Genomic sequencing-based detection of large deletions in Rhodococcus rhodochrous strain B-276(MICROBIAL PHYSIOLOGY AND BIOTECHNOLOGY)

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概要

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• Bacteria of the genus Rhodococcus (Actinomycetes) have the ability to catabolize various organic compounds and are therefore considered potential genetic resources for applications such as bioremediation. We investigated a next-generation sequencing-based procedure to rapidly identify candidate functional gene(s) from rhodococci on the basis of their frequent genome recombination. The Rhodococcus rhodochrous strain B-276 and its alkene monooxygenase (AMO) gene cluster were the focus of our investigation. Firstly, 2 types of cultures of the R. rhodochrous strain B-276 were prepared, one of which was supplied with propene, which requires AMO genes for its assimilation, whereas the other was supplied with glucose as the sole energy source. The latter culture was anticipated to have a lower gene frequency of AMO genes because of their deletion during cultivation. We then conducted whole genome shotgun sequencing of the genomic DNA extracted from both cultures. Next, all sequence data were pooled and assembled into contiguous sequences (contigs). Finally, the abundance of each contig was quantified in order to detect contigs that were highly biased between the 2 cultures. We identified contigs that were overrepresented by 2 orders of magnitude in the AMO-required culture and successfully identified an AMO gene cluster among these contigs. We propose this procedure as an efficient method for the rapid detection and sequencing of deleted region, which contributes to identification of functional genes in rhodococci.

• 公益社団法人日本生物工学会の論文

著者

• Matsui Toru

  Tropical Biosphere Research Center, University of the Ryukyus

• Saitoh Seikoh

  Tropical Biosphere Research Center, University of the Ryukyus

• Aoyama Hiroaki

  Tropical Biosphere Research Center, University of the Ryukyus

• Akutsu Masako

  Tropical Biosphere Research Center, University of the Ryukyus

• Nakano Kazuma

  Tropical Biosphere Research Center, University of the Ryukyus

• Shinzato Naoya

  Tropical Biosphere Research Center, University of the Ryukyus

• Aoyama Hiroaki

  Tropical Biosphere Research Center, University of the Ryukyus:Laboratory of Cell and Functional Biology, Faculty of Science, University of the Ryukyus

関連論文

• Genomic sequencing-based detection of large deletions in Rhodococcus rhodochrous strain B-276(MICROBIAL PHYSIOLOGY AND BIOTECHNOLOGY)

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