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Draft genome sequence and detailed analysis of Pantoea eucrina strain Russ and implication for opportunistic pathogenesis

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ABSTRACT

The genus Pantoea is a predominant member of host-associated microbiome. We here report on the genomic analysis of Pantoea eucrina strain Russ that was isolated from a trashcan at Oklahoma State University, Stillwater, OK. The draft genome of Pantoea eucrina strain Russ consists of 3,939,877 bp of DNA with 3704 protein-coding genes and 134 RNA genes. This is the first report of a genome sequence of a member of Pantoea eucrina. Genomic analysis revealed metabolic versatility with genes involved in the metabolism and transport of all amino acids as well as glucose, fructose, mannose, xylose, arabinose and galactose, suggesting the organism is a versatile heterotroph. The genome also encodes an extensive secretory machinery including types I, II, III, IV, and Vb secretion systems, and several genes for pili production including the new usher/chaperone system (pfam 05,229). The implications of these systems for opportunistic pathogenesis are discussed.

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Comparative genomics of Pantoea eucrina strain Russ and 21 closely related genomes. (A) KEGG profile clustering of the genomes compared in this study. (B) PCA biplot of the genomic features and COG category distribution in the genomes compared. Genomes are represented by stars, where the strain name is depicted. Arrows represent genomic features or COG categories used for comparison. The arrow directions follow the maximal abundance, and their lengths are proportional to the maximal rate of change between genomes. The first two components explained 75% of variation.
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f0015: Comparative genomics of Pantoea eucrina strain Russ and 21 closely related genomes. (A) KEGG profile clustering of the genomes compared in this study. (B) PCA biplot of the genomic features and COG category distribution in the genomes compared. Genomes are represented by stars, where the strain name is depicted. Arrows represent genomic features or COG categories used for comparison. The arrow directions follow the maximal abundance, and their lengths are proportional to the maximal rate of change between genomes. The first two components explained 75% of variation.

Mentions: When the genome of Pantoea eucrina Russ was compared to 22 closely related genomes based on their KEGG profiles, the genome clustered with Pantoea sp. PSNIH1 previously isolated from patients in a hospital setting and shown to carry several plasmids with antibiotic resistance cassettes [24] (Fig. 3A). This genomic similarity was confirmed when several genomic features (including the genome size, the number of genes, the number of transporters identified, the GC content, the number of non-coding bases, the number of genes belonging to COG categories, as well as the number of genes belonging to each COG category) were used to compare Pantoea eucrina Russ genome to the 22 other closely related genomes. The Russ genome was shown to cluster with the genomes of strains PSNIH1, PSNIH2, IMH, and B40 based on the lower number of genes belonging to the COG categories E, K, G, R, and P in these genomes (Fig. 3B).


Draft genome sequence and detailed analysis of Pantoea eucrina strain Russ and implication for opportunistic pathogenesis
Comparative genomics of Pantoea eucrina strain Russ and 21 closely related genomes. (A) KEGG profile clustering of the genomes compared in this study. (B) PCA biplot of the genomic features and COG category distribution in the genomes compared. Genomes are represented by stars, where the strain name is depicted. Arrows represent genomic features or COG categories used for comparison. The arrow directions follow the maximal abundance, and their lengths are proportional to the maximal rate of change between genomes. The first two components explained 75% of variation.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5037212&req=5

f0015: Comparative genomics of Pantoea eucrina strain Russ and 21 closely related genomes. (A) KEGG profile clustering of the genomes compared in this study. (B) PCA biplot of the genomic features and COG category distribution in the genomes compared. Genomes are represented by stars, where the strain name is depicted. Arrows represent genomic features or COG categories used for comparison. The arrow directions follow the maximal abundance, and their lengths are proportional to the maximal rate of change between genomes. The first two components explained 75% of variation.
Mentions: When the genome of Pantoea eucrina Russ was compared to 22 closely related genomes based on their KEGG profiles, the genome clustered with Pantoea sp. PSNIH1 previously isolated from patients in a hospital setting and shown to carry several plasmids with antibiotic resistance cassettes [24] (Fig. 3A). This genomic similarity was confirmed when several genomic features (including the genome size, the number of genes, the number of transporters identified, the GC content, the number of non-coding bases, the number of genes belonging to COG categories, as well as the number of genes belonging to each COG category) were used to compare Pantoea eucrina Russ genome to the 22 other closely related genomes. The Russ genome was shown to cluster with the genomes of strains PSNIH1, PSNIH2, IMH, and B40 based on the lower number of genes belonging to the COG categories E, K, G, R, and P in these genomes (Fig. 3B).

View Article: PubMed Central - PubMed

ABSTRACT

The genus Pantoea is a predominant member of host-associated microbiome. We here report on the genomic analysis of Pantoea eucrina strain Russ that was isolated from a trashcan at Oklahoma State University, Stillwater, OK. The draft genome of Pantoea eucrina strain Russ consists of 3,939,877 bp of DNA with 3704 protein-coding genes and 134 RNA genes. This is the first report of a genome sequence of a member of Pantoea eucrina. Genomic analysis revealed metabolic versatility with genes involved in the metabolism and transport of all amino acids as well as glucose, fructose, mannose, xylose, arabinose and galactose, suggesting the organism is a versatile heterotroph. The genome also encodes an extensive secretory machinery including types I, II, III, IV, and Vb secretion systems, and several genes for pili production including the new usher/chaperone system (pfam 05,229). The implications of these systems for opportunistic pathogenesis are discussed.

No MeSH data available.


Related in: MedlinePlus