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Genome sequence of the halotolerant bacterium Corynebacterium halotolerans type strain YIM 70093(T) (= DSM 44683(T)).

Rückert C, Albersmeier A, Al-Dilaimi A, Niehaus K, Szczepanowski R, Kalinowski J - Stand Genomic Sci (2012)

Bottom Line: C. halotolerans, isolated from a saline soil, belongs to the non-lipophilic, non-pathogenic corynebacteria.It displays a high tolerance to salts (up to 25%) and is related to the pathogenic corynebacteria C. freneyi and C. xerosis.As this is a type strain in a subgroup of Corynebacterium without complete genome sequences, this project describing the 3.14 Mbp long chromosome and the 86.2 kbp plasmid pCha1 with their 2,865 protein-coding and 65 RNA genes will aid the Genomic Encyclopedia ofBacteria andArchaea project.

View Article: PubMed Central - PubMed

Affiliation: Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany.

ABSTRACT
Corynebacterium halotolerans Chen et al. 2004 is a member of the genus Corynebacterium which contains Gram-positive bacteria with a high G+C content. C. halotolerans, isolated from a saline soil, belongs to the non-lipophilic, non-pathogenic corynebacteria. It displays a high tolerance to salts (up to 25%) and is related to the pathogenic corynebacteria C. freneyi and C. xerosis. As this is a type strain in a subgroup of Corynebacterium without complete genome sequences, this project describing the 3.14 Mbp long chromosome and the 86.2 kbp plasmid pCha1 with their 2,865 protein-coding and 65 RNA genes will aid the Genomic Encyclopedia ofBacteria andArchaea project.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree highlighting the position of C. halotolerans relative to type strains of other species within the genus Corynebacterium as selected by Chen et al. [1]. In addition, the recently described C. maris, C. marinum, and C. humireducens were added, as they were shown to be closely related. Furthermore, the type strain of the genus, C. diphtheriae [11], was included. Species with at least one publicly available genome sequence (not necessarily the type strain) are highlighted in bold face. The tree is based on sequences aligned by the RDP aligner, utilizes the Jukes-Cantor corrected distance model to construct a distance matrix based on alignment model positions without the use of alignment inserts, and uses a minimum comparable position of 200. The tree is built with RDP Tree Builder, which uses Weighbor [12] with an alphabet size of 4 and length size of 1,000. The building of the tree also involves a bootstrapping process repeated 100 times to generate a majority consensus tree [13]. Rhodococcus equi (X80614) was used as an outgroup.
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f1: Phylogenetic tree highlighting the position of C. halotolerans relative to type strains of other species within the genus Corynebacterium as selected by Chen et al. [1]. In addition, the recently described C. maris, C. marinum, and C. humireducens were added, as they were shown to be closely related. Furthermore, the type strain of the genus, C. diphtheriae [11], was included. Species with at least one publicly available genome sequence (not necessarily the type strain) are highlighted in bold face. The tree is based on sequences aligned by the RDP aligner, utilizes the Jukes-Cantor corrected distance model to construct a distance matrix based on alignment model positions without the use of alignment inserts, and uses a minimum comparable position of 200. The tree is built with RDP Tree Builder, which uses Weighbor [12] with an alphabet size of 4 and length size of 1,000. The building of the tree also involves a bootstrapping process repeated 100 times to generate a majority consensus tree [13]. Rhodococcus equi (X80614) was used as an outgroup.

Mentions: Figure 1 shows the phylogenetic neighborhood of C. halotolerans in a 16S rRNA based tree. The sequences of the four identical 16S rRNA gene copies in the genome differ by eight nucleotides from the previously published 16S rRNA sequence (AY226509), which contains two ambiguous bases.


Genome sequence of the halotolerant bacterium Corynebacterium halotolerans type strain YIM 70093(T) (= DSM 44683(T)).

Rückert C, Albersmeier A, Al-Dilaimi A, Niehaus K, Szczepanowski R, Kalinowski J - Stand Genomic Sci (2012)

Phylogenetic tree highlighting the position of C. halotolerans relative to type strains of other species within the genus Corynebacterium as selected by Chen et al. [1]. In addition, the recently described C. maris, C. marinum, and C. humireducens were added, as they were shown to be closely related. Furthermore, the type strain of the genus, C. diphtheriae [11], was included. Species with at least one publicly available genome sequence (not necessarily the type strain) are highlighted in bold face. The tree is based on sequences aligned by the RDP aligner, utilizes the Jukes-Cantor corrected distance model to construct a distance matrix based on alignment model positions without the use of alignment inserts, and uses a minimum comparable position of 200. The tree is built with RDP Tree Builder, which uses Weighbor [12] with an alphabet size of 4 and length size of 1,000. The building of the tree also involves a bootstrapping process repeated 100 times to generate a majority consensus tree [13]. Rhodococcus equi (X80614) was used as an outgroup.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3569386&req=5

f1: Phylogenetic tree highlighting the position of C. halotolerans relative to type strains of other species within the genus Corynebacterium as selected by Chen et al. [1]. In addition, the recently described C. maris, C. marinum, and C. humireducens were added, as they were shown to be closely related. Furthermore, the type strain of the genus, C. diphtheriae [11], was included. Species with at least one publicly available genome sequence (not necessarily the type strain) are highlighted in bold face. The tree is based on sequences aligned by the RDP aligner, utilizes the Jukes-Cantor corrected distance model to construct a distance matrix based on alignment model positions without the use of alignment inserts, and uses a minimum comparable position of 200. The tree is built with RDP Tree Builder, which uses Weighbor [12] with an alphabet size of 4 and length size of 1,000. The building of the tree also involves a bootstrapping process repeated 100 times to generate a majority consensus tree [13]. Rhodococcus equi (X80614) was used as an outgroup.
Mentions: Figure 1 shows the phylogenetic neighborhood of C. halotolerans in a 16S rRNA based tree. The sequences of the four identical 16S rRNA gene copies in the genome differ by eight nucleotides from the previously published 16S rRNA sequence (AY226509), which contains two ambiguous bases.

Bottom Line: C. halotolerans, isolated from a saline soil, belongs to the non-lipophilic, non-pathogenic corynebacteria.It displays a high tolerance to salts (up to 25%) and is related to the pathogenic corynebacteria C. freneyi and C. xerosis.As this is a type strain in a subgroup of Corynebacterium without complete genome sequences, this project describing the 3.14 Mbp long chromosome and the 86.2 kbp plasmid pCha1 with their 2,865 protein-coding and 65 RNA genes will aid the Genomic Encyclopedia ofBacteria andArchaea project.

View Article: PubMed Central - PubMed

Affiliation: Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany.

ABSTRACT
Corynebacterium halotolerans Chen et al. 2004 is a member of the genus Corynebacterium which contains Gram-positive bacteria with a high G+C content. C. halotolerans, isolated from a saline soil, belongs to the non-lipophilic, non-pathogenic corynebacteria. It displays a high tolerance to salts (up to 25%) and is related to the pathogenic corynebacteria C. freneyi and C. xerosis. As this is a type strain in a subgroup of Corynebacterium without complete genome sequences, this project describing the 3.14 Mbp long chromosome and the 86.2 kbp plasmid pCha1 with their 2,865 protein-coding and 65 RNA genes will aid the Genomic Encyclopedia ofBacteria andArchaea project.

No MeSH data available.


Related in: MedlinePlus