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May 1, 2020 - New paper published

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

Abraham Morales-Cruz, Shahin S. Ali, Andrea Minio, Rosa Figueroa-Balderas, Jadran F. García, Takao Kasuga, Alina S. Puig, Jean-Philippe Marelli, Bryan A. Bailey and Dario Cantu

G3: GENES, GENOMES, GENETICS Early online April 30, 2020;

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 (SMRT). 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 towards 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.

May 1, 2020 - is now live is now live

The University of California Davis, USDA ARS, and Mars, Incorporated have teamed up to develop genomic resources for the major fungal and oomycete pathogens of cacao.
This repository provides public access to genome references, resequencing and gene expression data. These resources are being used by Mars, Incorporated and collaborators to study the evolution, geographical diversity, host-specificity and biology of the causal agents of cacao black pod (Phytophthora megakarya, P. palmivora), witches' broom (Moniliophthora perniciosa), and frosty pod (Moniliophthora roreri).