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Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method.

Uchino Y, Miura T, Hosoyama A, Ohji S, Yamazoe A, Ito M, Takahata Y, Suzuki K, Fujita N - Stand Genomic Sci (2015)

Bottom Line: A novel Dehalococcoides sp. strain UCH007 was isolated from the groundwater polluted with chlorinated ethenes in Japan.This strain is capable of dechlorinating trichloroethene, cis-1,2-dichloroethene and vinyl chloride to ethene.Strain UCH007 is the first strain in the Victoria subgroup found to possess the pceA, tceA and vcrA genes.

View Article: PubMed Central - PubMed

Affiliation: Biological Resource Center, National Institute of Technology and Evaluation, 2-10-49 Nishihara, Tokyo, 151-0066 Japan.

ABSTRACT
A novel Dehalococcoides sp. strain UCH007 was isolated from the groundwater polluted with chlorinated ethenes in Japan. This strain is capable of dechlorinating trichloroethene, cis-1,2-dichloroethene and vinyl chloride to ethene. Dehalococcoides bacteria are hardly cultivable, so genome sequencing has presented a challenge. In this study, we developed a differential reads picking method for mixed genomic DNA obtained from a co-culture, and applied it to the sequencing of strain UCH007. The genome of strain UCH007 consists of a 1,473,548-bp chromosome that encodes 1509 coding sequences including 29 putative reductive dehalogenase genes. Strain UCH007 is the first strain in the Victoria subgroup found to possess the pceA, tceA and vcrA genes.

No MeSH data available.


Related in: MedlinePlus

The scheme of the differential reads picking method for sequencing of Dehalococcoides sp. strain UCH007
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Fig3: The scheme of the differential reads picking method for sequencing of Dehalococcoides sp. strain UCH007

Mentions: It was difficult to obtain sufficient genomic DNA for direct shotgun sequencing from the pure culture of strain UCH007. It was also difficult to construct a complete genome sequence using reads generated by WGA because of the high abundance of chimeric reads. Therefore, direct shotgun sequencing was performed using the mixed genomic DNA obtained from the co-culture. Then, the differential reads picking method (Fig. 3) was applied to pick up reads that originated from strain UCH007.Fig. 3


Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method.

Uchino Y, Miura T, Hosoyama A, Ohji S, Yamazoe A, Ito M, Takahata Y, Suzuki K, Fujita N - Stand Genomic Sci (2015)

The scheme of the differential reads picking method for sequencing of Dehalococcoides sp. strain UCH007
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4644273&req=5

Fig3: The scheme of the differential reads picking method for sequencing of Dehalococcoides sp. strain UCH007
Mentions: It was difficult to obtain sufficient genomic DNA for direct shotgun sequencing from the pure culture of strain UCH007. It was also difficult to construct a complete genome sequence using reads generated by WGA because of the high abundance of chimeric reads. Therefore, direct shotgun sequencing was performed using the mixed genomic DNA obtained from the co-culture. Then, the differential reads picking method (Fig. 3) was applied to pick up reads that originated from strain UCH007.Fig. 3

Bottom Line: A novel Dehalococcoides sp. strain UCH007 was isolated from the groundwater polluted with chlorinated ethenes in Japan.This strain is capable of dechlorinating trichloroethene, cis-1,2-dichloroethene and vinyl chloride to ethene.Strain UCH007 is the first strain in the Victoria subgroup found to possess the pceA, tceA and vcrA genes.

View Article: PubMed Central - PubMed

Affiliation: Biological Resource Center, National Institute of Technology and Evaluation, 2-10-49 Nishihara, Tokyo, 151-0066 Japan.

ABSTRACT
A novel Dehalococcoides sp. strain UCH007 was isolated from the groundwater polluted with chlorinated ethenes in Japan. This strain is capable of dechlorinating trichloroethene, cis-1,2-dichloroethene and vinyl chloride to ethene. Dehalococcoides bacteria are hardly cultivable, so genome sequencing has presented a challenge. In this study, we developed a differential reads picking method for mixed genomic DNA obtained from a co-culture, and applied it to the sequencing of strain UCH007. The genome of strain UCH007 consists of a 1,473,548-bp chromosome that encodes 1509 coding sequences including 29 putative reductive dehalogenase genes. Strain UCH007 is the first strain in the Victoria subgroup found to possess the pceA, tceA and vcrA genes.

No MeSH data available.


Related in: MedlinePlus