Genome Sequencing and Comparative Genomics of Rhodococcus sp. strain DK17, a Superb Aromatic Hydrocarbon Degrader

Abstract

The metabolically versatile Rhodococcus sp. strain DK17 has the capability to utilize various derivatives of benzene (e.g. BTEX, n-propyl to n-hexylbenzenes, phenol, and phthalates) and bicyclics containing both aromatic and alicyclic moieties (e.g. indan and tetralin) as sole carbon and energy sources. In an effort to fully understand the metabolic versatility of DK17, its genome was sequenced using Roche/454 FLX technology and assembled with Newbler assembler version 2.3 software and CLC Genomics Workbench 4.5.1. Optical mapping was performed to confirm the assembly output. The 9,155,319-bp draft genome sequence with a G+C content of 66% consists of 135 contigs in 27 scaffolds and contains 9,407 ORFs. The ORF annotation by COG and RAST results in the classification into 22 COG categories (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V) with a total of 6,238 COGs. Comparison to other Rhodococcus species indicated that DK17 is most closely related to Rhodococcus jostii RHA1 among 11 Rhodococcus species whose genome sequences are available in the NCBI database. Sequence alignment between ORFs from DK17 and RHA1 revealed that 74% of the ORFs (6,966) share over 90% identity with each other while 23% of the ORFs (2,157) are only present in DK17. Among the remaining 284 ORFs, 63, 39, 16, and 86 ORFs share identity ranging from 80~89, 70~79, 60~69, and 50~59% with those of RHA1oieties (e.g. indan and tetralin) as sole carbon and energy sources.