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Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2(T)).

Lapidus A, Nolan M, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Brambilla EM, Rohde M, Abt B, Verbarg S, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T - Stand Genomic Sci (2011)

Bottom Line: Larkin and Shinabarger 1983 is the type species of the genus Thiothrix in the family Thiotrichaceae.The species is of interest not only because of its isolated location in the yet to be genomically characterized region of the tree of life, but also because of its life-style with gliding gonidia, the multilayer sheath, rosettes, and the embedded sulfur granules.This is the first completed (improved-high-quality-draft) genome sequence to be published of a member of the family Thiotrichaceae.

View Article: PubMed Central - PubMed

ABSTRACT
Thiothrix nivea (Rabenhorst 1865) Winogradsky 1888 (Approved Lists 1980) emend. Larkin and Shinabarger 1983 is the type species of the genus Thiothrix in the family Thiotrichaceae. The species is of interest not only because of its isolated location in the yet to be genomically characterized region of the tree of life, but also because of its life-style with gliding gonidia, the multilayer sheath, rosettes, and the embedded sulfur granules. Strain JP2(T) is the neotype strain of the species which was first observed by Rabenhorst in 1865 and later reclassified by Winogradsky in 1888 into the then novel genus Thiothrix. This is the first completed (improved-high-quality-draft) genome sequence to be published of a member of the family Thiotrichaceae. The genome in its current assembly consists of 15 contigs in four scaffolds with a total of 4,691,711 bp bearing 4,542 protein-coding and 52 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree highlighting the position of T. nivea relative to the other type strains within the family Thiotrichaceae. The tree was inferred from 1,332 aligned characters [10,11] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [12]. Rooting was done initially using the midpoint method [13] and then checked for its agreement with the current classification (Table 1). The branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 200 ML bootstrap replicates [14] (left) and from 1,000 maximum parsimony bootstrap replicates [15] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [16] are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks.
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f1: Phylogenetic tree highlighting the position of T. nivea relative to the other type strains within the family Thiotrichaceae. The tree was inferred from 1,332 aligned characters [10,11] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [12]. Rooting was done initially using the midpoint method [13] and then checked for its agreement with the current classification (Table 1). The branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 200 ML bootstrap replicates [14] (left) and from 1,000 maximum parsimony bootstrap replicates [15] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [16] are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks.

Mentions: Figure 1 shows the phylogenetic neighborhood of T. nivea in a 16S rRNA based tree. The sequences of the two identical 16S rRNA gene copies in the genome do not differ from the previously published 16S rRNA sequence (L40993), which contains six ambiguous base calls.


Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2(T)).

Lapidus A, Nolan M, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Huntemann M, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Brambilla EM, Rohde M, Abt B, Verbarg S, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T - Stand Genomic Sci (2011)

Phylogenetic tree highlighting the position of T. nivea relative to the other type strains within the family Thiotrichaceae. The tree was inferred from 1,332 aligned characters [10,11] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [12]. Rooting was done initially using the midpoint method [13] and then checked for its agreement with the current classification (Table 1). The branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 200 ML bootstrap replicates [14] (left) and from 1,000 maximum parsimony bootstrap replicates [15] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [16] are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368414&req=5

f1: Phylogenetic tree highlighting the position of T. nivea relative to the other type strains within the family Thiotrichaceae. The tree was inferred from 1,332 aligned characters [10,11] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [12]. Rooting was done initially using the midpoint method [13] and then checked for its agreement with the current classification (Table 1). The branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 200 ML bootstrap replicates [14] (left) and from 1,000 maximum parsimony bootstrap replicates [15] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [16] are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks.
Mentions: Figure 1 shows the phylogenetic neighborhood of T. nivea in a 16S rRNA based tree. The sequences of the two identical 16S rRNA gene copies in the genome do not differ from the previously published 16S rRNA sequence (L40993), which contains six ambiguous base calls.

Bottom Line: Larkin and Shinabarger 1983 is the type species of the genus Thiothrix in the family Thiotrichaceae.The species is of interest not only because of its isolated location in the yet to be genomically characterized region of the tree of life, but also because of its life-style with gliding gonidia, the multilayer sheath, rosettes, and the embedded sulfur granules.This is the first completed (improved-high-quality-draft) genome sequence to be published of a member of the family Thiotrichaceae.

View Article: PubMed Central - PubMed

ABSTRACT
Thiothrix nivea (Rabenhorst 1865) Winogradsky 1888 (Approved Lists 1980) emend. Larkin and Shinabarger 1983 is the type species of the genus Thiothrix in the family Thiotrichaceae. The species is of interest not only because of its isolated location in the yet to be genomically characterized region of the tree of life, but also because of its life-style with gliding gonidia, the multilayer sheath, rosettes, and the embedded sulfur granules. Strain JP2(T) is the neotype strain of the species which was first observed by Rabenhorst in 1865 and later reclassified by Winogradsky in 1888 into the then novel genus Thiothrix. This is the first completed (improved-high-quality-draft) genome sequence to be published of a member of the family Thiotrichaceae. The genome in its current assembly consists of 15 contigs in four scaffolds with a total of 4,691,711 bp bearing 4,542 protein-coding and 52 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

No MeSH data available.


Related in: MedlinePlus