Tohama from Combined Oxford Nanopore and Illumina Sequencing

Microbiology Resource Announcements ◽

10.1128/mra.01207-18 ◽

2018 ◽

Vol 7 (19) ◽

Cited By ~ 4

Author(s):

Valérie Bouchez ◽

Sarah Louise Baines ◽

Sophie Guillot ◽

Sylvain Brisse

Keyword(s):

Clinical Isolate ◽

Bordetella Pertussis ◽

Complete Genome ◽

Reference Strain ◽

Sequence Data ◽

Hybrid Approach ◽

Genome Sequences ◽

Content Type ◽

Oxford Nanopore ◽

Oxford Nanopore Technologies

Here, we describe the complete genome sequences of two Bordetella pertussis strains, FR5810, a clinical isolate recovered from the respiratory tract of an infant, and Tohama, a key reference strain for the species. Sequences were obtained using a hybrid approach combining Oxford Nanopore Technologies MinION and Illumina NextSeq 500 sequence data.

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Complete Genome Sequences of Four Putatively Antibiotic-Producing Bacteria Isolated from Soil in Arkansas, USA

Microbiology Resource Announcements ◽

10.1128/mra.00745-21 ◽

2022 ◽

Author(s):

Ruth Plymale ◽

Griffin Hopkins ◽

Taylor Johnson ◽

Taylor Savage ◽

Danielle Schaal

Keyword(s):

Complete Genome ◽

Soil Bacteria ◽

Hybrid Approach ◽

Antimicrobial Compounds ◽

Research Experience ◽

Genome Sequences ◽

Valuable Source ◽

Oxford Nanopore ◽

Complete Genomes ◽

Oxford Nanopore Technologies

Soil bacteria can be a valuable source of antimicrobial compounds. Here, we report the complete genomes of four soil bacteria that were isolated by undergraduate microbiology students as part of a course-based research experience. These genomes were assembled using a hybrid approach combining paired-end Illumina reads with Oxford Nanopore Technologies MinION reads.

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A draft genome of grass pea (Lathyrus sativus), a resilient diploid legume

10.1101/2020.04.24.058164 ◽

2020 ◽

Author(s):

Peter M. F. Emmrich ◽

Abhimanyu Sarkar ◽

Isaac Njaci ◽

Gemy George Kaithakottil ◽

Noel Ellis ◽

...

Keyword(s):

Draft Genome ◽

Lathyrus Sativus ◽

Grass Pea ◽

Total Length ◽

Gene Space ◽

Mate Pair ◽

Oxford Nanopore ◽

Long Read ◽

Paired End Sequencing ◽

Oxford Nanopore Technologies

AbstractWe have sequenced the genome of grass pea (Lathyrus sativus), a resilient diploid (2n=14) legume closely related to pea (Pisum sativum). We determined the genome size of the sequenced European accession (LS007) as 6.3 Gbp. We generated two assemblies of this genome, i) EIv1 using Illumina PCR-free paired-end sequencing and assembly followed by long-mate-pair scaffolding and ii) Rbp using Oxford Nanopore Technologies long-read sequencing and assembly followed by polishing with Illumina paired-end data. EIv1 has a total length of 8.12 Gbp (including 1.9 billion Ns) and scaffold N50 59,7 kbp. Annotation has identified 33,819 high confidence genes in the assembly. Rbp has a total length of 6.2 Gbp (with no Ns) and a contig N50 of 155.7 kbp. Gene space assessment using the eukaryote BUSCO database showed completeness scores of 82.8 % and 89.8%, respectively.

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High quality genome assembly of the amitochondriate eukaryote Monocercomonoides exilis

Microbial Genomics ◽

10.1099/mgen.0.000745 ◽

2021 ◽

Vol 7 (12) ◽

Author(s):

Sebastian Cristian Treitli ◽

Priscila Peña-Diaz ◽

Paweł Hałakuc ◽

Anna Karnkowska ◽

Vladimír Hampl

Keyword(s):

Genome Assembly ◽

Complete Genome ◽

Untranslated Region ◽

Gene Prediction ◽

Draft Genome ◽

High Quality ◽

Kozak Sequence ◽

Oxford Nanopore ◽

High Quality Genome ◽

Polyadenylation Signals

Monocercomonoides exilis is considered the first known eukaryote to completely lack mitochondria. This conclusion is based primarily on a genomic and transcriptomic study which failed to identify any mitochondrial hallmark proteins. However, the available genome assembly has limited contiguity and around 1.5 % of the genome sequence is represented by unknown bases. To improve the contiguity, we re-sequenced the genome and transcriptome of M. exilis using Oxford Nanopore Technology (ONT). The resulting draft genome is assembled in 101 contigs with an N50 value of 1.38 Mbp, almost 20 times higher than the previously published assembly. Using a newly generated ONT transcriptome, we further improve the gene prediction and add high quality untranslated region (UTR) annotations, in which we identify two putative polyadenylation signals present in the 3′UTR regions and characterise the Kozak sequence in the 5′UTR regions. All these improvements are reflected by higher BUSCO genome completeness values. Regardless of an overall more complete genome assembly without missing bases and a better gene prediction, we still failed to identify any mitochondrial hallmark genes, thus further supporting the hypothesis on the absence of mitochondrion.

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