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Complete genome sequence of the halophilic and highly halotolerant Chromohalobacter salexigens type strain (1H11(T)).

Copeland A, O'Connor K, Lucas S, Lapidus A, Berry KW, Detter JC, Del Rio TG, Hammon N, Dalin E, Tice H, Pitluck S, Bruce D, Goodwin L, Han C, Tapia R, Saunders E, Schmutz J, Brettin T, Larimer F, Land M, Hauser L, Vargas C, Nieto JJ, Kyrpides NC, Ivanova N, Göker M, Klenk HP, Csonka LN, Woyke T - Stand Genomic Sci (2011)

Bottom Line: Chromohalobacter salexigens is one of nine currently known species of the genus Chromohalobacter in the family Halomonadaceae.C. salexigens strain 1H11(T) and Halomonas elongata are the first and the second members of the family Halomonadaceae with a completely sequenced genome.The 3,696,649 bp long chromosome with a total of 3,319 protein-coding and 93 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2004.

View Article: PubMed Central - PubMed

ABSTRACT
Chromohalobacter salexigens is one of nine currently known species of the genus Chromohalobacter in the family Halomonadaceae. It is the most halotolerant of the so-called 'moderately halophilic bacteria' currently known and, due to its strong euryhaline phenotype, it is an established model organism for prokaryotic osmoadaptation. C. salexigens strain 1H11(T) and Halomonas elongata are the first and the second members of the family Halomonadaceae with a completely sequenced genome. The 3,696,649 bp long chromosome with a total of 3,319 protein-coding and 93 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2004.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree highlighting the position of C. salexigens relative to the type strains of the other species within the genus and the type species of the other genera within the family Halomonadaceae. The tree was inferred from 1,440 aligned characters [13,14] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [15]. Rooting was done initially using the midpoint method [16] 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 1,000 ML bootstrap replicates [17] (left) and from 1,000 maximum parsimony bootstrap replicates [18] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [19] are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks [20].
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f1: Phylogenetic tree highlighting the position of C. salexigens relative to the type strains of the other species within the genus and the type species of the other genera within the family Halomonadaceae. The tree was inferred from 1,440 aligned characters [13,14] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [15]. Rooting was done initially using the midpoint method [16] 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 1,000 ML bootstrap replicates [17] (left) and from 1,000 maximum parsimony bootstrap replicates [18] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [19] are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks [20].

Mentions: Figure 1 shows the phylogenetic neighborhood of C. salexigens in a 16S rRNA based tree. The sequences of the five identical 16S rRNA gene copies in the genome differ by two nucleotides from the previously published 16S rRNA sequence (AJ295146), which contains three ambiguous base calls.


Complete genome sequence of the halophilic and highly halotolerant Chromohalobacter salexigens type strain (1H11(T)).

Copeland A, O'Connor K, Lucas S, Lapidus A, Berry KW, Detter JC, Del Rio TG, Hammon N, Dalin E, Tice H, Pitluck S, Bruce D, Goodwin L, Han C, Tapia R, Saunders E, Schmutz J, Brettin T, Larimer F, Land M, Hauser L, Vargas C, Nieto JJ, Kyrpides NC, Ivanova N, Göker M, Klenk HP, Csonka LN, Woyke T - Stand Genomic Sci (2011)

Phylogenetic tree highlighting the position of C. salexigens relative to the type strains of the other species within the genus and the type species of the other genera within the family Halomonadaceae. The tree was inferred from 1,440 aligned characters [13,14] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [15]. Rooting was done initially using the midpoint method [16] 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 1,000 ML bootstrap replicates [17] (left) and from 1,000 maximum parsimony bootstrap replicates [18] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [19] are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks [20].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368415&req=5

f1: Phylogenetic tree highlighting the position of C. salexigens relative to the type strains of the other species within the genus and the type species of the other genera within the family Halomonadaceae. The tree was inferred from 1,440 aligned characters [13,14] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [15]. Rooting was done initially using the midpoint method [16] 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 1,000 ML bootstrap replicates [17] (left) and from 1,000 maximum parsimony bootstrap replicates [18] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [19] are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks [20].
Mentions: Figure 1 shows the phylogenetic neighborhood of C. salexigens in a 16S rRNA based tree. The sequences of the five identical 16S rRNA gene copies in the genome differ by two nucleotides from the previously published 16S rRNA sequence (AJ295146), which contains three ambiguous base calls.

Bottom Line: Chromohalobacter salexigens is one of nine currently known species of the genus Chromohalobacter in the family Halomonadaceae.C. salexigens strain 1H11(T) and Halomonas elongata are the first and the second members of the family Halomonadaceae with a completely sequenced genome.The 3,696,649 bp long chromosome with a total of 3,319 protein-coding and 93 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2004.

View Article: PubMed Central - PubMed

ABSTRACT
Chromohalobacter salexigens is one of nine currently known species of the genus Chromohalobacter in the family Halomonadaceae. It is the most halotolerant of the so-called 'moderately halophilic bacteria' currently known and, due to its strong euryhaline phenotype, it is an established model organism for prokaryotic osmoadaptation. C. salexigens strain 1H11(T) and Halomonas elongata are the first and the second members of the family Halomonadaceae with a completely sequenced genome. The 3,696,649 bp long chromosome with a total of 3,319 protein-coding and 93 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2004.

No MeSH data available.


Related in: MedlinePlus