We report here the 4.9-Mb genome sequence of a quinoline-degrading bacterium, Rhodococcus sp. strain ATCC 49988. The draft genome data will enable the identification of genes and future genetic modification to enhance traits relevant to heteroaromatic compound degradation.
ABSTRACT
We report here the 4.9-Mb genome sequence of a quinoline-degrading bacterium, Rhodococcus sp. strain ATCC 49988. The draft genome data will enable the identification of genes and future genetic modification to enhance traits relevant to heteroaromatic compound degradation.
ANNOUNCEMENT
Quinoline is a nitrogen-containing heterocyclic compound that is used as a solvent in the chemical industry and occurs widely in coal tar, oil shale, and plant alkaloids. It is known to be a mutagenic and carcinogenic compound (1). Due to its widespread use and toxic properties, the degradation of quinoline by microorganisms has been studied extensively. Rhodococcus sp. strain ATCC 49988 was isolated from soil by enrichment culture using quinoline as a dominant carbon, nitrogen, and energy source (2). In order to understand the genetic basis of quinoline degradation and other abilities of this strain, genome sequence analysis of Rhodococcus sp. strain ATCC 49988 was carried out.
Rhodococcus sp. strain ATCC 49988 was obtained from the ATCC. It was grown in tryptic soy broth at 30°C with shaking at 200 rpm for 16 h, after which DNA for whole-genome sequencing was isolated using a DNeasy PowerSoil kit (catalog number 12888-50; Qiagen), followed by preparation of an Illumina Nextera XT paired-end library. Whole-genome sequencing was performed using a MiSeq system (Illumina) and produced 13,615,724 (average length, 160 bp) paired-end reads. The raw sequence was processed using the KBase (3) platform (https://narrative.kbase.us/narrative/ws.39490.obj.1), and the sequence was uploaded in FASTQ format. During analysis, default parameters were used for all software, unless otherwise specified. The read quality was assessed using FastQC v 0.11.5 (4), and the adaptor sequences specific to the Nextera DNA library were trimmed using Trimmomatic v 0.36 (5). De novo assembly conducted using SPAdes v 3.12.0 (6) yielded 27 contigs. The draft genome sequence has a total length of 4,970,306 bp (N50, 792,857 bp) and a GC content of 67.87%. The genome coverage was 155.0×. Genome assembly statistics were computed using QUAST v 0.0.4 (7). The assembled contigs ranged in size from 805 bp to 1,052,617 bp. The assembly was evaluated for completeness and contamination using CheckM v 1.0.8 (8), which characterized the assembly as 99.4% complete with 0% contamination.
The genome sequence of this Rhodococcus sp. strain was first annotated using Prokka v 1.12 (9), which predicted a total of 4,508 protein-coding genes in the genome (https://narrative.kbase.us/#dataview/39490/15/1). Next, the genome was functionally annotated using Rapid Annotations using Subsystems Technology (RAST) v 0.1.1 (10; https://narrative.kbase.us/#dataview/39490/17/1), which assigned 1,406 (31%) of the genes to SEED subsystems. Several putative polycyclic aromatic hydrocarbon (PAH) catabolic enzymes (11), such as monooxygenase, dioxygenases, dehydrogenases, and cytochrome P450, were found in the Rhodococcus genome. However, genes for quinoline 2-oxidoreductase were not annotated in the genome, indicating that this species uses a different enzyme to convert quinoline to 2-hydroxyquinoline. The genomic information of this Rhodococcus sp. strain will not only facilitate our understanding of the metabolism for recalcitrant heteroaromatic compounds but will also expand our knowledge of the physiology of the Rhodococcus genus.
Data availability.
The draft genome sequence of this Rhodococcus sp. strain has been deposited in GenBank under the accession numbers SDMJ01000001 to SDMJ01000026, and the raw sequencing reads are available in the Sequence Read Archive under accession number SRP179964.
ACKNOWLEDGMENT
This work was supported by ExxonMobil via cooperative research and development agreement (CRADA) number C1400201.
REFERENCES
- 1.Felczak A, Zawadzka K, Lisowska K. 2014. Efficient biodegradation of quinolone—factors determining the process. Int Biodeterior Biodegradation 96:127–134. doi: 10.1016/j.ibiod.2014.08.004. [DOI] [Google Scholar]
- 2.O’Loughlin EJ, Kehrmeyer SR, Sims GK. 1996. Isolation, characterization and substrate utilization of a quinoline-degrading bacterium. Int Biodeterior Biodegradation 38:107–118. doi: 10.1016/S0964-8305(96)00032-7. [DOI] [Google Scholar]
- 3.Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, Kamimura RT, Kumari S, Drake MM, Brettin TS, Glass EM, Chivian D, Gunter D, Weston DJ, Allen BH, Baumohl J, Best AA, Bowen B, Brenner SE, Bun CC, Chandonia J-M, Chia J-M, Colasanti R, Conrad N, Davis JJ, Davison BH, DeJongh M, Devoid S, Dietrich E, Dubchak I, Edirisinghe JN, Fang G, Faria JP, Frybarger PM, Gerlach W, Gerstein M, Greiner A, Gurtowski J, Haun HL, He F, Jain R, et al. 2018. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nat Biotechnol 36:566–569. doi: 10.1038/nbt.4163. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Brown J, Pirrung M, McCue LA. 2017. FQC Dashboard: integrates FastQC results into a Web-based, interactive, and extensible FASTQ quality control tool. Bioinformatics 33:3137–3139. doi: 10.1093/bioinformatics/btx373. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi: 10.1093/bioinformatics/btu170. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi: 10.1089/cmb.2012.0021. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Mikheenko A, Valin G, Prjibelski A, Saveliev V, Gurevich A. 2016. Icarus: visualizer for de novo assembly evaluation. Bioinformatics 32:3321–3323. doi: 10.1093/bioinformatics/btw379. [DOI] [PubMed] [Google Scholar]
- 8.Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055. doi: 10.1101/gr.186072.114. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. doi: 10.1093/bioinformatics/btu153. [DOI] [PubMed] [Google Scholar]
- 10.Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. doi: 10.1186/1471-2164-9-75. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Haritash AK, Kaushik CP. 2009. Biodegradation aspects of polycyclic aromatic hydrocarbons (PAHs): a review. J Hazard Mater 169:1–15. doi: 10.1016/j.jhazmat.2009.03.137. [DOI] [PubMed] [Google Scholar]
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Data Availability Statement
The draft genome sequence of this Rhodococcus sp. strain has been deposited in GenBank under the accession numbers SDMJ01000001 to SDMJ01000026, and the raw sequencing reads are available in the Sequence Read Archive under accession number SRP179964.