Abstract

Complete genomes of xenobiotic-degrading microorganisms provide valuable resources for researchers to understand molecular mechanisms involved in bioremediation. Despite the well-known ability of Sphingomonas paucimobilis to degrade persistent xenobiotic compounds, a complete genome sequencing is lacking for this organism. In line with this, we report the first complete genome sequence of Sphingomonas paucimobilis (strain AIMST S2), an organophosphate and hydrocarbon-degrading bacterium isolated from oil-polluted soil at Kedah, Malaysia. The genome was derived from a hybrid assembly of short and long reads generated by Illumina HiSeq and MinION, respectively. The assembly resulted in a single contig of 4,005,505 bases which consisted of 3,612 CDS and 56 tRNAs. An array of genes involved in xenobiotic degradation and plant-growth promoters were identified, suggesting its’ potential role as an effective microorganism in bioremediation and agriculture. Having reported the first complete genome of the species, this study will serve as a stepping stone for comparative genome analysis of Sphingomonas strains and other xenobiotic-degrading microorganisms as well as gene expression studies in organophosphate biodegradation.

Alternate abstract:

Measurement(s)genome • sequence_assemblyTechnology Type(s)DNA sequencing • genome assemblySample Characteristic - OrganismSphingomonas paucimobilisSample Characteristic - Environmentoil contaminated soilSample Characteristic - LocationMalaysia

Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.9971711

Details

Title
Complete genome sequence of Sphingomonas paucimobilis AIMST S2, a xenobiotic-degrading bacterium
Author
Ravintheran, Suganniiya K 1 ; Sivaprakasam, Sumitra 1 ; Loke, Stella 2   VIAFID ORCID Logo  ; Su Yin Lee 1 ; Ravichandran Manickam 1 ; Yahya, Adibah 3 ; Croft, Lawrence 4 ; Millard, Andrew 5 ; Parimannan, Sivachandran 1   VIAFID ORCID Logo  ; Rajandas, Heera 1 

1  Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong, Malaysia 
2  School of Life and Environmental Sciences, Deakin University, Burwood Campus, Burwood, Australia 
3  Biorefinery Technology Laboratory, Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai, Malaysia 
4  Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin, University, Geelong, Australia 
5  Department of Genetics and Genome Biology, University of Leicester, Leicester, UK 
Pages
1-6
Publication year
2019
Publication date
Dec 2019
Publisher
Nature Publishing Group
e-ISSN
20524463
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1038/s41597-019-0289-x
ProQuest document ID
2317918927
Copyright
© 2019. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.