Fig. 1

A gene cluster containing most of the genes of the PhnCDEFGHIJKLMNOP operon [14] and the corresponding PQ-tree. The Phn operon encodes proteins that utilize phosphonate as a nutritional source of phosphorus in prokaryotes. The genes PhnCDE encode a phosphonate transporter, the genes PhnGHIJKLM encode proteins responsible for the conversion of phosphonates to phosphate, and the gene PhnF encodes a regulator. (1)–(3). The three distinct gene orders found among 47 chromosomal instances of the Phn gene cluster. (4) A PQ-tree representing the Phn gene cluster, constructed from its three known gene orders shown in (1)–(3). (5) An example of a Phn gene cluster instance identified by the PQ-tree shown in (4), and the one-to-one mapping between the leaves of the PQ-tree and the genes comprising the instance (indicated by the colored lines). The instance genes are rearranged differently from the gene orders shown in (1)-(3) and yet can be derived from the PQ-tree. In this mapping, gene F is substituted by gene R, gene N is an intruding gene (i.e., deleted from the instance string), and gene K is a missing gene (i.e., deleted from the PQ-tree)