Genome analysis of Ceratobasidium theobromae and its causal association with cassava witches’ broom disease in the Philippines

Cassava witches’ broom disease (CWBD) has been present in the Philippines from the early 2010s and has since been considered a phytoplasma-caused disease. This assumption has guided CWBD diagnostics and management, yielding mixed results. However, recent results in continental Southeast Asia (SEA) indicate that the disease is rather associated with the fungus Ceratobasidium theobromae, the causal agent of Vascular Streak Dieback (VSD) of cacao, another important disease occurring in the Philippines. Field surveys showed that CWBD was present in all cassava-growing regions, reaching field level incidence values above 50%. C. theobromae was detected in symptomatic samples using a standard PCR assay, with a sensitivity of 91.79% and a specificity of 95.24%, supporting its causal association with CWBD, in contrast to phytoplasma detection, which failed to yield positive results. Genome analyses of C. theobromae, supported by an improved reference genome, indicate that Philippine isolates, whether infecting cassava or cacao, are more closely related to each other than to isolates from continental SEA. Furthermore, isolates from the recent outbreak in the Americas are more closely related to those from continental SEA than to those from the Philippines.