Figure 3

Protocol used to obtain the ancestral gene order and sequence of a Yersinia pestis ancestor. A) Extraction and filtering of gene families from extant genomes and alignment. B) Reconstruction of the species tree using a concatenate of the variant positions of 1971 universal gene families. C) ML reconstruction of gene trees followed by the collapse of any non-supported branch (bootstrap <99) and the resolution of the created polytomies using the species tree as a guide. D) Inference of ancestral gene adjacencies using DeCo. E) Detection and correction of wrongly inferred gene trees based on the ancestral adjacency graph linearity. F) Reconstruction of the ancestral sequence of each gene adjacency from their extant descendants. G) Alignment of the consecutive ancestral adjacency sequences to assemble the ancestral genome. Similar colors indicates homology. Dots represent a gene as a node in an adjacency graph while oriented segments represent a gene as a sequence.