Complete Genome Sequence of Gordonia sp. 135, a Promising Dibenzothiophene- and Hydrocarbon-Degrading Strain

Gordonia sp. strain 135 is a promising dibenzothiophene-desulfurizing and hydrocarbon-degrading bacterium. It can utilize dibenzothiophene as the sole sulfur source. The genome of strain 135 was completely sequenced; it consists of a 5,039,827-bp circular chromosome and a 164,963-bp circular plasmid.

G ordonia bacteria encompass a rich reservoir of metabolic diversity, which makes them attractive candidates for crude oil bioremediation (1). Most of the species present in this genus are capable of utilizing hydrocarbons and sulfur-containing organic compounds such as dibenzothiophene (DBT) (2,3). The strain Gordonia sp. 135 was isolated from oil-polluted soil (in Moscow, Russia). It is capable of crude oil and DBT degradation (strain certificate VKM Ac-2849D). For long-term storage, the strain was kept in glycerol (40%) stocks at Ϫ70° . For short-term maintenance, the strain was cultured on lysogeny broth agar plates at 27°C.
Genomic DNA was isolated from a fresh culture biomass (a colony) of Gordonia sp. 135 grown on LB agar using a DNeasy blood and tissue kit (catalog number 69506; Qiagen). Sequencing was performed using a MinION sequencer with the flow cell FLO-MIN106 (Oxford Nanopore Technologies [ONT]) (BioSpark, Moscow, Russia). A library was prepared with a rapid sequencing kit (catalog number SQK-RAD004). Guppy (version 3.2.4) software was used for base calling, which yielded a total of 100 Mbp distributed in 29,042 reads with a Q score of Ͼ10. Additionally, the same DNA sample was sequenced with an Illumina NovaSeq 6000 platform using an S2 reagent kit (catalog number 20012861; 2 ϫ 100 bp). A paired-end library was prepared with the Kapa HyperPlus kit (Roche). The Illumina and Nanopore reads were used for hybrid assembly with SPAdes (version 3.13.1) (4). The Nanopore reads were assembled into 4 contigs using Flye assembler version 2.6 (5). Next, SPAdes contigs were combined into two replicons with the help of Flye data which were used as reference sequences. The Illumina reads were used to correct Nanopore or assembly errors using Bowtie2 version 2.3.5.1 (6) and Pilon version 1.23 (7) software. Default parameters were used for all software.
The strain 135 genome was annotated with the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) version 4.6 (9). The chromosome contained 4,492 coding sequences, 4 rRNA clusters (5S, 16S, and 23S), and 51 tRNAs. The genome of Gordonia sp. 135 has no alkane hydroxylase gene (alkB) but does have 3 copies of cytochrome P450 hydroxylase (CYP153). So, we reasoned that alkane-degrading capabilities of the strain are associated mainly with the cytochrome P450 hydroxylase activity (10). The genes that may be responsible for DBT degradation were also detected.
The antiSMASH search for secondary metabolite clusters found 15 clusters on the chromosome, including clusters of ectoine and carotenoid production (11). The genome sequence data of Gordonia sp. 135 will enhance our understanding of the metabolic capabilities of Gordonia strains.
Data availability. This genome project has been deposited at GenBank under the accession numbers NZ_CP046257 for the chromosome and NZ_CP046258 for the plasmid and under BioSample number SAMN13326465, BioProject number PRJNA590456, and SRA accession number PRJNA590456.

ACKNOWLEDGMENT
This work was financially supported by the Russian Science Foundation (grant number 19-74-00097).