Draft Genome Sequence and Comparative Analysis of the Superb Aromatic-Hydrocarbon Degrader Rhodococcus sp. Strain DK17

Abstract

Rhodococcus sp. strain DK17 is capable of utilizing various derivatives of benzene and bicyclics containing both aromatic and alicyclic moieties as sole carbon and energy sources. Here, we present the 9,107,362-bp draft genome sequence of DK17 and its genomic analysis in comparison with other members of the genus Rhodococcus.

GENOME ANNOUNCEMENT

Members of the genus Rhodococcus demonstrate a remarkable ability to utilize a wide variety of natural organic and xenobiotic compounds, including aliphatic, aromatic, and alicyclic hydrocarbons (7). Rhodococcus sp. strain DK17 was isolated from a crude oil-contaminated site in Yeochon, South Korea, for the ability to grow on o-xylene as the sole source of carbon and energy and was later found to also have the ability to grow on benzene, toluene, ethylbenzene, isopropylbenzene, n-propyl- to n-hexylbenzenes, phenol, indan, tetralin, and phthalates (3, 5, 6). Strain DK17 possesses three linear megaplasmids (380-kb pDK1, 330-kb pDK2, and 750-kb pDK3). The genes for alkylbenzene degradation are present on pDK2, while the gene clusters for phthalate degradation are duplicated and found on both pDK2 and pDK3 (2, 4).

In an effort to fully understand the metabolic versatility of DK17, its genome was sequenced using Roche/454 GS FLX (577,562 reads) and Illumina GAIIx (32,685,616 reads) systems and assembled with Newbler assembler version 2.3 software (454 Life Sciences) and CLC Genomics Workbench version 4.5.1 (Illumina GAIIx) with totals of 9,107,362 bases in paired-end reads (totaling ∼9 Mb; ∼567-fold coverage of the genome). Optical mapping was performed to confirm the assembly output. The annotation was done by merging the results obtained from the RAST (Rapid Annotation using Subsystem Technology) server (1) and COG (Cluster of Orthologous Groups) database (8). Analysis of the unclosed draft genome sequence of strain DK17, consisting of 135 contigs in 27 scaffolds, showed that the G+C content is 67.15% and that the sequence contains 9,266 open reading frames (ORFs). Additionally, at least 48 tRNA genes and 4 rRNA operons were predicted in the draft genome. The ORF annotation by COG and RAST results in classification into 18 COG categories (J, K, L, D, O, M, N, P, T, C, G, E, F, H, I, Q, R, and S) with a total of 6,124 genes.

Comparison to the genome sequences of other Rhodococcus species indicated that DK17 is most closely related to the polychlorinated-biphenyl-degrading Rhodococcus jostii RHA1 among 14 Rhodococcus species whose genome sequences are available in the NCBI database. Sequence alignment between ORFs from DK17 and RHA1 using blastp (protein-protein BLAST) revealed that 75% of the ORFs (6,927) share over 90% identity with each other while 9% of the ORFs (824) are present only in DK17. Among the remaining 1,515 ORFs, 245, 130, 130, 99, and 491 ORFs share identity ranging from 80 to 89, 70 to 79, 60 to 69, 50 to 59, and less than 50% with those of RHA1, respectively, while the remaining 420 have nonreciprocal matches. The DK17-specific ORFs are not randomly distributed over the genome, but rather, they occur in groups or clusters. Analysis of the DK17-specific ORFs indicates that many encode proteins likely to be involved in catabolism or transport of organics, including aromatic hydrocarbons.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. AJLQ00000000. The version described in this paper is the first version, AJLQ01000000.