Figure 3

Phylogenetic analysis of chromosomal rearrangement in A. gossypii chromosome I and gene segments with homologues in S. cerevisiae and K. waltii chromosomes (A) and tree reconstructions under alternative WGD models (B). The common ancestral gene arrangement sequence of A. gossypii, S. cerevisiae, and K. waltii ( containing eight segments) was reconstructed (open circle) and genes were transformed into corresponding chromosomal segments (see Fig. 1). Thus, the common ancestral gene sequences embedded in the 8 chromosomal segments of the ancestor were tracked through the corresponding extant sequences of A. gossypii, S. cerevisiae, and K. waltii. Visual inspection reveals interleaving arrangements of differently colored segments. A detailed analysis of gene order and orientation confirms these interleaving arrangements are synteny patterns. The reconstruction of an ancestor allowed evaluation of which of the competing hypotheses (WGD and PGD) was more parsimonious in lineages leading to extant species. Note that the branches of the trees do not reflect actual lengths, the arrowhead shows the root of the tree based on Kurtzman and Robnett [47], and the star identifies the branch in which the putative WGD occurred [1,12]. The star is also used to indicate the branch defining alternative WGD scenarios.