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High quality genome sequence and description of Enterobacter mori strain 5-4, isolated from a mixture of formation water and crude-oil.

Zhang F, Su S, Yu G, Zheng B, Shu F, Wang Z, Xiang T, Dong H, Zhang Z, Hou D, She Y - Stand Genomic Sci (2015)

Bottom Line: To date, there is only one E. mori genome has been sequenced and very little knowledge about the mechanism of E. mori adapted to the petroleum reservoir.Here, we report the second E. mori genome sequence and annotation, together with the description of features for this organism.The 4,621,281 bp assembly genome exhibits a G + C content of 56.24% and contains 4,317 protein-coding and 65 RNA genes, including 5 rRNA genes.

View Article: PubMed Central - PubMed

Affiliation: The Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism, School of Energy Resources, China University of Geosciences, Beijing, China.

ABSTRACT
Enterobacter mori strain 5-4 is a Gram-negative, motile, rod shaped, and facultatively anaerobic bacterium, which was isolated from a mixture of formation water (also known as oil-reservior water) and crude-oil in Karamay oilfield, China. To date, there is only one E. mori genome has been sequenced and very little knowledge about the mechanism of E. mori adapted to the petroleum reservoir. Here, we report the second E. mori genome sequence and annotation, together with the description of features for this organism. The 4,621,281 bp assembly genome exhibits a G + C content of 56.24% and contains 4,317 protein-coding and 65 RNA genes, including 5 rRNA genes.

No MeSH data available.


Related in: MedlinePlus

Genome comparison betweenE. mori5–4andE. moriLMG 25706T. (A). Alignment is represented as local colinear blocks (colored) filled with a similarity plot. Height of the similarity plot indicates nucleotide identity of both assemblies; (B). Numbers inside the Venn diagrams indicate the number of genes found to be shared among the indicated genomes.
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Fig3: Genome comparison betweenE. mori5–4andE. moriLMG 25706T. (A). Alignment is represented as local colinear blocks (colored) filled with a similarity plot. Height of the similarity plot indicates nucleotide identity of both assemblies; (B). Numbers inside the Venn diagrams indicate the number of genes found to be shared among the indicated genomes.

Mentions: Genome alignment between E. mori 5–4 (JFHW00000000) and E. mori type strain LMG 25706 T (AEXB00000000) was performed by using Mauve [42]. Orthology identification was carried out by a modified method introduced by Lerat [43]. Genome alignment showed that some functional regions are highly homologous between these two assemblies. The alignment also reveals some discrepancies between them, some short stretches of LMG 25706 T genome absent from the contigs in 5–4 (Figure 3A). However, two alkane 1-monooxygenase, one alkanesulfonate monooxygenase, one putative alkanesulfonate transporter, one putative sulfate permease and one alkanesulfonate transporter permease subunit were identified in the genome. Alkane 1-monooxygenase was found as one of the key enzymes responsible for the aerobic transformation of n-alkanes [44]. Moreover, alkanesulfonate monooxygenase and alkanesulfonate transporter may be responsible for organosulfur compound degradation [45]. Comparison of these two strains revealed the presence of a large core-genome (Figure 3B). They shared 3555 CDS in the genome. In addition, 759 CDS from the 5–4 genome were classified as unique, while 1097 CDS from the LMG 25706 T genome were classified as unique. Our genomic data will provide an excellent platform for further improvement of this organism for potential application in bioremediation.Figure 3


High quality genome sequence and description of Enterobacter mori strain 5-4, isolated from a mixture of formation water and crude-oil.

Zhang F, Su S, Yu G, Zheng B, Shu F, Wang Z, Xiang T, Dong H, Zhang Z, Hou D, She Y - Stand Genomic Sci (2015)

Genome comparison betweenE. mori5–4andE. moriLMG 25706T. (A). Alignment is represented as local colinear blocks (colored) filled with a similarity plot. Height of the similarity plot indicates nucleotide identity of both assemblies; (B). Numbers inside the Venn diagrams indicate the number of genes found to be shared among the indicated genomes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4940761&req=5

Fig3: Genome comparison betweenE. mori5–4andE. moriLMG 25706T. (A). Alignment is represented as local colinear blocks (colored) filled with a similarity plot. Height of the similarity plot indicates nucleotide identity of both assemblies; (B). Numbers inside the Venn diagrams indicate the number of genes found to be shared among the indicated genomes.
Mentions: Genome alignment between E. mori 5–4 (JFHW00000000) and E. mori type strain LMG 25706 T (AEXB00000000) was performed by using Mauve [42]. Orthology identification was carried out by a modified method introduced by Lerat [43]. Genome alignment showed that some functional regions are highly homologous between these two assemblies. The alignment also reveals some discrepancies between them, some short stretches of LMG 25706 T genome absent from the contigs in 5–4 (Figure 3A). However, two alkane 1-monooxygenase, one alkanesulfonate monooxygenase, one putative alkanesulfonate transporter, one putative sulfate permease and one alkanesulfonate transporter permease subunit were identified in the genome. Alkane 1-monooxygenase was found as one of the key enzymes responsible for the aerobic transformation of n-alkanes [44]. Moreover, alkanesulfonate monooxygenase and alkanesulfonate transporter may be responsible for organosulfur compound degradation [45]. Comparison of these two strains revealed the presence of a large core-genome (Figure 3B). They shared 3555 CDS in the genome. In addition, 759 CDS from the 5–4 genome were classified as unique, while 1097 CDS from the LMG 25706 T genome were classified as unique. Our genomic data will provide an excellent platform for further improvement of this organism for potential application in bioremediation.Figure 3

Bottom Line: To date, there is only one E. mori genome has been sequenced and very little knowledge about the mechanism of E. mori adapted to the petroleum reservoir.Here, we report the second E. mori genome sequence and annotation, together with the description of features for this organism.The 4,621,281 bp assembly genome exhibits a G + C content of 56.24% and contains 4,317 protein-coding and 65 RNA genes, including 5 rRNA genes.

View Article: PubMed Central - PubMed

Affiliation: The Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism, School of Energy Resources, China University of Geosciences, Beijing, China.

ABSTRACT
Enterobacter mori strain 5-4 is a Gram-negative, motile, rod shaped, and facultatively anaerobic bacterium, which was isolated from a mixture of formation water (also known as oil-reservior water) and crude-oil in Karamay oilfield, China. To date, there is only one E. mori genome has been sequenced and very little knowledge about the mechanism of E. mori adapted to the petroleum reservoir. Here, we report the second E. mori genome sequence and annotation, together with the description of features for this organism. The 4,621,281 bp assembly genome exhibits a G + C content of 56.24% and contains 4,317 protein-coding and 65 RNA genes, including 5 rRNA genes.

No MeSH data available.


Related in: MedlinePlus