Abstract
We present the complete genome sequence of Sphingomonas sp. gentR, a strain exhibiting high-level resistance to gentamicin (MIC = 40 mg/mL). The genome was assembled from hybrid Illumina and Nanopore sequencing data into a gap-free sequence of 4.0 Mbp, comprising one chromosome and two plasmids. A total of 3,692 coding sequences were predicted, with comprehensive functional annotation revealing genes associated with antibiotic resistance, stress adaptation, and metabolic diversity. Three confirmed resistance genes—ANT(2″)-Ia, ANT(3″)-IIa, and Sul1—were co-localized within a genomic island on plasmid B. This dataset provides insight into the genetic basis of high-level aminoglycoside resistance in Sphingomonas and serves as a valuable resource for studying horizontal gene transfer, environmental adaptation, and bioremediation potential. The genome sequence is publicly available under GenBank accessions CP144670–CP144672 and China National Genomics Data Center (accession number GWHDOHA00000000).
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Data availability
The sequencing data and assembled genome sequence generated in this study have been deposited in publicly accessible repositories. The details are as follows:
Raw sequencing reads
The datasets have been deposited in the NCBI Sequence Read Archive (SRA) under BioProject accession number PRJNA1072271 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1072271). The data are organized under BioSample SAMN39740430 and SRA experiment accession SRR3618163746. The repository contains the following files:
• JNDY-SC.fq.gz – Compressed FASTQ file containing Nanopore long reads.
• JNDY-SC_1.clean.fq.gz – Compressed FASTQ file containing paired-end Illumina short reads (read 1).
• JNDY-SC_2.clean.fq.gz – Compressed FASTQ file containing paired-end Illumina short reads (read 2).
Assembled Genome Sequence
The complete, annotated genome assembly of Sphingomonas sp. gentR has been deposited in the NCBI GenBank database under the same BioProject PRJNA1072271 and BioSample SAMN39740430. The assembly is available as a FASTA file (assembly.fna) and is organized into three records:
• CP144670: Chromosome sequence.
• CP144671: Plasmid A sequence.
• CP144672: Plasmid B sequence.
Genome Warehouse Access
The complete genome sequence is also available in the Genome Warehouse of the China National Genomics Data Center under accession number GWHDOHA00000000 (https://ngdc.cncb.ac.cn/gwh).
These datasets are freely accessible and can be used to explore the genomic basis of high-level gentamicin resistance and other functional traits in Sphingomonas sp. gentR.
Code availability
All software tools used in this study have been properly cited or accompanied by relevant website links. Unless otherwise specified in the manuscript, all data analyses were performed using default parameters as described in the respective software manuals. The running codes for genome assembly and annotation using Unicycler and prokka, respectively, have been uploaded as a supplementary information (SI1) to Figshare.
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Acknowledgements
This work was financially supported by the National Natural Science Foundation of China (Grant No. 32360880, 31360553).
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Jinhua Zhang and Baosheng Liu conceived the project. Yi Liu, Lijing Jiang and Qiufen Li collected the samples, performed the genome assembly, gene annotation and other bioinformatics analysis. Yi Liu and Lijing Jiang wrote the manuscript. Qiufen Li and Baosheng Liu revised the manuscript. Yi Liu and Lijing Jiang contributed equally to this work.
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Liu, Y., Jiang, L., Zhang, J. et al. Complete genome sequence of Sphingomonas sp. gentR, a high-level gentamicin-resistant bacterium. Sci Data (2026). https://doi.org/10.1038/s41597-026-06723-4
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DOI: https://doi.org/10.1038/s41597-026-06723-4
