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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]

In the genome of the heterocystous cyanobacterium Calothrix sp. NIES-4101 (NIES-4101), the four genes essential for nitrogen fixation (nifB, nifH, nifD and nifK) are highly fragmented into 13 parts in a 350-kb chromosomal region, and four of these parts are encoded in the reverse strand. Such a complex fragmentation feature makes it difficult to restore the intact nifBHDK genes by the excision mechanism found in the nifD gene of the Anabaena sp. PCC 7120 heterocyst. To examine the nitrogen-fixing ability of NIES-4101, we confirmed that NIES-4101 grew well on a combined nitrogen-free medium and showed high nitrogenase activity, which strongly suggested that the complete nifBHDK genes are restored by a complex recombination process in heterocysts. Next, we resequenced the genome prepared from cells grown under nitrogen-fixing conditions. Two contigs covering the complete nifHDK and nifB genes were found by de novo assembly of the sequencing reads. In addition, the DNA fragments covering the nifBHDK operon were successfully amplified by PCR. We propose that the process of nifBHDK restoration occurs as follows. First, the nifD–nifK genes are restored by four excision events. Then, the complete nifH and nifB genes are restored by two excision events followed by two successive inversion events between the inverted repeat sequences and one excision event, forming the functional nif gene cluster, nifB-fdxN-nifS-nifU-nifH-nifD-nifK. All genes coding recombinases responsible for these nine recombination events are located close to the terminal repeat sequences. The restoration of the nifBHDK genes in NIES-4101 is the most complex genome reorganization reported in heterocystous cyanobacteria. [ABSTRACT FROM AUTHOR]

Basal plant immune responses are activated by the recognition of conserved microbe‐associated molecular patterns (MAMPs), or breakdown molecules released from the plants after damage by pathogen penetration, so‐called damage‐associated molecular patterns (DAMPs). While chitin‐oligosaccharide (CHOS), a primary component of fungal cell walls, is most known as MAMP, plant cell wall‐derived oligosaccharides, cello‐oligosaccharides (COS) from cellulose, and xylo‐oligosaccharide (XOS) from hemicellulose are representative DAMPs. In this study, elicitor activities of COS prepared from cotton linters, XOS prepared from corn cobs, and chitin‐oligosaccharide (CHOS) from crustacean shells were comparatively investigated. In Arabidopsis, COS, XOS, or CHOS treatment triggered typical defense responses such as reactive oxygen species (ROS) production, phosphorylation of MAP kinases, callose deposition, and activation of the defense‐related transcription factor WRKY33 promoter. When COS, XOS, and CHOS were used at concentrations with similar activity in inducing ROS production and callose depositions, CHOS was particularly potent in activating the MAPK kinases and WRKY33 promoters. Among the COS and XOS with different degrees of polymerization, cellotriose and xylotetraose showed the highest activity for the activation of WRKY33 promoter. Gene ontology enrichment analysis of RNAseq data revealed that simultaneous treatment of COS, XOS, and CHOS (oligo‐mix) effectively activates plant disease resistance. In practice, treatment with the oligo‐mix enhanced the resistance of tomato to powdery mildew, but plant growth was not inhibited but rather tended to be promoted, providing evidence that treatment with the oligo‐mix has beneficial effects on improving disease resistance in plants, making them a promising class of compounds for practical application. [ABSTRACT FROM AUTHOR]

Beet necrotic yellow vein virus (BNYVV) is the causal agent of rhizomania, the most serious sugar beet disease worldwide. Since the first finding in Japan in 1969, BNYVV became widespread throughout Hokkaido in a few decades and led to the introduction of Rz1‐resistant sugar beet cultivars in the 1990s. Here, we report the historical progress of the BNYVV epidemic in Hokkaido from 1969 to 2019. Previous analysis on samples from 1991 showed that BNYVV isolates were classified into three strains (named O, D, and T) based on the RNA3‐encoded p25 gene. The O‐type viruses were widely detected in Hokkaido, while the D‐ and T‐type viruses were detected in limited areas. The RNA5, encoding the p26 gene, was initially contained in some D‐ and O‐type isolates but not in any T‐type isolates. Interestingly, recent sample analysis revealed that RNA5‐containing T‐type viruses, seemingly more virulent than the other two strains, were widely detected in Hokkaido. Additionally, a small group of virus isolates harbouring a new p25 gene (named C) was found in limited areas. These results suggest that the T‐type viruses, which accompanied RNA5, have been preferentially spread from a limited area to other districts over the last few decades and that this spread might be strongly associated with the recent introduction of Rz1‐resistant sugar beet cultivars. BNYVV‐positive samples also contained mainly beet soil‐borne virus and traces of beet virus Q, both of which are the first to be recorded in Japan. [ABSTRACT FROM AUTHOR]