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Complete genome sequencing and analysis of Saprospira grandis str. Lewin, a predatory marine bacterium.

Saw JH, Yuryev A, Kanbe M, Hou S, Young AG, Aizawa S, Alam M - Stand Genomic Sci (2012)

Bottom Line: Genome analysis revealed incomplete pathways for the biosynthesis of nine essential amino acids but presence of a large number of peptidases.The genome encodes multiple copies of sensor globin-coupled rsbR genes thought to be essential for stress response and the presence of such sensor globins in Bacteroidetes is unprecedented.A total of 429 spacer sequences within the three CRISPR repeat regions were identified in the genome and this number is the largest among all the Bacteroidetes sequenced to date.

View Article: PubMed Central - PubMed

ABSTRACT
Saprospira grandis is a coastal marine bacterium that can capture and prey upon other marine bacteria using a mechanism known as 'ixotrophy'. Here, we present the complete genome sequence of Saprospira grandis str. Lewin isolated from La Jolla beach in San Diego, California. The complete genome sequence comprises a chromosome of 4.35 Mbp and a plasmid of 54.9 Kbp. Genome analysis revealed incomplete pathways for the biosynthesis of nine essential amino acids but presence of a large number of peptidases. The genome encodes multiple copies of sensor globin-coupled rsbR genes thought to be essential for stress response and the presence of such sensor globins in Bacteroidetes is unprecedented. A total of 429 spacer sequences within the three CRISPR repeat regions were identified in the genome and this number is the largest among all the Bacteroidetes sequenced to date.

No MeSH data available.


Related in: MedlinePlus

Clustered heatmap representations of S. grandis str. Lewin and other completely sequenced Bacteroidetes species based on the presence or absence of 14,228 orthologous genes identified.
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Related In: Results  -  Collection


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f3: Clustered heatmap representations of S. grandis str. Lewin and other completely sequenced Bacteroidetes species based on the presence or absence of 14,228 orthologous genes identified.

Mentions: In order to better understand the ecophysiology and phylogeny of S. grandis, we profiled the complete genomes of 46 Bacteroidetes (including S. grandis str. Lewin) and 1 Chlorobi based on 14,228 orthologous groups identified between them. ORFs from these genomes were searched against each other using reciprocal BLAST hit (RBH) method. Orthologous genes shared between the organisms were identified by the Markov Clustering method using OrthoMCL [41,42]. A 14,228 × 47 matrix table based on the presence or absence of these orthologs was then imported to R program [43] and “gplots” package was used to calculate the Pearson correlation and to represent the correlation matrix using a heatmap plot (Figure 3).


Complete genome sequencing and analysis of Saprospira grandis str. Lewin, a predatory marine bacterium.

Saw JH, Yuryev A, Kanbe M, Hou S, Young AG, Aizawa S, Alam M - Stand Genomic Sci (2012)

Clustered heatmap representations of S. grandis str. Lewin and other completely sequenced Bacteroidetes species based on the presence or absence of 14,228 orthologous genes identified.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3368406&req=5

f3: Clustered heatmap representations of S. grandis str. Lewin and other completely sequenced Bacteroidetes species based on the presence or absence of 14,228 orthologous genes identified.
Mentions: In order to better understand the ecophysiology and phylogeny of S. grandis, we profiled the complete genomes of 46 Bacteroidetes (including S. grandis str. Lewin) and 1 Chlorobi based on 14,228 orthologous groups identified between them. ORFs from these genomes were searched against each other using reciprocal BLAST hit (RBH) method. Orthologous genes shared between the organisms were identified by the Markov Clustering method using OrthoMCL [41,42]. A 14,228 × 47 matrix table based on the presence or absence of these orthologs was then imported to R program [43] and “gplots” package was used to calculate the Pearson correlation and to represent the correlation matrix using a heatmap plot (Figure 3).

Bottom Line: Genome analysis revealed incomplete pathways for the biosynthesis of nine essential amino acids but presence of a large number of peptidases.The genome encodes multiple copies of sensor globin-coupled rsbR genes thought to be essential for stress response and the presence of such sensor globins in Bacteroidetes is unprecedented.A total of 429 spacer sequences within the three CRISPR repeat regions were identified in the genome and this number is the largest among all the Bacteroidetes sequenced to date.

View Article: PubMed Central - PubMed

ABSTRACT
Saprospira grandis is a coastal marine bacterium that can capture and prey upon other marine bacteria using a mechanism known as 'ixotrophy'. Here, we present the complete genome sequence of Saprospira grandis str. Lewin isolated from La Jolla beach in San Diego, California. The complete genome sequence comprises a chromosome of 4.35 Mbp and a plasmid of 54.9 Kbp. Genome analysis revealed incomplete pathways for the biosynthesis of nine essential amino acids but presence of a large number of peptidases. The genome encodes multiple copies of sensor globin-coupled rsbR genes thought to be essential for stress response and the presence of such sensor globins in Bacteroidetes is unprecedented. A total of 429 spacer sequences within the three CRISPR repeat regions were identified in the genome and this number is the largest among all the Bacteroidetes sequenced to date.

No MeSH data available.


Related in: MedlinePlus