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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

Venn diagram showing a comparison of three different Desulfotomaculum genomes, D. ruminis DSM 2154T, D. acetoxidans DSM 771T and D. nigrificans DSM 564T. The number of overlapping protein genes is given inside the areas of the circles and the total number of derived protein sequences used for each strain is shown in parentheses. The figure was created using the program Venn diagram plotter available from the Pacific Northwest National Laboratory Software Distribution Center [51].
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f4: Venn diagram showing a comparison of three different Desulfotomaculum genomes, D. ruminis DSM 2154T, D. acetoxidans DSM 771T and D. nigrificans DSM 564T. The number of overlapping protein genes is given inside the areas of the circles and the total number of derived protein sequences used for each strain is shown in parentheses. The figure was created using the program Venn diagram plotter available from the Pacific Northwest National Laboratory Software Distribution Center [51].

Mentions: We analyzed the fraction of shared genes in three genomes of Desulfotomaculum species with validly published names. The genomes of D. acetoxidans [50] and D. ruminis [10] are complete, whereas the genome of the type species D. nigrificans is only available as a draft sequence. D. nigrificans has the smallest genome with 3,014 protein coding sequences. The resulting data are illustrated in the Venn diagram shown in [Figure 4]. The largest overlap is found between the strains D. nigrificans DSM 574T and D. ruminis DSM 2154T, which share 2,359 homologous proteins corresponding to 78.3% of the DSM 574T genes and 60.5% of the DSM 2154T genes. Thus, a closer relationship between D. ruminis DSM 2154T and D. nigrificans DSM 574T than between D. acetoxidans DSM 771T and D. nigrificans DSM 574T, as suggested by the 16S rRNA based phylogenetic tree, is confirmed by 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)

Venn diagram showing a comparison of three different Desulfotomaculum genomes, D. ruminis DSM 2154T, D. acetoxidans DSM 771T and D. nigrificans DSM 564T. The number of overlapping protein genes is given inside the areas of the circles and the total number of derived protein sequences used for each strain is shown in parentheses. The figure was created using the program Venn diagram plotter available from the Pacific Northwest National Laboratory Software Distribution Center [51].
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f4: Venn diagram showing a comparison of three different Desulfotomaculum genomes, D. ruminis DSM 2154T, D. acetoxidans DSM 771T and D. nigrificans DSM 564T. The number of overlapping protein genes is given inside the areas of the circles and the total number of derived protein sequences used for each strain is shown in parentheses. The figure was created using the program Venn diagram plotter available from the Pacific Northwest National Laboratory Software Distribution Center [51].
Mentions: We analyzed the fraction of shared genes in three genomes of Desulfotomaculum species with validly published names. The genomes of D. acetoxidans [50] and D. ruminis [10] are complete, whereas the genome of the type species D. nigrificans is only available as a draft sequence. D. nigrificans has the smallest genome with 3,014 protein coding sequences. The resulting data are illustrated in the Venn diagram shown in [Figure 4]. The largest overlap is found between the strains D. nigrificans DSM 574T and D. ruminis DSM 2154T, which share 2,359 homologous proteins corresponding to 78.3% of the DSM 574T genes and 60.5% of the DSM 2154T genes. Thus, a closer relationship between D. ruminis DSM 2154T and D. nigrificans DSM 574T than between D. acetoxidans DSM 771T and D. nigrificans DSM 574T, as suggested by the 16S rRNA based phylogenetic tree, is confirmed by 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