Assembling the ZnDsv-02 genome

Sequencing libraries for the ZnDsv-02 genome were prepared using the TruSeq DNA PCR-Free Library Prep Kit and the Nextera Mate Pair Library Prep Kit (Illumina, Madison, WI, USA). Sequencing was performed using the MiSeq Reagent Kit v3 (600 cycles) on the Illumina MiSeq platform. After adapter removal and quality trimming using cutadapt [41 ] and prinseq [42 (link)], respectively, the resulting reads were assembled into contigs using SPAdes 3.10.1 [43 (link)]. The contigs and mate-pair reads were used to generate scaffolds with SCARPA 0.241 [44 (link)]. Contigs and scaffolds exhibiting the highest similarity to genome sequences of the genus Desulfovibrio or ‘Ca. Adiutrix intracellularis’ Adiu1 (LQAA00000000) by BLASTn searching against the NCBI non-redundant (nr) nucleotide database were extracted and treated as ‘trusted contigs.’ Sequence reads of 2–5 kb in length, which were obtained on a PacBio RSII platform as described previously [4 (link)], were added and re-assembled with the ‘trusted contigs’ using SPAdes 3.10.1. The resulting assemblies were manually inspected and curated as needed. After these processes, the Desulfovibrio genome was still fragmented to 55 contigs. Thus, we incorporated an assembling process as described in the Supplementary methods, and the final contig set was then obtained.