Genome Assembly and Annotation of Rhodobacter

Genome analysis was performed as previously described [15 (link)]. Genomic DNA was isolated from mid-log phase cell culture in marine broth using the DNeasy Blood and Tissue Kit (Qiagen, Germantown, MD, USA). Samples were prepped for Illumina 250-bp paired-end sequencing using Nextera sample prep kit (Illumina, Inc., San Diego, CA, USA), and sequenced on Illumina MiSeq platform with V2 chemistry. Reads were quality checked and adapter trimmed using Trimmomatic version 0.33 using default parameters for paired-end reads [18 (link)]. Reads were de novo assembled using CLC Genomics Workbench (CLC Bio-Qiagen, Aarhaus, Denmark), and scaffolds generated using MeDuSa [19 (link)] and R. sulfidophilum DSM 2351 as an alignment guide. Alignment of reads to R. sulfidophilum DSM 2351 was performed using Bowtie2 version 2.2.29 [20 (link)] short read mapper, and annotated with National Center for Biotechnology Information Prokaryotic Genome Annotation Pipeline [21 (link)].