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Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95(T)).

Kiss H, Nett M, Domin N, Martin K, Maresca JA, Copeland A, Lapidus A, Lucas S, Berry KW, Glavina Del Rio T, Dalin E, Tice H, Pitluck S, Richardson P, Bruce D, Goodwin L, Han C, Detter JC, Schmutz J, Brettin T, Land M, Hauser L, Kyrpides NC, Ivanova N, Göker M, Woyke T, Klenk HP, Bryant DA - Stand Genomic Sci (2011)

Bottom Line: H. aurantiacus cells are organized in filaments which can rapidly glide.The species is of interest not only because of its rather isolated position in the tree of life, but also because Herpetosiphon ssp. were identified as predators capable of facultative predation by a wolf pack strategy and of degrading the prey organisms by excreted hydrolytic enzymes.The 6,346,587 bp long chromosome and the two 339,639 bp and 99,204 bp long plasmids with a total of 5,577 protein-coding and 77 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2005.

View Article: PubMed Central - PubMed

ABSTRACT
Herpetosiphon aurantiacus Holt and Lewin 1968 is the type species of the genus Herpetosiphon, which in turn is the type genus of the family Herpetosiphonaceae, type family of the order Herpetosiphonales in the phylum Chloroflexi. H. aurantiacus cells are organized in filaments which can rapidly glide. The species is of interest not only because of its rather isolated position in the tree of life, but also because Herpetosiphon ssp. were identified as predators capable of facultative predation by a wolf pack strategy and of degrading the prey organisms by excreted hydrolytic enzymes. The genome of H. aurantiacus strain 114-95(T) is the first completely sequenced genome of a member of the family Herpetosiphonaceae. The 6,346,587 bp long chromosome and the two 339,639 bp and 99,204 bp long plasmids with a total of 5,577 protein-coding and 77 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2005.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree highlighting the position of H. aurantiacus relative to the other type strains within the phylum Chloroflexi. The tree was inferred from 1,350 aligned characters [11,12] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [13]. Rooting was done initially using the midpoint method [14] 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 100 ML bootstrap replicates [15] (left) and from 1,000 maximum parsimony bootstrap replicates [16] (right) if the value is larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [17] are labeled with one asterisk, and those also listed as 'Complete and Published' with two asterisks (see [18,19] and AP012029 for Anaerolinea thermophila, CP002084 for Dehalogenimonas lykanthroporepellens, CP001337 for Chloroflexus aggregans, CP000909 C. aurantiacus, and CP000804 for Roseiflexus castenholzii).
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f1: Phylogenetic tree highlighting the position of H. aurantiacus relative to the other type strains within the phylum Chloroflexi. The tree was inferred from 1,350 aligned characters [11,12] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [13]. Rooting was done initially using the midpoint method [14] 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 100 ML bootstrap replicates [15] (left) and from 1,000 maximum parsimony bootstrap replicates [16] (right) if the value is larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [17] are labeled with one asterisk, and those also listed as 'Complete and Published' with two asterisks (see [18,19] and AP012029 for Anaerolinea thermophila, CP002084 for Dehalogenimonas lykanthroporepellens, CP001337 for Chloroflexus aggregans, CP000909 C. aurantiacus, and CP000804 for Roseiflexus castenholzii).

Mentions: Figure 1 shows the phylogenetic neighborhood of H. aurantiacus in a tree based upon 16S rRNA. The sequences of the five 16S rRNA gene copies in the genome differ from each other by up to two nucleotides, and differ by up to seven nucleotides from the previously published 16S rRNA sequence (M34117), which contains 64 ambiguous base calls.


Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95(T)).

Kiss H, Nett M, Domin N, Martin K, Maresca JA, Copeland A, Lapidus A, Lucas S, Berry KW, Glavina Del Rio T, Dalin E, Tice H, Pitluck S, Richardson P, Bruce D, Goodwin L, Han C, Detter JC, Schmutz J, Brettin T, Land M, Hauser L, Kyrpides NC, Ivanova N, Göker M, Woyke T, Klenk HP, Bryant DA - Stand Genomic Sci (2011)

Phylogenetic tree highlighting the position of H. aurantiacus relative to the other type strains within the phylum Chloroflexi. The tree was inferred from 1,350 aligned characters [11,12] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [13]. Rooting was done initially using the midpoint method [14] 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 100 ML bootstrap replicates [15] (left) and from 1,000 maximum parsimony bootstrap replicates [16] (right) if the value is larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [17] are labeled with one asterisk, and those also listed as 'Complete and Published' with two asterisks (see [18,19] and AP012029 for Anaerolinea thermophila, CP002084 for Dehalogenimonas lykanthroporepellens, CP001337 for Chloroflexus aggregans, CP000909 C. aurantiacus, and CP000804 for Roseiflexus castenholzii).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368417&req=5

f1: Phylogenetic tree highlighting the position of H. aurantiacus relative to the other type strains within the phylum Chloroflexi. The tree was inferred from 1,350 aligned characters [11,12] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [13]. Rooting was done initially using the midpoint method [14] 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 100 ML bootstrap replicates [15] (left) and from 1,000 maximum parsimony bootstrap replicates [16] (right) if the value is larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [17] are labeled with one asterisk, and those also listed as 'Complete and Published' with two asterisks (see [18,19] and AP012029 for Anaerolinea thermophila, CP002084 for Dehalogenimonas lykanthroporepellens, CP001337 for Chloroflexus aggregans, CP000909 C. aurantiacus, and CP000804 for Roseiflexus castenholzii).
Mentions: Figure 1 shows the phylogenetic neighborhood of H. aurantiacus in a tree based upon 16S rRNA. The sequences of the five 16S rRNA gene copies in the genome differ from each other by up to two nucleotides, and differ by up to seven nucleotides from the previously published 16S rRNA sequence (M34117), which contains 64 ambiguous base calls.

Bottom Line: H. aurantiacus cells are organized in filaments which can rapidly glide.The species is of interest not only because of its rather isolated position in the tree of life, but also because Herpetosiphon ssp. were identified as predators capable of facultative predation by a wolf pack strategy and of degrading the prey organisms by excreted hydrolytic enzymes.The 6,346,587 bp long chromosome and the two 339,639 bp and 99,204 bp long plasmids with a total of 5,577 protein-coding and 77 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2005.

View Article: PubMed Central - PubMed

ABSTRACT
Herpetosiphon aurantiacus Holt and Lewin 1968 is the type species of the genus Herpetosiphon, which in turn is the type genus of the family Herpetosiphonaceae, type family of the order Herpetosiphonales in the phylum Chloroflexi. H. aurantiacus cells are organized in filaments which can rapidly glide. The species is of interest not only because of its rather isolated position in the tree of life, but also because Herpetosiphon ssp. were identified as predators capable of facultative predation by a wolf pack strategy and of degrading the prey organisms by excreted hydrolytic enzymes. The genome of H. aurantiacus strain 114-95(T) is the first completely sequenced genome of a member of the family Herpetosiphonaceae. The 6,346,587 bp long chromosome and the two 339,639 bp and 99,204 bp long plasmids with a total of 5,577 protein-coding and 77 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2005.

No MeSH data available.


Related in: MedlinePlus