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

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...

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Autores principales: Uchino, Yoshihito, Miura, Takamasa, Hosoyama, Akira, Ohji, Shoko, Yamazoe, Atsushi, Ito, Masako, Takahata, Yoh, Suzuki, Ken-ichiro, Fujita, Nobuyuki
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4644273/
https://www.ncbi.nlm.nih.gov/pubmed/26568785
http://dx.doi.org/10.1186/s40793-015-0095-9
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author Uchino, Yoshihito
Miura, Takamasa
Hosoyama, Akira
Ohji, Shoko
Yamazoe, Atsushi
Ito, Masako
Takahata, Yoh
Suzuki, Ken-ichiro
Fujita, Nobuyuki
author_facet Uchino, Yoshihito
Miura, Takamasa
Hosoyama, Akira
Ohji, Shoko
Yamazoe, Atsushi
Ito, Masako
Takahata, Yoh
Suzuki, Ken-ichiro
Fujita, Nobuyuki
author_sort Uchino, Yoshihito
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40793-015-0095-9) contains supplementary material, which is available to authorized users.
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spelling pubmed-46442732015-11-15 Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method Uchino, Yoshihito Miura, Takamasa Hosoyama, Akira Ohji, Shoko Yamazoe, Atsushi Ito, Masako Takahata, Yoh Suzuki, Ken-ichiro Fujita, Nobuyuki Stand Genomic Sci Short Genome Report 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40793-015-0095-9) contains supplementary material, which is available to authorized users. BioMed Central 2015-11-14 /pmc/articles/PMC4644273/ /pubmed/26568785 http://dx.doi.org/10.1186/s40793-015-0095-9 Text en © Uchino et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Short Genome Report
Uchino, Yoshihito
Miura, Takamasa
Hosoyama, Akira
Ohji, Shoko
Yamazoe, Atsushi
Ito, Masako
Takahata, Yoh
Suzuki, Ken-ichiro
Fujita, Nobuyuki
Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method
title Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method
title_full Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method
title_fullStr Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method
title_full_unstemmed Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method
title_short Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method
title_sort complete genome sequencing of dehalococcoides sp. strain uch007 using a differential reads picking method
topic Short Genome Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4644273/
https://www.ncbi.nlm.nih.gov/pubmed/26568785
http://dx.doi.org/10.1186/s40793-015-0095-9
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