Fig. 5: A tRNA-associated hypervariable region (‘plasticity zone’) encodes gene cassettes for metabolic pathways used for biotyping within S. marcescens.
The gene arrangement between the conserved tRNA-Proggg and tRNA-Sertga in S. marcescens is plotted against a maximum-likelihood sub-phylogeny from the tree in Fig. 1. Clades for which all descending tips represent strains that have an identical set of genes in the locus depicted are collapsed and denoted by a diamond shape within the tree. The size of the diamond represents the number of tips in each collapsed clade. Tips lacking a completely assembled gene locus between tRNA-Proggg and tRNA-Sertga have been pruned from the tree. Each tip number represents a unique combination of genes in the locus. Genes are coloured according to their role, or in the absence of any predicted function, named according to the group number assigned by Panaroo in the pan-genome (Fig. 2). Prophage regions and the closest related prophage sequence determined by PHASTER are indicated.
