Computational protocol: Draft Genome Sequence of Shewanella decolorationis S12, a Dye-Degrading Bacterium Isolated from a Wastewater Treatment Plant

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Protocol publication

[…] The genus Shewanella is famous for bioremediation of environments contaminated with toxic organic and inorganic chemicals and has been found in water, sediment, and surfaces of shale and sandstone (). Recent studies have demonstrated that Shewanella decolorationis is a powerful species to degrade diverse manufactured textile dyes, including azo and anthraquinone dye, which are carcinogenic to humans (–). S. decolorationis S12 was isolated in 2002 from activated sludge of a textile-printing wastewater treatment plant in Guangzhou, China (). Whole-genome sequences of S. decolorationis have not been available, which is a limitation to the genetic study of this useful species.Genomic DNA extracted from S. decolorationis S12 was sequenced on an Illumina Miseq sequencer according to Illumina’s recommendations. A total of 16,692,489 paired-end 250-base reads were generated. The draft genome was assembled using Velvet () and Newbler, containing 77 contigs of >250 bp each after manual curation, with a total of 4,843,449 bases, an N50 of 155.5 kbp, and a G+C content of 47.1%. The draft genome sequence of strain S12 was annotated using Blast2GO () and the NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP) (, ).The draft genome sequence contains 4,305 genes, including 4,219 predicted coding sequences (CDS), 9 rRNA genes, and 77 tRNA genes. A total of 3,184 CDS were classified using the Cluster of Orthologous Groups (COG) database (). The most abundant groups of proteins were those that are involved in signal transduction (COG category T [9.5%]), amino acid metabolism and transport (COG category E [9.0%]), transcription (COG category K [8.5%]), and energy production and conversion (COG category C [7.8%]). The genome sequence of S. decolorationis S12 serves as a basis for further investigation of the molecular basis of its potential in dye degradation.Currently, the genus Shewanella contains 45 type species, and 28 strains from 15 type species have been sequenced for the whole genomes. Unlike these species from natural environments, S. decolorationis S12 was isolated from a human-altered and highly contaminated system, and thus its genetic evolution and cell responses might be different. Comparative genomics analysis showed that S. decolorationis S12 was closest to Shewanella sp. strain ANA-3 (89% coding sequence similarity), followed by Shewanella sp. strain MR-7 (88%) and Shewanella sp. strain MR-4 (88%). Further analysis will provide a better understanding of the S. decolorationis genome and shed more light on genomic evolution of the Shewanella genus. […]

Pipeline specifications

Software tools Velvet, Newbler, Blast2GO, PGAP
Applications Phylogenetics, WGS analysis