A systematic study of the whole genome sequence of strain 239 provides an insight into its physiological and taxonomic properties which correlate with its position in the genus.

The complete genome of methanol-utilizing strain 239 was generated, revealing a single 7,237,391 nucleotide circular chromosome with 7074 annotated protein-coding sequences (CDSs). Comparative analyses against the complete genome sequences of strain MG417-CF17, strain U32 and strain HCCB10007 revealed a broad spectrum of genomic structures, including various genome sizes, core/quasi-core/non-core configurations and different kinds of episomes. Although polyketide synthase gene clusters were absent from the genome, 12 gene clusters related to the biosynthesis of other specialized (secondary) metabolites were identified. Complete pathways attributable to the facultative methylotrophic physiology of strain 239, including both the / encoded methanol oxidation and the / encoded formaldehyde assimilation the ribulose monophosphate cycle, were identified together with evidence that the latter might be the result of horizontal gene transfer. Phylogenetic analyses based on 16S rDNA or orthologues of , a novel actinobacterial class-specific conserved gene against 62 or 18 type strains, respectively, revealed three major phyletic lineages, namely the mesophilic or moderately thermophilic subclade (AOS), the mesophilic subclade (ATS) and the thermophilic subclade (AMS). The distinct growth temperatures of members of the subclades correlated with corresponding genetic variations in their encoded compatible solutes. This study shows the value of integrating conventional taxonomic with whole genome sequence data.