Computational protocol: Draft Genome Sequence of the Crude Oil-Degrading and Biosurfactant-Producing Strain Cobetia sp. QF-1

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Protocol publication

[…] The Cobetia genus is 1 of 11 genera of the family Halomonadaceae and is most closely related to members of the genus Halomonas (). The type strain has been described as aerobic, Gram-negative, motile, rod-shaped, and slightly halophilic (). Cobetia sp. QF-1 can degrade crude oil and produce biosurfactants at 0°C. Although some isolated marine bacteria can degrade oil efficiently around 0°C, most of them have been isolated from polar environments (, ); a few have been isolated from China. Several genomes of Cobetia strains have been sequenced before (), but a marine Cobetia strain from China with the capacity to degrade hydrocarbons and produce biosurfactants at 0°C is lacking. Here, we report the draft genome sequence of Cobetia sp. QF-1, isolated from the seawater of Yellow Sea, China.The genome sequencing of Cobetia sp. QF-1 was performed using the Illumina HiSeq platform at NovogenBio, Beijing, China. Reads were assembled using SOAPdenovo software version 2.21 (). Protein-coding sequences were functionally annotated with the Clusters of Orthologous Groups of Proteins (COG) (), Gene Ontology (GO) (), and KEGG databases (). tRNAs and rRNAs were detected using tRNAscan-SE () and rRNAmmer software (), respectively.The genome of Cobetia sp. QF-1 was 4,084,184 bp with a 57.44% GC content. The genome contained 3,513 predicted protein-coding sequences, and the total length of the genes was 3,470,121 bp, which accounted for 84.96% of the genome. The genome also encoded 71 tRNAs and 5 rRNAs.According to the annotation results, many genes involved in petroleum hydrocarbon degradation, biosurfactant production, and cold adaption were found in the genome of Cobetia sp. QF-1. This draft genome sequence of Cobetia sp. QF-1 will help in understanding the genetic basis of crude oil degradation and biosurfactant production by Cobetia spp. […]

Pipeline specifications

Software tools SOAPdenovo, tRNAscan-SE
Databases COGs KEGG
Application Genome annotation