Instructions for use Title Genome Sequence of Rhodococcus erythropolis Type Strain JCM

Rhodococcus erythropolis JCM 3201 can express several recombinant proteins that are difficult to express in Escherichia coli. It is used as one of the hosts for protein expression and bioconversion. Here, we report the draft genome sequence of R. erythropolis JCM 3201. Rhodococci remarkably degrade various xenobiotics (1–3). The type strain of Rhodococcus erythropolis, JCM 3201, was originally isolated from soil as a degrader of aromatics (4). A lysozyme-sensitive mutant of JCM 3201, strain L88, has been used as an expression host of recombinant proteins that are difficult to express in Escherichia coli (5–9). JCM 3201 is also useful to the host for bioconversion of chemicals such as vitamin D3 to hydroxyvitamin D3 (10–12). To optimize these processes thorough metabolic pathway engineering, its genomic information will be essential. The draft genome of JCM 3201 was previously deposited with 67 contigs (GenBank accession number BCRM00000000). However, this sequence lacks information about the numbers and structural type of its chromosomes and plasmids. To improve the genome assembly level, we resequenced the JCM 3201 genome. We cultured the strain in LB broth containing 1% glycine, lysed cells with 2 mg ml 1 lysozyme, and extracted the genomic DNA by the phenol-chloroform method (13). We prepared three libraries with the TruSeq DNA PCR-free library prep kit (Illumina), the Nextera mate pair sample preparation kit (Illumina), and the DNA template prep kit version 1.0 (PacBio). The genome was sequenced using (i) an Illumina HiSeq 2500 platform with 350-bp paired-end and 8-kbp mate pair libraries and (ii) a PacBio RS II platform. The PacBio raw reads were filtered with SMRT Analysis version 2.3. 0 with the following parameters: minimum subread length, 500; minimum polymerase read quality, 0.80; and minimum polymerase read length, 100. We obtained 98,981 subreads and assembled them with the Hierarchical Genome Assembly Process (HGAP) version 2 (14), resulting in a 6.33-Mbp circular sequence with a mean coverage of 84-fold. The paired-end and mate pair reads were filtered with Trimmomatic version 0.38 with the parameters SLIDINGWINDOW:20:20 and MINLEN:50 (15), resulting in 14,661,238 and 9,431,622 reads, respectively. We assembled these reads using Velvet version 1.2. 08 (16) and obtained 52 contigs. Among these contigs, 12 did not match the circular PacBio assembly, which showed the highest similarities to plasmid sequences of other R. erythropolis strains (17). To confirm the possibility that these contigs were derived from plasmid sequences, we examined their connectivity by PCR and finally obtained another 85-kb circular sequence and a 241-kb linear sequence. Based on their sizes, we predicted that these two sequences were plasmids. One end of the linear sequence showed similarity to end sequences of linear plasmids in rhodococci. However, the Citation Yoshida K, Kitagawa W, Ishiya K, Mitani Y, Nakashima N, Aburatani S, Tamura T. 2019. Genome sequence of Rhodococcus erythropolis type strain JCM 3201. Microbiol Resour Announc 8:e01730-18. https://doi.org/10.1128/ MRA.01730-18. Editor Jason E. Stajich, University of California, Riverside Copyright © 2019 Yoshida et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Tomohiro Tamura, t-tamura@aist.go. jp. Received 3 January 2019 Accepted 27 February 2019 Published 4 April 2019 GENOME SEQUENCES