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Simple Summary: Cassava witches' broom disease (CWBD) is a major threat to cassava production, and it is believed to be caused by phytoplasma, an unculturable bacterial pathogen. However, recent findings suggest that other pathogens, such as viruses or fungi, may cause witches' broom disease in other crops. This study aims to investigate CWBD in the Philippines, specifically its status, and identify its potential pathogen(s). Currently, CWBD has spread nationwide and causes severe symptoms, such as leaf clustering and drying, as well as the browning of stems and roots. Polymerase chain reaction (PCR) and next-generation sequencing (NGS) showed consistent detection and a high abundance of Ceratobasidium sp., but an inconsistent and low detection rate of phytoplasma (Candidatus Phytoplasma luffae) in Philippine cassava samples. These findings challenge existing notions about CWBD and its causal agent. Confirming the causality and understanding Ceratobasidium sp. involvement can lead to better disease diagnosis and control strategies for ensuring food security. Cassava witches' broom disease (CWBD) is one of the most devastating diseases of cassava (Manihot esculenta Crantz), and it threatens global production of the crop. In 2017, a phytoplasma, Candidatus Phytoplasma luffae (Ca. P. luffae), was reported in the Philippines, and it has been considered as the causal agent, despite unknown etiology and transmission of CWBD. In this study, the nationwide occurrence of CWBD was assessed, and detection of CWBD's pathogen was attempted using polymerase chain reaction (PCR) and next-generation sequencing (NGS) techniques. The results showed that CWBD has spread and become severe, exhibiting symptoms such as small leaf proliferation, shortened internodes, and vascular necrosis. PCR analysis revealed a low phytoplasma detection rate, possibly due to low titer, uneven distribution, or absence in the CWBD-symptomatic cassava. In addition, NGS techniques confirm the PCR results, revealing the absence or extremely low phytoplasma read counts, but a surprisingly high abundance of fastidious and xylem-limited fungus, Ceratobasidium sp. in CWBD-symptomatic plants. These findings cast doubt over the involvement of phytoplasma in CWBD and instead highlight the potential association of Ceratobasidium sp., strongly supporting the recent findings in mainland Southeast Asia. Further investigations are needed to verify the etiology of CWBD and identify infection mechanisms of Ceratobasidium sp. to develop effective diagnostic and control methods for disease management. [ABSTRACT FROM AUTHOR]

Epichloë species are endophytic fungi that systemically colonize grass species. Here, we report the genome sequences of Epichloë bromicola strains HS and DP isolated for the first time from Elymus ciliaris in Nagoya, Japan., Competing Interests: The authors declare no conflict of interest.