Sequencing libraries for the ‘Ca. Desulfovibrio trichonymphae' genome were prepared using the TruSeq DNA PCR-free Sample Prep Kit and the Nextera Mate Pair Sample Prep Kit (Illumina, San Diego, CA, USA). Sequencing was performed using the MiSeq Reagent Kit v3 (600 cycles) on an Illumina MiSeq platform. The generated reads were processed for adapter and quality trimming using programs cutadapt and prinseq, respectively (Martin, 2011 ; Schmieder and Edwards, 2011 (link)). The reads were assembled into contigs, using SPAdes 3.0 (Bankevich et al., 2012 (link)), and the contigs and the mate-pair reads were used to generate scaffolds with SCARPA 0.241 (Donmez and Brudno, 2013 (link)). Finding and functional annotation of genes were performed using MiGAP (http://www.migap.org), and the result was curated manually. Pseudogenes were manually identified as described previously (Hongoh et al., 2008a (link)). Metabolic pathways were reconstructed using the KEGG automatic annotation server (KAAS; Moriya et al., 2007 (link)). Genes were assigned to functional categories based on non-supervised orthologous groups (NOG) (Powell et al., 2014 (link)). Clustered regularly interspaced short palindromic repeat (CRISPR) loci were identified using CRISPRFinder (Grissa et al., 2007 (link)).