Phylogenetic context and inference of homoeologous expression evolution in Gossypium. (A) Phylogentic relationships among the cotton accessions used in this study. An allopolyploidy event between A- and D-genome diploid species (red star) created modern allopolyploid Gossypium hirsutum (AD1). Using models of the ancenstral genome donors (A2 and D5), an interspecific diploid hybrid (F1) was created (blue star). Although not a perfect match, the model A- and D-genome donors are the best modern representatives of the diploids that underwent allopolyploidization to form AD1 and, as such, provide the best available reconstruction this ancient event. (B) Possible expression phenotypes and associated evolutionary inference. The far left pie represents equal expression among model diploid progenitor species (denoted by A2 and D5). Given this starting condition, several expression states are possible following allopolyploidy or hybridization. Some potential outcomes are indicated by the five pies on the right (At and Dt denote co-resident genomes, either in the hybrid or allopolyploid). (C) Detection of conserved homoeolog-specific single nucleotide polymorphism (SNPs). Given an alignment of expressed sequence tag (EST) sequences from orthologous genes from both diploid and allopolyploid genomes, species- and genome-specific SNPs (all SNPs highlighted in gray) can be detected. The middle SNP is an example of a genome-specific SNP. With this conserved SNP, homoeolog- and allele-specific microarray probes can be generated (potential microarray probe region highlighted in blue), and used to assay expression in allopolyploid and hybrid species.