Premise: Allopolyploid species are the result of hybridization-induced whole-genome duplications, in which the hybrid-genome of the resulting offspring lineage consists of two distinct subgenomes: one from each progenitor. In meiosis, the extent to which chromosomes pair with their proper homolog vs. with the chromosome descended from the opposing progenitor (i.e., homoeolog), varies across allopolyploid taxa, such that recombination and gene flow between homoeologous chromosomes is also expected to vary across distinct allopolyploid lineages.
Methods: While the D-statistic, commonly referred to as the ABBA/BABA test, has traditionally been employed to test for evidence of introgression between the genomes of two diverged species, we used it to characterize the extent and direction of gene flow between homoeologs of the subgenomes in allotetraploid Coffea arabica.
Results: We found that genome-wide patterns of homoeologous conversion were slightly, but not significantly, maternally biased, indicating that both subgenomes are donors and recipients of homoeologous gene flow (HGF). Because C. eugenioides represents the cytoplasmic ancestor of C. arabica, we also tested whether HGF was maternally biased in nuclear-encoded genes that interact with cytoplasmically-encoded genes. In contrast to genome-wide patterns, we found that patterns of HGF were highly maternally biased in plastid', but not mitochondrially targeted genes.
Discussion: This observation is consistent with a scenario in which selection favors overwriting of paternally derived alleles by maternally derived alleles to ameliorate plastid-nuclear incompatibilities. These analyses indicate that natural selection shapes the direction and intensity of HGF in allopolyploid coffee, and this work represents a proof-of-principle for a simple method to detect HGF in allopolyploid genomes.