Here, we report the draft genome sequence of Rhodococcus aetherivorans JCM 14343T, which possesses the versatile ability to degrade recalcitrant noncyclic and cyclic ether compounds. The 4.2-Mbp genome of this bacterium contains alkane hydroxylase and propane monooxygenase genes involved in the degradation of noncyclic and cyclic ethers, respectively.
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