Genome Sequence of Rhodococcus sp. Strain PML026, a Trehalolipid Biosurfactant Producer and Biodegrader of Oil and Alkanes.

Rhodococcus sp. strain PML026 produces an array of trehalolipid biosurfactant compounds in order to utilize hydrophobic carbon sources, such as oils and alkanes. Here, we report the high-quality draft genome sequence of this strain, which has a total length of 5,168,404 bp containing 4,835 protein-coding sequences, 12 rRNAs, and 45 tRNAs.

GENOME ANNOUNCEMENT

Members of the Rhodococcus genus are well known for their ability to produce cell-bound and extracellular trehalolipid biosurfactant compounds in the presence of hydrophobic substrates (1–3). Trehalolipids exhibit a range of potential bioactivities (4–9) and are excellent emulsifying compounds with applications in microbe-enhanced oil recovery and oil spill treatment (10, 11). Rhodococcus sp. strain PML026 is a novel marine bacterium that was recently isolated and shown to produce a range of trehalolipid compounds in order to assimilate oil and alkanes (12). To better understand the trehalolipid production and other abilities of this strain, a genome sequence analysis of Rhodococcus sp. PML026 was carried out.

Using the Illumina HiSeq 2500 platform, two paired-end libraries (insert sizes, 250 bp and 500 bp) and two mate-pair libraries (insert sizes, 9 kbp and 11 kbp) were sequenced, generating 146,696,910 pairs of sequence reads (100 bp) from the two paired-end libraries and 73,808,154 read pairs (100 bp) from the two mate-pair libraries. After duplicate removal using FastUniq (13) and filtering and trimming using Trim Galore, 93% of the read pairs (136,458,888) from the paired-end libraries were retained, and 78% of the read pairs (57,494,134) from the mate-pair libraries remained. Using subsets of the two paired-end libraries, ~5 million trimmed and filtered reads per library were used for genome assembly with SPAdes (version 3.1.1) (14) using the parameter --careful with k-mers of 21, 33, 55, 77, 99, and 127. Further scaffolding was performed with SSPACE (version 3) (15) using all trimmed and filtered paired-end reads and mate-pair reads. Finally, GapFiller (version 1-10) (16) was used to close 19 gaps, and incorrect scaffolds were split using REAPR (version 1.0.17). The resulting assembly consisted of 37 contigs in 16 scaffolds with a total length of 5,168,404 bp. Annotation was performed using Prokka (version 1.10) (17) using a genus database generated from four Rhodococcus sp. genomes, R. erythropolis PR4 (GenBank accession no. NC_012490), R. jostii RHA1 (GenBank accession no. NC_008268), R. opacus B4 (GenBank accession no. NC_012522), and R. pyridinivorans SB3094 (GenBank accession no. NC_023150). tRNAs and transfer-messenger RNAs (tmRNAs) were predicted using Aragorn (version 1.2), ribosomal RNAs with Barrnap (version 0.5), and coding sequences with Prodigal (version 2.60). The genome contains 4,835 protein-coding sequences, 12 rRNAs, and 45 tRNAs.

Nucleotide sequence accession number.

The genome sequence and annotation data for Rhodococcus sp. PML026 have been submitted to GenBank under the accession no. JZIS00000000.