Independent Whole-Genome Duplications Define the Architecture of the Genomes of the Devastating West African Cacao Black Pod Pathogen <i>Phytophthora megakarya</i> and Its Close Relative <i>Phytophthora palmivora</i>

Abstract

<i>Phytophthora megakarya</i> and <i>P. palmivora</i> are oomycete pathogens that cause black pod rot of cacao (<i>Theobroma cacao</i>), the most economically important disease on cacao globally. While <i>P. palmivora</i> is a cosmopolitan pathogen, <i>P. megakarya</i>, which is more aggressive on cacao than <i>P. palmivora</i>, has been reported only in West and Central Africa where it has been spreading and devastating cacao farms since the 1950s. In this study, we reconstructed the complete diploid genomes of multiple isolates of both species using single-molecule real-time sequencing. Thirty-one additional genotypes were sequenced to analyze inter- and intra-species genomic diversity. The <i>P. megakarya</i> genome is exceptionally large (222 Mbp) and nearly twice the size of <i>P. palmivora</i> (135 Mbp) and most known <i>Phytophthora</i> species (∼100 Mbp on average). Previous reports pointed toward a whole-genome duplication (WGD) in <i>P. palmivora</i> In this study, we demonstrate that both species underwent independent and relatively recent WGD events. In <i>P. megakarya</i> we identified a unique combination of WGD and large-scale transposable element driven genome expansion, which places this genome in the upper range of <i>Phytophthora</i> genome sizes, as well as effector pools with 1,382 predicted RxLR effectors. Finally, this study provides evidence of adaptive evolution of effectors like RxLRs and Crinklers, and discusses the implications of effector expansion and diversification.