Complete Genome Sequencing and Assembly

The quality of the DNA was assessed by gel-electrophoresis and the quantity was estimated using the Quant-iT PicoGreen dsDNA kit (Invitrogen) and the Tecan Infinite 200 Microplate Reader (Tecan Deutschland GmbH, Mainz, Germany). To obtain the complete genome sequence, a whole-genome-shotgun PCRfree (Nextera DNA Sample Prep Kit; Illumina, Munich, Germany) and an 8 K mate pair library (Nextera Mate Pair Sample Preparation Kit; Illumina) were generated based on the manufacturer’s protocol. After sequencing and processing of the raw data, a de novo assembly was performed using the GS De Novo Assembler software release version 2.8 (Roche, Mannheim, Germany) with default settings. In our approach, we used a 2 x 300 bp paired end sequencing run. For quality-control and filtering, a pipeline including trimmomatic (Bolger et al. [45 (link)]), r2cat [46 (link)] and contig-length vs. read-count analysis [47, 48] was implemented. The resulting data set was manually inspected and improved.