scholarly journals High-quality complete genome resource of plant pathogenic bacterium Pectobacterium atrosepticum strain Green1 isolated from potato (Solanum tuberosum L.) in Greenland

2021 ◽  
Author(s):  
Robert Czajkowski ◽  
Lukasz Rabalski ◽  
Maciej Kosinski ◽  
Eigil de Neergaard ◽  
Susanne Harding
Keyword(s):  
Solanum Tuberosum ◽  
Solanum Tuberosum L ◽  
Pathogenic Bacterium ◽  
Rrna Genes ◽  
Comparative Genomic ◽  
Trna Genes ◽  
Plant Pathogenic Bacterium ◽  
High Quality ◽  
Ecological Fitness ◽  
Pectobacterium Atrosepticum

Pectobacterium atrosepticum is a narrow host range pectinolytic plant pathogenic bacterium causing blackleg of potato (Solanum tuberosum L.) worldwide. Till present, several P. atrosepticum genomes have been sequenced and characterized in detail; all of these genomes have come, however, from P. atrosepticum strains isolates from plants grown in temperate zones, not from hosts cultivated under different climatic conditions. Herewith, we present the first complete, high-quality genome of the P. atrosepticum strain Green1 isolated from potato plants grown under subarctic climate in Greenland. The genome of P. atrosepticum strain Green1 consists of one chromosome of 4,959,719 bp., with a GC content of 51% and no plasmids. The genome contains 4531 annotated features, including 4179 protein-coding genes (CDSs), 22 rRNA genes, 70 tRNA genes, 8 ncRNA genes, 2 CRISPRs and 126 pseudogenes. We believe that the information of this first, high-quality, complete, closed genome of P. atrosepticum strain isolated from host plant grown in subarctic agricultural region will provide resources for comparative genomic studies and for analyses targeting climatic adaptation and ecological fitness mechanisms present in P. atrosepticum.

scholarly journals High-quality complete genome resource of plant pathogenic bacterium Pectobacterium atrosepticum strain Green1 isolated from potato (Solanum tuberosum L.) in Greenland

2021 ◽  
Author(s):  
Robert Czajkowski ◽  
Lukasz Rabalski ◽  
Maciej Kosinski ◽  
Eigil de Neergaard ◽  
Susanne Harding
Keyword(s):  
Solanum Tuberosum ◽  
Solanum Tuberosum L ◽  
Pathogenic Bacterium ◽  
Rrna Genes ◽  
Comparative Genomic ◽  
Trna Genes ◽  
Plant Pathogenic Bacterium ◽  
High Quality ◽  
Ecological Fitness ◽  
Pectobacterium Atrosepticum

Pectobacterium atrosepticum is a narrow host range pectinolytic plant pathogenic bacterium causing blackleg of potato (Solanum tuberosum L.) worldwide. Till present, several P. atrosepticum genomes have been sequenced and characterized in detail; all of these genomes have come, however, from P. atrosepticum strains isolates from plants grown in temperate zones, not from hosts cultivated under different climatic conditions. Herewith, we present the first complete, high-quality genome of the P. atrosepticum strain Green1 isolated from potato plants grown under subarctic climate in Greenland. The genome of P. atrosepticum strain Green1 consists of one chromosome of 4,959,719 bp., with a GC content of 51% and no plasmids. The genome contains 4531 annotated features, including 4179 protein-coding genes (CDSs), 22 rRNA genes, 70 tRNA genes, 8 ncRNA genes, 2 CRISPRs and 126 pseudogenes. We believe that the information of this first, high-quality, complete, closed genome of P. atrosepticum strain isolated from host plant grown in subarctic agricultural region will provide resources for comparative genomic studies and for analyses targeting climatic adaptation and ecological fitness mechanisms present in P. atrosepticum.

scholarly journals High-quality complete genome resource of plant pathogenic bacterium Dickeya solani strain IPO 2019 isolated from Hyacinthus orientalis

2021 ◽  
Author(s):  
Robert Czajkowski ◽  
Lukasz Rabalski ◽  
Przemysław Bartnik ◽  
Sylwia Jafra
Keyword(s):  
Gc Content ◽  
Pathogenic Bacterium ◽  
Rrna Genes ◽  
Comparative Genomic ◽  
Trna Genes ◽  
Plant Pathogenic Bacterium ◽  
High Quality ◽  
Ecological Fitness ◽  
Hyacinthus Orientalis ◽  
Dickeya Solani

AbstractDickeya solani is an emerging plant pathogenic bacterium, causing disease symptoms in a variety of agriculturally relevant crop species worldwide. To date a number of D. solani genomes have been sequenced and characterized, the great majority of these genomes have however come from D. solani strains isolated from potato (Solanum tuberosum L.) and not from other plant hosts. Herewith, we present the first complete, high-quality genome of D. solani strain IPO 2019 (LMG 25990) isolated from ornamental plant Hyacinthus orientalis. The genome of D. solani strain IPO 2019 consists of one chromosome of 4,919,542 bp., with a GC content of 56.2% and no plasmids. The genome contains 4502 annotated features, 22 rRNA genes, 73 tRNA genes and 1 CRISPRS. We believe that the information of this high-quality, complete, closed genome of D. solani strain isolated from host plant different than potato (i.e. hyacinth) will provide resources for comparative genomic studies as well as for analyses targeting adaptation and ecological fitness mechanisms present in Dickeya solani species.

scholarly journals High-quality complete genome resource of plant pathogenic bacterium Dickeya solani strain IPO 2019 isolated from Hyacinthus orientalis

2021 ◽  
Author(s):  
Robert Czajkowski ◽  
Lukasz Rabalski ◽  
Przemyslaw Bartnik ◽  
Sylwia Jafra
Keyword(s):  
Gc Content ◽  
Pathogenic Bacterium ◽  
Rrna Genes ◽  
Comparative Genomic ◽  
Trna Genes ◽  
Plant Pathogenic Bacterium ◽  
High Quality ◽  
Ecological Fitness ◽  
Hyacinthus Orientalis ◽  
Dickeya Solani

Dickeya solani is an emerging plant pathogenic bacterium, causing disease symptoms in a variety of agriculturally relevant crop species worldwide. To date a number of D. solani genomes have been sequenced and characterized, the great majority of these genomes have however come from D. solani strains isolated from potato (Solanum tuberosum L.) and not from other plant hosts. Herewith, we present the first complete, high-quality genome of D. solani strain IPO 2019 (LMG 25990) isolated from ornamental plant Hyacinthus orientalis. The genome of D. solani strain IPO 2019 consists of one chromosome of 4,919,542 bp., with a GC content of 56.2% and no plasmids. The genome contains 4502 annotated features, 22 rRNA genes, 73 tRNA genes and 1 CRISPRS. We believe that the information of this high-quality, complete, closed genome of D. solani strain isolated from host plant different than potato (i.e. hyacinth) will provide resources for comparative genomic studies as well as for analyses targeting adaptation and ecological fitness mechanisms present in Dickeya solani species.

scholarly journals Characterization and Analysis of the Mitochondrial Genome of Common Bean (Phaseolus vulgaris) by Comparative Genomic Approaches

2020 ◽  
Vol 21 (11) ◽  
pp. 3778
Author(s):  
Changwei Bi ◽  
Na Lu ◽  
Yiqing Xu ◽  
Chunpeng He ◽  
Zuhong Lu
Keyword(s):  
Phaseolus Vulgaris ◽  
Mitochondrial Genome ◽  
Common Bean ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Comparative Genomic ◽  
Trna Genes ◽  
Leguminous Plants ◽  
The Common

The common bean (Phaseolus vulgaris) is a major source of protein and essential nutrients for humans. To explore the genetic diversity and phylogenetic relationships of P. vulgaris, its complete mitochondrial genome (mitogenome) was sequenced and assembled. The mitogenome is 395,516 bp in length, including 31 unique protein-coding genes (PCGs), 15 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes. Among the 31 PCGs, four genes (mttB, nad1, nad4L, and rps10) use ACG as initiation codons, which are altered to standard initiation codons by RNA editing. In addition, the termination codon CGA in the ccmFC gene is converted to UGA. Selective pressure analysis indicates that the ccmB, ccmFC, rps1, rps10, and rps14 genes were under evolutionary positive selection. The proportions of five amino acids (Phe, Leu, Pro, Arg, and Ser) in the whole amino acid profile of the proteins in each mitogenome can be used to distinguish angiosperms from gymnosperms. Phylogenetic analyses show that P. vulgaris is evolutionarily closer to the Glycininae than other leguminous plants. The results of the present study not only provide an important opportunity to conduct further genomic breeding studies in the common bean, they also provide valuable information for future evolutionary and molecular studies of leguminous plants.

scholarly journals Microbial Conversion of Tomato by a Plant Pathogenic Bacterium Pectobacterium atrosepticum: A Plant-Microbial Approach to Control Pathogenic Candida Species

2012 ◽  
Vol 7 (1) ◽  
pp. 1934578X1200700
Author(s):  
Vivek K. Bajpai ◽  
Sun Chul Kang ◽  
Soon-Gu Lee ◽  
Kwang-Hyun Baek
Keyword(s):  
Candida Species ◽  
Fungal Pathogens ◽  
Pharmaceutical Preparations ◽  
Pathogenic Bacterium ◽  
Plant Pathogenic Bacterium ◽  
Microbial Conversion ◽  
Pectobacterium Atrosepticum ◽  
Minimum Fungicidal Concentration ◽  
Therapeutic Uses

This study was carried out to produce bioconverted products by microbial fermentation of tomato using a plant pathogenic bacterium Pectobacterium atrosepticum and to evaluate their in vitro antimycotic effect against pathogenic Candida species. The bioconverted products (500 μg/disc) provoked promising antimycotic effects against pathogenic isolates of Candida species as shown by the diameters of zones of inhibition (9 ± 0.6 to 14 ± 0.4 mm), along with their respective minimum inhibitory and minimum fungicidal concentration values, which increased from 250 to 1000 and 250 to 2000 μg/mL, respectively. With the viable counts of the tested fungal pathogens, exposure of the bioconverted products revealed a remarkable antimycotic effect. In addition, the morphology of a clinical isolate of C. glabrata KBN06P00368, visualized by scanning electron microscopy, showed a severe detrimental effect produced by the bioconverted products at the minimum inhibitory concentration (250 μg/mL). The bioconverted products significantly inhibited the in vitro growth of all the tested clinical and pathogenic laboratory isolates of Candida species. This study confirmed the potent antimycotic efficacy of the bioconverted products of tomato, hence justifying the therapeutic uses of bioconverted products in pharmaceutical preparations as an alternative approach to support the antifungal activity of conventional antimycotics.

scholarly journals Long-Read Metagenomics to Retrieve High-Quality Metagenome-Assembled Genomes from Canine Feces

2020 ◽  
Author(s):  
Anna Cusco ◽  
Daniel Perez ◽  
Joaquim Viñes ◽  
Olga Francino
Keyword(s):  
Molecular Weight ◽  
High Molecular Weight ◽  
Dna Extraction ◽  
Rrna Genes ◽  
Trna Genes ◽  
High Quality ◽  
High Molecular Weight Dna ◽  
Fecal Microbiome ◽  
Long Read ◽  
Gene Similarity

Abstract Background. Metagenomics is a powerful and rapidly developing approach that provides new biological insights into the microbes inhabiting underexplored environments, such as canine fecal microbiome. We investigate long-read metagenomics with Nanopore sequencing to profile the fecal microbiome and to retrieve high-quality metagenome-assembled genomes (HQ MAGs) from a healthy dog.Results. More than 99% of total classified reads corresponded to Bacteria. The most abundant phylum was Bacteroidetes (~80% of total reads), followed by Firmicutes, Proteobacteria, and Fusobacteria. Prevotella (>50%) and Bacteroides (>20%) are the more abundant genera, followed by Fusobacterium, Megamonas, Sutterella, and other fecal-related genera, (each representing <5% of the total bacterial composition). We retrieved eight single-contig HQ MAGs and three medium-quality MAGs, after combining several metagenome dataset assemblies. The HQ MAGs corresponded to Succinivibrio, Sutterella, Prevotellamassilia, Phascolarctobacterium, Enterococcus, Blautia, and Catenibacterium genera. Succinivibrio HQ MAG represents a novel candidate bacterial species. Sutterella HQ MAG is potentially the first reported genome assembly for Sutterella stercoricanis, as assigned by 16S rRNA gene similarity. Prevotellamassilia, Phascolarctobacterium, Catenibacterium, and Blautia sp900541345 HQ MAGs improved the contiguity of previously reported genome assemblies in their respective genera, and the number of rRNA genes and tRNA genes. Finally, Enterococcus hirae and Blautia sp003287895 HQ MAGs represented species that already have a complete reference genome. At the technical level, we demonstrated that a high-molecular weight DNA extraction improved the taxonomic classification of the raw unassembled reads, the metagenomics assembly contiguity, and the retrieval of longer and circular contigs, which are potential HQ MAGs. Conclusions. Long-read metagenomics allowed us to recover HQ MAGs from canine feces of a healthy dog. The high-molecular weight DNA extraction to improve contiguity and the correction of the insertions and deletions to reduce frameshift errors ensure the retrieval of complete single-contig HQ MAGs.

scholarly journals Draft Genome Sequence of Corynebacterium ulcerans Strain 04-3911, Isolated from Humans

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Luis C. Guimarães ◽  
Marcus V. C. Viana ◽  
Leandro J. Benevides ◽  
Diego C. B. Mariano ◽  
Adooney A. O. Veras ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Pathogenic Bacterium ◽  
Draft Genome Sequence ◽  
Rrna Genes ◽  
Trna Genes ◽  
Coding Sequences ◽  
Domesticated Animals ◽  
Corynebacterium Ulcerans ◽  
The World

Corynebacterium ulcerans is a pathogenic bacterium infecting wild and domesticated animals; some infection cases in humans have increased throughout the world. The current study describes the draft genome of strain 04-3911, isolated from humans. The draft genome has 2,492,680 bp, 2,143 coding sequences, 12 rRNA genes, and 50 tRNA genes.

scholarly journals Pectobacterium parmentieri SCC 3193 Mutants with Altered Synthesis of Cell Surface Polysaccharides are Resistant to N4-Like Lytic Bacteriophage ϕA38 (vB_Ppp_A38) but Express Decreased Virulence in Potato (Solanum tuberosum L.) Plants

2021 ◽  
Vol 22 (14) ◽  
pp. 7346
Author(s):  
Przemyslaw Bartnik ◽  
Sylwia Jafra ◽  
Magdalena Narajczyk ◽  
Paulina Czaplewska ◽  
Robert Czajkowski
Keyword(s):  
Solanum Tuberosum ◽  
Biological Control Agent ◽  
Solanum Tuberosum L ◽  
Sugar Metabolism ◽  
Nitrogen Sources ◽  
Control Agent ◽  
Plant Colonization ◽  
Lytic Phage ◽  
Lytic Bacteriophage ◽  
Ecological Fitness

Pectobacterium parmentieri is a Gram-negative plant-pathogenic bacterium able to infect potato (Solanum tuberosum L.). Little is known about lytic bacteriophages infecting P. parmentieri and how phage-resistance influences the environmental fitness and virulence of this species. A lytic phage vB_Ppp_A38 (ϕA38) has been previously isolated and characterized as a potential biological control agent for the management of P. parmentieri. In this study, seven P. parmentieri SCC 3193 Tn5 mutants were identified that exhibited resistance to infection caused by vB_Ppp_A38 (ϕA38). The genes disrupted in these seven mutants encoded proteins involved in the assembly of O-antigen, sugar metabolism, and the production of bacterial capsule exopolysaccharides. The potential of A38-resistant P. parmentieri mutants for plant colonization and pathogenicity as well as other phenotypes expected to contribute to the ecological fitness of P. parmentieri, including growth rate, use of carbon and nitrogen sources, production of pectinolytic enzymes, proteases, cellulases, and siderophores, swimming and swarming motility, presence of capsule and flagella as well as the ability to form biofilm were assessed. Compared to the wild-type P. parmentieri strain, all phage-resistant mutants exhibited a reduced ability to colonize and to cause symptoms in growing potato (S. tuberosum L.) plants. The implications of bacteriophage resistance on the ecological fitness of P. parmentieri are discussed.

scholarly journals Preferential Colonization of Solanum tuberosum L. Roots by the Fungus Glomus intraradices in Arable Soil of a Potato Farming Area

2008 ◽  
Vol 74 (18) ◽  
pp. 5776-5783 ◽  
Author(s):  
Patrizia Cesaro ◽  
Diederik van Tuinen ◽  
Andrea Copetta ◽  
Odile Chatagnier ◽  
Graziella Berta ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Glomus Intraradices ◽  
Solanum Tuberosum L ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Fungal Communities ◽  
Bulk Soil ◽  
Rrna Genes ◽  
Fungal Abundance ◽  
Lsu Rrna

ABSTRACT The symbiosis between plant roots and arbuscular mycorrhizal (AM) fungi has been shown to affect both the diversity and productivity of agricultural communities. In this study, we characterized the AM fungal communities of Solanum tuberosum L. (potato) roots and of the bulk soil in two nearby areas of northern Italy, in order to verify if land use practices had selected any particular AM fungus with specificity to potato plants. The AM fungal large-subunit (LSU) rRNA genes were subjected to nested PCR, cloning, sequencing, and phylogenetic analyses. One hundred eighty-three LSU rRNA sequences were analyzed, and eight monophyletic ribotypes, belonging to Glomus groups A and B, were identified. AM fungal communities differed between bulk soil and potato roots, as one AM fungal ribotype, corresponding to Glomus intraradices, was much more frequent in potato roots than in soils (accounting for more than 90% of sequences from potato samples and less than 10% of sequences from soil samples). A semiquantitative heminested PCR with specific primers was used to confirm and quantify the AM fungal abundance observed by cloning. Overall results concerning the biodiversity of AM fungal communities in roots and in bulk soils from the two studied areas suggested that potato roots were preferentially colonized by one AM fungal species, G. intraradices.

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