TY - JOUR

T1 - Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), 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

AU - Scheuner, Carmen

AU - Tindall, Brian J.

AU - Lu, Megan

AU - Nolan, Matt

AU - Lapidus, Alla

AU - Cheng, Jan Fang

AU - Goodwin, Lynne

AU - Pitluck, Sam

AU - Huntemann, Marcel

AU - Liolios, Konstantinos

AU - Pagani, Ioanna

AU - Mavromatis, Konstantinos

AU - Ivanova, Natalia

AU - Pati, Amrita

AU - Chen, Amy

AU - Palaniappan, Krishna

AU - Jeffries, Cynthia D.

AU - Hauser, Loren

AU - Land, Miriam

AU - Mwirichia, Romano

AU - Rohde, Manfred

AU - Abt, Birte

AU - Detter, John C.

AU - Woyke, Tanja

AU - Eisen, Jonathan A.

AU - Markowitz, Victor

AU - Hugenholtz, Philip

AU - Göker, Markus

AU - Kyrpides, Nikos C.

AU - Klenk, Hans Peter

PY - 2014/12/8

Y1 - 2014/12/8

N2 - 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 1448T, 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 Genomic Encyclopedia 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.

AB - 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 1448T, 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 Genomic Encyclopedia 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.

KW - GEBA

KW - Gram-negative

KW - Halotolerant

KW - Non-peptidoglycan bacteria

KW - Planctomycetales

KW - Planctomycetes

KW - Stalked bacteria

KW - Taxonomic descriptions

UR - http://www.scopus.com/inward/record.url?scp=84971201884&partnerID=8YFLogxK

U2 - 10.1186/1944-3277-9-10

DO - 10.1186/1944-3277-9-10

M3 - Article

AN - SCOPUS:84971201884

VL - 9

JO - Standards in Genomic Sciences

JF - Standards in Genomic Sciences

SN - 1944-3277

IS - 1

M1 - 10

ER -