Figure 1.

(A) Visualization of the circular genome of S. panacis DCY99^T. The genome is shown with a base pair (bp) ruler on the outer ring. The S. panacis DCY99^T main chromosome is 5,003,808 bp in size; the plasmid is 319,133 bp in size. The chromosome is arranged clockwise. The two outer circles represent S. panacis DCY99^T CDSs on the forward and reverse strands, respectively. The next circle indicates GC% content and next three circles indicate rRNA, tRNA, and sRNA, respectively. The S. panacis DCY99^T plasmid does not contain the three RNAs. (B) Sphingomonas pan-genome statistics. The Sphingomonas pan-genome can be subdivided into three categories: (i) the core-genome (the set of genes shared by all genomes), (ii) the accessory-genome (the set of genes present in some but not all genomes), and (iii) the unique-genome (genes that are unique to a single genome). The function of each gene in a group was classified using COGs. COG categories are as follows. For cellular processes and signaling, D: cell cycle control, cell division, and chromosome partitioning; M: cell wall/membrane/envelope biogenesis, N: cell motility; O: posttranslational modification, chaperones and protein turnover, T: signal transduction mechanisms, U: intracellular trafficking, secretion, and vesicular transport, V: defense mechanisms. For information storage and processing, J: translation, ribosomal structure, and biogenesis, K: transcription, L: replication, recombination, and repair. For metabolism, C: energy production and conversion, G: carbohydrate transport and metabolism, E: amino acid transport and metabolism, F: nucleotide transport and metabolism, H: coenzyme transport and metabolism, I: lipid transport and metabolism, P: inorganic ion transport and metabolism, Q: secondary metabolites biosynthesis, transport, and catabolism, R: general function prediction only, and S: function unknown. (C) KEGG pathway distribution of the 159 Sphingomonas strains.