Limits...
Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T)).

Anderson I, Munk C, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin L, Pitluck S, Liolios K, Mavromatis K, Pagani I, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Tindall BJ, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Ivanova N - Stand Genomic Sci (2012)

Bottom Line: Niabella soli Weon et al. 2008 is a member of the Chitinophagaceae, a family within the class Sphingobacteriia that is poorly characterized at the genome level, thus far.Here we describe the features of this organism, together with the complete genome sequence and annotation.The 4,697,343 bp long chromosome with its 3,931 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia ofBacteria andArchaea project.

View Article: PubMed Central - PubMed

Affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.

ABSTRACT
Niabella soli Weon et al. 2008 is a member of the Chitinophagaceae, a family within the class Sphingobacteriia that is poorly characterized at the genome level, thus far. N. soli strain JS13-8(T) is of interest for its ability to produce a variety of glycosyl hydrolases. The genome of N. soli strain JS13-8(T) is only the second genome sequence of a type strain from the family Chitinophagaceae to be published, and the first one from the genus Niabella. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,697,343 bp long chromosome with its 3,931 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia ofBacteria andArchaea project.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree highlighting the position of N. soli relative to the type strains of the other species within the family Chitinophagaceae except for the genera Balneola and Gracilimonas. The tree was inferred from 1,395 aligned characters [8,9] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [10]. Rooting was done initially using the midpoint method [11] 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 950 ML bootstrap replicates [12] (left) and from 1,000 maximum-parsimony bootstrap replicates [13] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [14] are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks [15] (for Niastella koreensis see CP003178).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3569382&req=5

f1: Phylogenetic tree highlighting the position of N. soli relative to the type strains of the other species within the family Chitinophagaceae except for the genera Balneola and Gracilimonas. The tree was inferred from 1,395 aligned characters [8,9] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [10]. Rooting was done initially using the midpoint method [11] 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 950 ML bootstrap replicates [12] (left) and from 1,000 maximum-parsimony bootstrap replicates [13] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [14] are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks [15] (for Niastella koreensis see CP003178).

Mentions: A representative genomic 16S rRNA sequence of N. soli JS13-8T was compared using NCBI BLAST [4,5] under default settings (e.g., considering only the high-scoring segment pairs (HSPs) from the best 250 hits) with the most recent release of the Greengenes database [6]. The relative frequencies of taxa and keywords (reduced to their stem [7]) were determined, weighted by BLAST scores. The most frequently occurring genera were Niabella (34.8%), Terrimonas (21.0%), Flavobacterium (14.9%), 'Niablella' (8.5%; an apparent misspelling of Niabella) and Niastella (8.2%) (13 hits in total). Regarding the single hit to sequences from members of the species, the average identity within HSPs was 99.7%, whereas the average coverage by HSPs was 96.8%. Among all other species, the one yielding the highest score was 'Niablella koreensis' (DQ457019; again a misnomer, see Figure 1), which corresponded to an identity of 95.1% and an HSP coverage of 99.9%. (Note that the Greengenes database uses the INSDC (= EMBL/NCBI/DDBJ) annotation, which is not an authoritative source for nomenclature or classification.) The highest-scoring environmental sequence was JF167633 ('skin antecubital fossa clone ncd2016g05c1'), which showed an identity of 95.3% and an HSP coverage of 95.7%. The most frequently occurring keywords within the labels of all environmental samples which yielded hits were 'sludg' (3.6%), 'activ' (2.6%), 'skin' (2.3%), 'wast' (1.8%) and 'soil' (1.8%) (236 hits in total) and reveal no deeper insight into the usual habitat of close relatives of the strain. Environmental samples which yielded hits of a higher score than the highest scoring species were not found, indicating that N. soli itself is rarely found in environmental screenings.


Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T)).

Anderson I, Munk C, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin L, Pitluck S, Liolios K, Mavromatis K, Pagani I, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Tindall BJ, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Ivanova N - Stand Genomic Sci (2012)

Phylogenetic tree highlighting the position of N. soli relative to the type strains of the other species within the family Chitinophagaceae except for the genera Balneola and Gracilimonas. The tree was inferred from 1,395 aligned characters [8,9] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [10]. Rooting was done initially using the midpoint method [11] 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 950 ML bootstrap replicates [12] (left) and from 1,000 maximum-parsimony bootstrap replicates [13] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [14] are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks [15] (for Niastella koreensis see CP003178).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3569382&req=5

f1: Phylogenetic tree highlighting the position of N. soli relative to the type strains of the other species within the family Chitinophagaceae except for the genera Balneola and Gracilimonas. The tree was inferred from 1,395 aligned characters [8,9] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [10]. Rooting was done initially using the midpoint method [11] 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 950 ML bootstrap replicates [12] (left) and from 1,000 maximum-parsimony bootstrap replicates [13] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [14] are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks [15] (for Niastella koreensis see CP003178).
Mentions: A representative genomic 16S rRNA sequence of N. soli JS13-8T was compared using NCBI BLAST [4,5] under default settings (e.g., considering only the high-scoring segment pairs (HSPs) from the best 250 hits) with the most recent release of the Greengenes database [6]. The relative frequencies of taxa and keywords (reduced to their stem [7]) were determined, weighted by BLAST scores. The most frequently occurring genera were Niabella (34.8%), Terrimonas (21.0%), Flavobacterium (14.9%), 'Niablella' (8.5%; an apparent misspelling of Niabella) and Niastella (8.2%) (13 hits in total). Regarding the single hit to sequences from members of the species, the average identity within HSPs was 99.7%, whereas the average coverage by HSPs was 96.8%. Among all other species, the one yielding the highest score was 'Niablella koreensis' (DQ457019; again a misnomer, see Figure 1), which corresponded to an identity of 95.1% and an HSP coverage of 99.9%. (Note that the Greengenes database uses the INSDC (= EMBL/NCBI/DDBJ) annotation, which is not an authoritative source for nomenclature or classification.) The highest-scoring environmental sequence was JF167633 ('skin antecubital fossa clone ncd2016g05c1'), which showed an identity of 95.3% and an HSP coverage of 95.7%. The most frequently occurring keywords within the labels of all environmental samples which yielded hits were 'sludg' (3.6%), 'activ' (2.6%), 'skin' (2.3%), 'wast' (1.8%) and 'soil' (1.8%) (236 hits in total) and reveal no deeper insight into the usual habitat of close relatives of the strain. Environmental samples which yielded hits of a higher score than the highest scoring species were not found, indicating that N. soli itself is rarely found in environmental screenings.

Bottom Line: Niabella soli Weon et al. 2008 is a member of the Chitinophagaceae, a family within the class Sphingobacteriia that is poorly characterized at the genome level, thus far.Here we describe the features of this organism, together with the complete genome sequence and annotation.The 4,697,343 bp long chromosome with its 3,931 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia ofBacteria andArchaea project.

View Article: PubMed Central - PubMed

Affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.

ABSTRACT
Niabella soli Weon et al. 2008 is a member of the Chitinophagaceae, a family within the class Sphingobacteriia that is poorly characterized at the genome level, thus far. N. soli strain JS13-8(T) is of interest for its ability to produce a variety of glycosyl hydrolases. The genome of N. soli strain JS13-8(T) is only the second genome sequence of a type strain from the family Chitinophagaceae to be published, and the first one from the genus Niabella. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,697,343 bp long chromosome with its 3,931 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia ofBacteria andArchaea project.

No MeSH data available.


Related in: MedlinePlus