Phytophthora megakarya and Phytophthora palmivora, Closely Related Causal Agents of Cacao Black Pod Rot, Underwent Increases in Genome Sizes and Gene Numbers by DifferentMechanisms

Phytophthoramegakarya (Pmeg) and Phytophthora palmivora (Ppal) are closely related species causing cacao blackpod rot. Although Ppal is a cosmopolitan pathogen, cacao is the only known host of economic importance for Pmeg. Pmeg is more virulent on cacao than Ppal. We sequenced and compared the Pmeg and Ppal genomes and identified virulence-related putative gene models (PGeneM) that may be responsible for their differences in host specificities and virulence. Pmeg and Ppal have estimated genome sizes of 126.88 and 151.23Mb and PGeneM numbers of 42,036 and 44,327, respectively. The evolutionary histories of Pmeg and Ppal appear quite different. Postspeciation, Ppal underwent whole-genome duplication whereas Pmeg has undergone selective increases in PGeneM numbers, likely through accelerated transposable element-driven duplications.Many PGeneMs in both species failed tomatch transcriptsandmay representpseudogenes or crypticgenetic reservoirs. Pmegappears tohave amplified specificgene families, some of which are virulence-related. Analysis of mycelium, zoospore, and in planta transcriptome expression profiles using neural network self-organizingmap analysis generated 24multivariate and nonlinear self-organizingmap classes. Many members of the RxLR, necrosis-inducing phytophthora protein, and pectinase genes familieswere specifically induced in planta. Pmeg displays a diverse virulence-related gene complement similar in size to and potentially of greater diversity than Ppal but it remains likely that the specific functions of the genes determine each species' unique characteristics as pathogens.