Maximum Entropy Niche Modelling to Estimate the Potential Distribution of Phytophthora megakarya (Brasier & M. J. Griffin) in Tropical Regions

Background: Phytophthora megakarya is an invasive pathogen endemic to Central and West Africa. This species causes the most devastating form of black pod disease. Despite the deleterious impacts of this disease on cocoa production, there is no information on the geographic distribution of P. megakarya. Aim: In this study, we investigated the potential geographic distribution of P. megakarya in cocoa-producing regions of the world using ecological niche modelling. Methods: Occurrence records of P. megakarya in Central and West Africa were compiled from published studies. We selected relevant climatic and edaphic predictor variables in the indigenous range of this species to generate 14 datasets of climate-only, soil-only, and a combination of both data types. For each dataset, we calibrated 100 candidate MaxEnt models using 20 regularisation multiplier values and five feature classes. The best model was selected from statistically significant candidates with an omission rate ≤ 5% and the lowest Akaike Information Criterion corrected for small sample sizes, and projected onto cocoa-producing regions in Southeast Asia, Central and South America. The risk of extrapolation in model transfer was measured using the mobility-oriented parity (MOP) metric. Results: We found an optimal goodness-of-fit and complexity for candidate models incorporating both climate and soil data. Predictions of the model with the best performance showed that nearly all of Central Africa, especially areas in Gabon, Equatorial Guinea, and southern Cameroon are at risk of black pod disease. In West Africa, suitable environments were observed along the Atlantic coast, from southern Nigeria to Gambia. Our analysis suggested that P. megakarya is capable of subsisting outside its native range, at least in terms of climatic and edaphic factors. Model projections identified likely suitable areas, especially in Brazil and Colombia, from southwestern Mexico down to Panama, and across the Caribbean islands in the Americas, and in Sri Lanka, Indonesia, Malaysia, and Papua New Guinea in Asia and adjacent areas Conclusion: The outcomes of this study would be useful for developing measures aimed at preventing the spread of this pathogen in the tropics.

Small but Deadly

This chapter looks at the first of several major diseases of cacao, black pod, which is responsible for huge losses in cacao production every year. It deals with the pathogens responsible, Phytophthora palmivora and Phytophthora megakarya, looking at their biology, and how understanding their biology and ecology can help in devising methods to control the disease and minimize its impact. The chapter takes us through the history of black pod research and the people involved in trying to understand this devastating disease. The need for vigilance is highlighted, since P. megakarya, which causes large losses in cacao production in West Africa, has not yet spread to other cacao-growing regions of the world.

Spatial and temporal analysis of Phytophthora megakarya epidemic in newly established cacao plantations

Studying spatial and temporal plant disease dynamics helps to understand pathogen dispersal processes and improve disease control recommendations. In this study, three cacao plots devoid of primary inoculum of Phytophthora megakarya (causal agent of cacao black pod rot disease) upon establishment in 2006 were monitored for presence of disease on a weekly basis from 2009 to 2016. Ripley’s K(r) function, join count statistics and Fisher Exact test were used to analyse spatial and temporal disease dynamics. Disease distribution maps showed aggregated disease patterns in all plots although for the years of disease onset, exogenous primary infections were mostly randomly distributed. The K(r) function confirmed these results indicating that inoculum generally disperses only over short distances. Moreover, significant positive spatial autocorrelations showed that diseased trees were often clustered up to a distance of 3-9 m. Temporal disease progression was low, meaning that endogenous inoculum failed to establish itself which is partly explained by rigorous phytosanitation and partly by unfavourable microclimatic conditions for disease development. Since P. megakarya had difficulty establishing itself in the plots, proximity to already infected cacao plantations drove infection dynamics. Thus, isolation of newly established cacao plantations from infected ones and rigorous phytosanitation as a preventive strategy appears to be an effective approach to control black pod for newly established cacao plantations.

APLIKASI KITOSAN UNTUK PENGENDALIAN PENYAKIT BUSUK BUAH KAKAO (Phytophthora megakarya L.)

Research on the effect of chitosan concentration on the severity of cocoa pod rot in three different sizes of cocoa pods carried out at the smallholder cocoa plantations in Taman Endah Village, East Lampung Regency using local hybrid cocoa. Data analysis was using analysis of variance (ANOVA) and continued with Duncan's multiple range test at 5% level. The results showed that the severity of fruit rot at cocoa pod sprayed with copper oxide 56% and chitosan 0.6% was lower than the severity of fruit rot with application of chitosan 0.2%, 0.4%, and 0.8% and control..Keywords: application, chitosan, cocoa pod rot disease

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

Phytophthora megakarya and P. palmivora are oomycete pathogens that cause black pod rot of cacao (Theobroma cacao), the most economically important disease on cacao globally. While P. palmivora is a cosmopolitan pathogen, P. megakarya, which is more aggressive on cacao than P. palmivora, 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 P. megakarya genome is exceptionally large (222 Mbp) and nearly twice the size of P. palmivora (135 Mbp) and most known Phytophthora species (∼100 Mbp on average). Previous reports pointed toward a whole-genome duplication (WGD) in P. palmivora. In this study, we demonstrate that both species underwent independent and relatively recent WGD events. In P. megakarya we identified a unique combination of WGD and large-scale transposable element driven genome expansion, which places this genome in the upper range of Phytophthora 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.