Transcriptome data of Shewanella WP2

Strand-specific transcriptome sequencing was performed at Magigene Biotechnology Co., Ltd. (Guangdong, China). First, ribosomal RNA (rRNA) was removed using an Epicentre Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA), and a cDNA library was prepared with a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA) according to the manufacturer's instructions. The initial quantification of the library was carried out using a Qubit Fluorometer (Life Technologies, Carlsbad, CA, USA), and the insertion fragment size of the library was determined with an Agilent 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA, USA). The effective concentration of the library was accurately quantified via qPCR (effective concentration >2 nM). The different libraries were pooled together in a flow cell according to the effective concentration and the target offline data volume. After clustering, the Illumina HiSeq sequencing platform (Illumina, San Diego, USA) was used for paired-end sequencing. The raw data were filtered and evaluated by fastp software (v0.19.7), after which the clean reads were mapped to the S. psychrophila WP2 genome (NZ_CP014782.1) by HISAT software (v2.1.0). RSEM (v1.3.1) was used to calculate the read counts per sample, and the sequencing results were evaluated in terms of quality, alignment, saturation, and distribution of reads on the reference genome by DEGseq (v1.36.0). Gene expression was calculated by the number of reads mapped to each gene using the fragments per kilobase per million mapped reads (FPKM) method and analysed by edgeR (v3.20.2). The DEGs were identified according to the following standards: a false discovery rate (FDR) < 0.05 and an FPKM fold change ≥ 2 between two samples. For each strain, three biologically independent samples were used for the RNA-seq analysis. The transcriptomic data were validated via RT-qPCR analysis, and a high correlation coefficient (R2=0.9593) was revealed, indicating that the transcriptomic data were reliable and could be used for follow-up analysis.