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Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DL(T)).

Spring S, Visser M, Lu M, Copeland A, Lapidus A, Lucas S, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Ivanova N, Land M, Hauser L, Larimer F, Rohde M, Göker M, Detter JC, Kyrpides NC, Woyke T, Schaap PJ, Plugge CM, Muyzer G, Kuever J, Pereira IA, Parshina SN, Bernier-Latmani R, Stams AJ, Klenk HP - Stand Genomic Sci (2012)

Bottom Line: Desulfotomaculum ruminis Campbell and Postgate 1965 is a member of the large genus Desulfotomaculum which contains 30 species and is contained in the family Peptococcaceae.Here we describe the features of D. ruminis together with the complete genome sequence and annotation.The 3,969,014 bp long chromosome with a total of 3,901 protein-coding and 85 RNA genes is the second completed genome sequence of a type strain of the genus Desulfotomaculum to be published, and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2009.

View Article: PubMed Central - PubMed

Affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.

ABSTRACT
Desulfotomaculum ruminis Campbell and Postgate 1965 is a member of the large genus Desulfotomaculum which contains 30 species and is contained in the family Peptococcaceae. This species is of interest because it represents one of the few sulfate-reducing bacteria that have been isolated from the rumen. Here we describe the features of D. ruminis together with the complete genome sequence and annotation. The 3,969,014 bp long chromosome with a total of 3,901 protein-coding and 85 RNA genes is the second completed genome sequence of a type strain of the genus Desulfotomaculum to be published, and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2009.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree of the dsrAB protein sequences. The trees (6A and 6B) were inferred from proteins sequences using RAxML (maximum-likelihood) in the software program ARB. The sequences of Archaeoglobus fulgidus, A. profundus, and A. veneficus were used as outgroup, but were pruned from the tree. The sequence of D. ruminis is written in bold. The black circles are bootstrap values between 100-75%, the white circles are values between 75-50%. The scale bar corresponds to 10% estimated sequence divergence.
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f6A: Phylogenetic tree of the dsrAB protein sequences. The trees (6A and 6B) were inferred from proteins sequences using RAxML (maximum-likelihood) in the software program ARB. The sequences of Archaeoglobus fulgidus, A. profundus, and A. veneficus were used as outgroup, but were pruned from the tree. The sequence of D. ruminis is written in bold. The black circles are bootstrap values between 100-75%, the white circles are values between 75-50%. The scale bar corresponds to 10% estimated sequence divergence.

Mentions: Figures 5A and 5B show the organization of dsrAB (A), qmoBA, aprAB and hdrBC (B) and neighboring genes for D. ruminis, “D. reducens” and D. acetoxidans. In Figure 5 dsrD is upstream of dsrAB in all three strains. However, no other neighboring genes are similar to each other. In contrast, Figure 5B shows remarkable homology in gene organization for the aprAB gene neighborhood for D. ruminis and “D. reducens”. Gene sequence is also very similar for that region (53-94% identity for the genes displayed including hypothetical proteins) which suggests horizontal gene transfer from a common ancestor. The dsrAB and aprBA proteins of D. ruminis are more closely related to “D. reducens” than to D. acetoxidans [Figure 6A and 6B]. This is in accordance with the 16SrRNA based phylogenetic tree and the whole-genome data.


Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DL(T)).

Spring S, Visser M, Lu M, Copeland A, Lapidus A, Lucas S, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Ivanova N, Land M, Hauser L, Larimer F, Rohde M, Göker M, Detter JC, Kyrpides NC, Woyke T, Schaap PJ, Plugge CM, Muyzer G, Kuever J, Pereira IA, Parshina SN, Bernier-Latmani R, Stams AJ, Klenk HP - Stand Genomic Sci (2012)

Phylogenetic tree of the dsrAB protein sequences. The trees (6A and 6B) were inferred from proteins sequences using RAxML (maximum-likelihood) in the software program ARB. The sequences of Archaeoglobus fulgidus, A. profundus, and A. veneficus were used as outgroup, but were pruned from the tree. The sequence of D. ruminis is written in bold. The black circles are bootstrap values between 100-75%, the white circles are values between 75-50%. The scale bar corresponds to 10% estimated sequence divergence.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3569383&req=5

f6A: Phylogenetic tree of the dsrAB protein sequences. The trees (6A and 6B) were inferred from proteins sequences using RAxML (maximum-likelihood) in the software program ARB. The sequences of Archaeoglobus fulgidus, A. profundus, and A. veneficus were used as outgroup, but were pruned from the tree. The sequence of D. ruminis is written in bold. The black circles are bootstrap values between 100-75%, the white circles are values between 75-50%. The scale bar corresponds to 10% estimated sequence divergence.
Mentions: Figures 5A and 5B show the organization of dsrAB (A), qmoBA, aprAB and hdrBC (B) and neighboring genes for D. ruminis, “D. reducens” and D. acetoxidans. In Figure 5 dsrD is upstream of dsrAB in all three strains. However, no other neighboring genes are similar to each other. In contrast, Figure 5B shows remarkable homology in gene organization for the aprAB gene neighborhood for D. ruminis and “D. reducens”. Gene sequence is also very similar for that region (53-94% identity for the genes displayed including hypothetical proteins) which suggests horizontal gene transfer from a common ancestor. The dsrAB and aprBA proteins of D. ruminis are more closely related to “D. reducens” than to D. acetoxidans [Figure 6A and 6B]. This is in accordance with the 16SrRNA based phylogenetic tree and the whole-genome data.

Bottom Line: Desulfotomaculum ruminis Campbell and Postgate 1965 is a member of the large genus Desulfotomaculum which contains 30 species and is contained in the family Peptococcaceae.Here we describe the features of D. ruminis together with the complete genome sequence and annotation.The 3,969,014 bp long chromosome with a total of 3,901 protein-coding and 85 RNA genes is the second completed genome sequence of a type strain of the genus Desulfotomaculum to be published, and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2009.

View Article: PubMed Central - PubMed

Affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.

ABSTRACT
Desulfotomaculum ruminis Campbell and Postgate 1965 is a member of the large genus Desulfotomaculum which contains 30 species and is contained in the family Peptococcaceae. This species is of interest because it represents one of the few sulfate-reducing bacteria that have been isolated from the rumen. Here we describe the features of D. ruminis together with the complete genome sequence and annotation. The 3,969,014 bp long chromosome with a total of 3,901 protein-coding and 85 RNA genes is the second completed genome sequence of a type strain of the genus Desulfotomaculum to be published, and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2009.

No MeSH data available.


Related in: MedlinePlus