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Draft genome sequence of Bacillus okhensis Kh10-101T, a halo-alkali tolerant bacterium from Indian saltpan.

Krishna PS, Sreenivas A, Singh DK, Shivaji S, Prakash JS - Genom Data (2015)

Bottom Line: This bacterium is a potential model to study the molecular response of bacteria to salt as well as alkaline stress, as it thrives under both high salt and high pH conditions.The draft genome consist of 4,865,284 bp with 38.2% G + C, 4952 predicted CDS, 157 tRNAs and 8 rRNAs.Sequence was deposited at DDBJ/EMBL/GenBank under the project accession JRJU00000000.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.

ABSTRACT
We report the 4.86-Mb draft genome sequence of Bacillus okhensis strain Kh10-101T, a halo-alkali tolerant rod shaped bacterium isolated from a salt pan near port of Okha, India. This bacterium is a potential model to study the molecular response of bacteria to salt as well as alkaline stress, as it thrives under both high salt and high pH conditions. The draft genome consist of 4,865,284 bp with 38.2% G + C, 4952 predicted CDS, 157 tRNAs and 8 rRNAs. Sequence was deposited at DDBJ/EMBL/GenBank under the project accession JRJU00000000.

No MeSH data available.


Related in: MedlinePlus

Subsystem category distribution statistics for B. okhensis strain Kh10-101T. The complete genome sequence of B. okhensis was annotated using the Rapid Annotation System Technology (RAST) server. The pie chart showed the count of each subsystem feature and the subsystem coverage. The green bar of the subsystem coverage corresponds to the percentage of the proteins included in the subsystems while the blue bar corresponds to the percentage of the proteins that are not included in the subsystems.
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f0005: Subsystem category distribution statistics for B. okhensis strain Kh10-101T. The complete genome sequence of B. okhensis was annotated using the Rapid Annotation System Technology (RAST) server. The pie chart showed the count of each subsystem feature and the subsystem coverage. The green bar of the subsystem coverage corresponds to the percentage of the proteins included in the subsystems while the blue bar corresponds to the percentage of the proteins that are not included in the subsystems.

Mentions: Genome sequencing resulted in a total of 3,18,628 high quality reads with approximately 28 × coverage of the entire genome. All reads were assembled using Newbler assembler (Roche Life sciences). Assembly resulted in an average contig size of 49,645 bp. N50 contig size is 115,121 bp and the largest contig size is 349,697 bp. Total 98 high quality contigs, with size greater than 500 bp were assembled. Final assembled draft genome size is 4,865,284 bp (4.86 Mb) with 38.2% GC content. The genome size of B. okhensis is relatively larger than its closest and sequenced relatives, Bacillus halodurans (4.2 Mb) and B. pseudofirmus (3.85 Mb) showing its evolutionary significance. Annotation with RAST has shown a total of 4952 coding sequences, (45% annotated and 55% hypothetical) (Fig. 1). 165 RNA coding genes and 8 rRNA (6 numbers of 5S rRNA, one 23S rRNA and one 16S rRNA) genes were present (Table 1). Of the total protein coding genes, genes involved in carbohydrate metabolism, amino acid metabolism, cofactors, vitamins, prosthetic groups, protein metabolism, nucleic acid metabolism, respiration were dominant (Fig. 1). In addition, RAST annotation server predicted 136 genes to be involved in various stress responses. However, none of these stress responsive genes coded for acid stress responsive proteins. Further, despite the fact that B. okhensis is aerobic, genes involved in fermentation and acid production were identified. In addition, 145 genes code for the proteins that are involved in transport across the membrane, such as ABC transporters and cation transport proteins. Interestingly, it was observed that though spore formation does not occur in high salt and high pH conditions in B. okhensis, its genome has 131 genes encoding proteins related to spore formation and dormancy. The B. okhensis strain Kh10-101T whole genome shot gun (WGS) project has been deposited at DDBJ/EMBL/GenBank under the project accession JRJU00000000. The project (01) has the accession number JRJU01000000 and consists of sequences JRJU01000001:JRJU01000098. The version described in this paper is the first version. Comparative genome analysis and genome wide transcriptomic analysis of this halo-alakli tolerant strain will be helpful in better understanding of the mechanisms involved in salt and high pH tolerance.


Draft genome sequence of Bacillus okhensis Kh10-101T, a halo-alkali tolerant bacterium from Indian saltpan.

Krishna PS, Sreenivas A, Singh DK, Shivaji S, Prakash JS - Genom Data (2015)

Subsystem category distribution statistics for B. okhensis strain Kh10-101T. The complete genome sequence of B. okhensis was annotated using the Rapid Annotation System Technology (RAST) server. The pie chart showed the count of each subsystem feature and the subsystem coverage. The green bar of the subsystem coverage corresponds to the percentage of the proteins included in the subsystems while the blue bar corresponds to the percentage of the proteins that are not included in the subsystems.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664779&req=5

f0005: Subsystem category distribution statistics for B. okhensis strain Kh10-101T. The complete genome sequence of B. okhensis was annotated using the Rapid Annotation System Technology (RAST) server. The pie chart showed the count of each subsystem feature and the subsystem coverage. The green bar of the subsystem coverage corresponds to the percentage of the proteins included in the subsystems while the blue bar corresponds to the percentage of the proteins that are not included in the subsystems.
Mentions: Genome sequencing resulted in a total of 3,18,628 high quality reads with approximately 28 × coverage of the entire genome. All reads were assembled using Newbler assembler (Roche Life sciences). Assembly resulted in an average contig size of 49,645 bp. N50 contig size is 115,121 bp and the largest contig size is 349,697 bp. Total 98 high quality contigs, with size greater than 500 bp were assembled. Final assembled draft genome size is 4,865,284 bp (4.86 Mb) with 38.2% GC content. The genome size of B. okhensis is relatively larger than its closest and sequenced relatives, Bacillus halodurans (4.2 Mb) and B. pseudofirmus (3.85 Mb) showing its evolutionary significance. Annotation with RAST has shown a total of 4952 coding sequences, (45% annotated and 55% hypothetical) (Fig. 1). 165 RNA coding genes and 8 rRNA (6 numbers of 5S rRNA, one 23S rRNA and one 16S rRNA) genes were present (Table 1). Of the total protein coding genes, genes involved in carbohydrate metabolism, amino acid metabolism, cofactors, vitamins, prosthetic groups, protein metabolism, nucleic acid metabolism, respiration were dominant (Fig. 1). In addition, RAST annotation server predicted 136 genes to be involved in various stress responses. However, none of these stress responsive genes coded for acid stress responsive proteins. Further, despite the fact that B. okhensis is aerobic, genes involved in fermentation and acid production were identified. In addition, 145 genes code for the proteins that are involved in transport across the membrane, such as ABC transporters and cation transport proteins. Interestingly, it was observed that though spore formation does not occur in high salt and high pH conditions in B. okhensis, its genome has 131 genes encoding proteins related to spore formation and dormancy. The B. okhensis strain Kh10-101T whole genome shot gun (WGS) project has been deposited at DDBJ/EMBL/GenBank under the project accession JRJU00000000. The project (01) has the accession number JRJU01000000 and consists of sequences JRJU01000001:JRJU01000098. The version described in this paper is the first version. Comparative genome analysis and genome wide transcriptomic analysis of this halo-alakli tolerant strain will be helpful in better understanding of the mechanisms involved in salt and high pH tolerance.

Bottom Line: This bacterium is a potential model to study the molecular response of bacteria to salt as well as alkaline stress, as it thrives under both high salt and high pH conditions.The draft genome consist of 4,865,284 bp with 38.2% G + C, 4952 predicted CDS, 157 tRNAs and 8 rRNAs.Sequence was deposited at DDBJ/EMBL/GenBank under the project accession JRJU00000000.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.

ABSTRACT
We report the 4.86-Mb draft genome sequence of Bacillus okhensis strain Kh10-101T, a halo-alkali tolerant rod shaped bacterium isolated from a salt pan near port of Okha, India. This bacterium is a potential model to study the molecular response of bacteria to salt as well as alkaline stress, as it thrives under both high salt and high pH conditions. The draft genome consist of 4,865,284 bp with 38.2% G + C, 4952 predicted CDS, 157 tRNAs and 8 rRNAs. Sequence was deposited at DDBJ/EMBL/GenBank under the project accession JRJU00000000.

No MeSH data available.


Related in: MedlinePlus