Whole genome of petroleum hydrocarbon degrading Rhodococcus indonesiensis isolated from Nacharam, Hyderabad, India

Petroleum pollution poses a critical environmental concern. Bioremediation has gained prominence as an eco-friendly approach for mitigating hydrocarbon pollution. This study reports the isolation and comprehensive characterization of a novel petroleum-degrading bacterium, Rhodococcus indonesiensis SARSHI1. Whole-genome sequencing was performed using a hybrid approach, integrating Oxford Nanopore Technologies (PromethION) and Illumina (NovaSeq 6000) platforms. The complete genome spans 5.7 Mbp and an additional plasmid of 159,118 bp, together encoding 5,150 coding sequences. Structural annotation identified 5220 genes, including 5094 protein-coding genes, one non-coding RNA, one CRISPR array, 56 pseudogenes, and 243 hypothetical proteins. Sequencing yielded 13,900,477 Illumina and 2,539,063 ONT reads, with 13,169,190 and 1,567,736 retained after quality processing, respectively. The assembly achieved 100% completeness with a coding density of 91.4%. Functional annotation revealed key hydrocarbon-degradation genes alkB, ahyA, and almA for long-chain alkanes, and bph, ben, and xylC for aromatics. Additionally, the presence of genes conferring multiple antibiotic resistances and those involved in secondary metabolite synthesis highlighted the strain's remarkable metabolic adaptability. The complete genome and plasmid sequences have been deposited in GenBank under accession numbers CP180630 and CP180631, respectively. The raw reads are available in the NCBI Sequence Read Archive (SRA) under accession numbers SRX27520007 (Illumina) and SRX27520006 (ONT).