Genome sequencing was performed by MicrobesNG (Birmingham) by Illumina NGS with a coverage of 30%. The reads were trimmed using Trimmomatic (Bolger et al., 2014 (link)) and de novo assembly was performed using SPAdes 3.7 (Bankevich et al., 2012 (link)). Annotation was undertaken using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v4.10 (Tatusova et al., 2016 (link)).
Average Nucleotide Identity (ANI) using MUMmer (Delcher et al., 2003 (link)) as the alignment algorithm (ANIm) or BLAST (ANIb) was calculated using the JSpeciesWS package (Richter and Rosselló-Móra, 2009 (link)). Pairwise comparisons were made between the genome sequences of the strains Re CFN42T (accessions CP000133.1–CP000138.1, U80928.5), Rp ATCC 14482T (accessions RJJV01000001–RJJV01000081) and Rlv UPM791 (accessions CP025505.1–CP025510.1) using a custom BLAST database on Geneious 10.0.9 (Biomatters). Clusters of orthologous groups (COGs) of proteins were predicted using the WebMGA server (Wu et al., 2011 (link)) and KAAS (KEGG Automatic Annotation Server) for the functional annotation of genes (Moriya et al., 2007 (link)). BLAST Ring Image Generator (BRIG) software was used to display circular genome comparisons (Alikhan et al., 2011 (link)).
The draft of this whole-genome shotgun project has been deposited in GenBank under the provisional accession no WNKD00000000.
Average Nucleotide Identity (ANI) using MUMmer (Delcher et al., 2003 (link)) as the alignment algorithm (ANIm) or BLAST (ANIb) was calculated using the JSpeciesWS package (Richter and Rosselló-Móra, 2009 (link)). Pairwise comparisons were made between the genome sequences of the strains Re CFN42T (accessions CP000133.1–CP000138.1, U80928.5), Rp ATCC 14482T (accessions RJJV01000001–RJJV01000081) and Rlv UPM791 (accessions CP025505.1–CP025510.1) using a custom BLAST database on Geneious 10.0.9 (Biomatters). Clusters of orthologous groups (COGs) of proteins were predicted using the WebMGA server (Wu et al., 2011 (link)) and KAAS (KEGG Automatic Annotation Server) for the functional annotation of genes (Moriya et al., 2007 (link)). BLAST Ring Image Generator (BRIG) software was used to display circular genome comparisons (Alikhan et al., 2011 (link)).
The draft of this whole-genome shotgun project has been deposited in GenBank under the provisional accession no WNKD00000000.
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