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

Abstract

Phytophthora megakarya (Pmeg) and Phytophthora palmivora (Ppal) are closely related species causing cacao black pod 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 151.23 Mb 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 to match transcripts and may represent pseudogenes or cryptic genetic reservoirs. Pmeg appears to have amplified specific gene families, some of which are virulence-related. Analysis of mycelium, zoospore, and in planta transcriptome expression profiles using neural network self-organizing map analysis generated 24 multivariate and nonlinear self-organizing map classes. Many members of the RxLR, necrosis-inducing phytophthora protein, and pectinase genes families were 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.

Modeling the temporal evolution of cocoa black pod rot disease caused by Phytophthora megakarya

“…Then, the DFE is GAS in Ω. To check condition (5), following the works of Varga 41 and Berman and Plemmons, 42 let us recall the following definition and theorem. For epidemiological models with periodic parameters, Wang and Zhao 31 generalized the results from the work of Van den Driessche and Watmough.…”

“…Through rain-splash or by certain insects such as ants, sporangia, or the motile biflagellate zoospores they contain, are transported onto pods where they can establish an infection. 9 Two factors that greatly contribute to the success of P. megakarya as cocoa pathogen is its ability to rapidly form appressoria (a flattened and thickened tip of a hyphal branch, that facilitates penetration of the host plant) in much greater quantities than P. palmivora 5 as well as its capability to shed zoospores earlier and twice as much than P. palmivora. 10 Successful infection then results in the generation of secondary inoculum, which gets dispersed again primarily through rain-splash, causing secondary infections.…”

“…Setting I = 0 in system (5), implies that S p,i , S p,e and the infections forces i (S p,e , S p,i ) are all equal to zero. Thus, we immediately deduce that…”

“…However, the most aggressive and damaging species is P. megakarya (C.M. Brasier & M.J. Griffin) (see related works 2,4,5 ).…”

The unique genome architecture of the devastating West African cacao black pod pathogen Phytophthora megakarya

“…1B)(3). In recent years, Pmeg has largely displaced Ppal as a major cause of BPR in some African nations (4).…”