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Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305(T)), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae.

Scheuner C, Tindall BJ, Lu M, Nolan M, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Huntemann M, Liolios K, Pagani I, Mavromatis K, Ivanova N, Pati A, Chen A, Palaniappan K, Jeffries CD, Hauser L, Land M, Mwirichia R, Rohde M, Abt B, Detter JC, Woyke T, Eisen JA, Markowitz V, Hugenholtz P, Göker M, Kyrpides NC, Klenk HP - Stand Genomic Sci (2014)

Bottom Line: A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera.Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions.In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.

View Article: PubMed Central - HTML - PubMed

Affiliation: DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.

ABSTRACT
Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448(T), were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree inferred from the MARE-filtered supermatrix under the maximum likelihood (ML) criterion [82] and rooted with Phycisphaera mikurensis . The branches are scaled in terms of the expected number of substitutions per site. Numbers above the branches (from left to right) are bootstrapping support values [87] (if larger than 60%) from ML/MP MARE-filtered supermatrix; ML/MP unfiltered (full) supermatrix; ML/MP core-genes supermatrix; ML/MP gene-content matrix; ML/MP ortholog-content matrix. Values larger than 95% are shown in bold; dots indicate branches with maximum support under all settings.
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Figure 4: Phylogenetic tree inferred from the MARE-filtered supermatrix under the maximum likelihood (ML) criterion [82] and rooted with Phycisphaera mikurensis . The branches are scaled in terms of the expected number of substitutions per site. Numbers above the branches (from left to right) are bootstrapping support values [87] (if larger than 60%) from ML/MP MARE-filtered supermatrix; ML/MP unfiltered (full) supermatrix; ML/MP core-genes supermatrix; ML/MP gene-content matrix; ML/MP ortholog-content matrix. Values larger than 95% are shown in bold; dots indicate branches with maximum support under all settings.

Mentions: The MARE-filtered supermatrix ML tree is shown in Figure 4 together with ML and MP bootstrap support values from all phylogenomic analyses if larger than 60%. All trees, except for the core-genes supermatrix MP tree, were topologically identical. The MP tree inferred from the core-gene matrix showed a distinct grouping of the clade that contained Gemmata obscuriglobus and Zavarzinella formosa, i.e. as sister clade of all other taxa but the outgroup, with maximal bootstrap support. Given that the majority of analyses supports the topology in Figure 4, the different core-genes MP topology might be caused by long branch attraction between the outgroup and the clade comprising Gemmata and Zavarzinella.


Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305(T)), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae.

Scheuner C, Tindall BJ, Lu M, Nolan M, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Huntemann M, Liolios K, Pagani I, Mavromatis K, Ivanova N, Pati A, Chen A, Palaniappan K, Jeffries CD, Hauser L, Land M, Mwirichia R, Rohde M, Abt B, Detter JC, Woyke T, Eisen JA, Markowitz V, Hugenholtz P, Göker M, Kyrpides NC, Klenk HP - Stand Genomic Sci (2014)

Phylogenetic tree inferred from the MARE-filtered supermatrix under the maximum likelihood (ML) criterion [82] and rooted with Phycisphaera mikurensis . The branches are scaled in terms of the expected number of substitutions per site. Numbers above the branches (from left to right) are bootstrapping support values [87] (if larger than 60%) from ML/MP MARE-filtered supermatrix; ML/MP unfiltered (full) supermatrix; ML/MP core-genes supermatrix; ML/MP gene-content matrix; ML/MP ortholog-content matrix. Values larger than 95% are shown in bold; dots indicate branches with maximum support under all settings.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4334474&req=5

Figure 4: Phylogenetic tree inferred from the MARE-filtered supermatrix under the maximum likelihood (ML) criterion [82] and rooted with Phycisphaera mikurensis . The branches are scaled in terms of the expected number of substitutions per site. Numbers above the branches (from left to right) are bootstrapping support values [87] (if larger than 60%) from ML/MP MARE-filtered supermatrix; ML/MP unfiltered (full) supermatrix; ML/MP core-genes supermatrix; ML/MP gene-content matrix; ML/MP ortholog-content matrix. Values larger than 95% are shown in bold; dots indicate branches with maximum support under all settings.
Mentions: The MARE-filtered supermatrix ML tree is shown in Figure 4 together with ML and MP bootstrap support values from all phylogenomic analyses if larger than 60%. All trees, except for the core-genes supermatrix MP tree, were topologically identical. The MP tree inferred from the core-gene matrix showed a distinct grouping of the clade that contained Gemmata obscuriglobus and Zavarzinella formosa, i.e. as sister clade of all other taxa but the outgroup, with maximal bootstrap support. Given that the majority of analyses supports the topology in Figure 4, the different core-genes MP topology might be caused by long branch attraction between the outgroup and the clade comprising Gemmata and Zavarzinella.

Bottom Line: A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera.Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions.In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.

View Article: PubMed Central - HTML - PubMed

Affiliation: DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.

ABSTRACT
Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448(T), were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.

No MeSH data available.


Related in: MedlinePlus