Genome-wide patterns of homoeologous gene flow in allotetraploid coffee

Premise: Allopolyploidy – a hybridization-induced whole-genome duplication event – has been a major driver of plant diversification. The extent to which chromosomes pair with their proper homolog vs. with their homoeolog in allopolyploids varies across taxa, and methods to detect homoeologous gene flow (HGF) are needed to understand how HGF has shaped polyploid lineages.Methods: The ABBA/BABA test represents a classic method for detecting introgression between closely related species, but here we used it to characterize the extent and direction of HGF in allotetraploid Coffea arabica. Results: We found that homoeologous conversion is abundant in the C. arabica genome, with both subgenomes serving as donors and recipients of HGF. We also found that HGF is highly maternally biased in plastid-targeted – but not mitochondrial-targeted – genes, as would be expected if plastid-nuclear incompatibilities exist between the two parent species.Discussion: Together our analyses provide a simple framework for detecting HGF and new evidence consistent with selection favoring overwriting of paternally derived alleles by maternally derived alleles to ameliorate plastid-nuclear incompatibilities. Natural selection therefore appears to shape the direction and intensity of HGF in allopolyploid coffee, indicating that cytoplasmic inheritance has long-term consequences for polyploid lineages.