Alternative splicing (AS) contributes to diversifying and regulating cellular responses to environmental conditions and developmental cues by differentially producing multiple mRNA and protein isoforms from a single gene. Previous studies on AS in pathogenic fungi focused on profiling AS isoforms under a limited number of conditions. We analysed AS profiles in the rice blast fungus Magnaporthe oryzae, a global threat to rice production, using high-quality transcriptome data representing its vegetative growth (mycelia) and multiple host infection stages. We identified 4,270 AS isoforms derived from 2,413 genes, including 499 genes presumably regulated by infection-specific AS. AS appears to increase during infection, with 32.7% of the AS isoforms being produced during infection but absent in mycelia. Analysis of the isoforms observed at each infection stage showed that 636 AS isoforms were more abundant than corresponding annotated mRNAs, especially after initial hyphal penetration into host cell. Many such dominant isoforms were predicted to encode regulatory proteins such as transcription factors and phospho-transferases. We also identified the genes encoding distinct proteins via AS and confirmed the translation of some isoforms via a proteomic analysis, suggesting potential AS-mediated neo-functionalization of some genes during infection. Comprehensive profiling of the pattern of genome-wide AS during multiple stages of rice-M. oryzae interaction established a foundational resource that will help investigate the role and regulation of AS during rice infection.

Using isolates collected over 2 decades, we determined the population structure and dynamics of the rice blast fungus, Magnaporthe grisea, in Korea at both the genotypic and phenotypic levels. Pathotype analysis on 6,315 isolates collected from 328 rice cultivars from 1981 to 2000 revealed the presence of a total of 91 pathotypes. Among these 91 patho-types, nine dominated, comprising 76.5% of the isolates. The expected number of pathotypes (corrected for sample size) increased significantly during the course of this study. On average, six (ranging from 0 to 20) new commercial cultivars were introduced annually between 1981 and 1998. However, the overall cultivar diversity, estimated using the Shannon index, was low. Most of the new cultivars were not planted to a large area because the seven most common cultivars each year occupied over 70% of the rice-cultivated area. The frequencies of the nine dominant patho-types from these seven cultivars were highly correlated with those from the entire set of cultivars. To understand genetic diversity within and between pathotypes, 176 isolates collected from 1984 to 1999 were randomly sampled and analyzed by DNA fingerprinting. High similarities were observed among isolates; overall similarities were greater than 63% in combined MGR586 and MAGGY DNA fingerprints. Unlike most other populations of M. grisea, DNA fingerprints showed no clear lineage structure. No groups were supported by bootstrap values greater than 10%. Furthermore, there was no significant correlation between DNA fingerprint similarities and pathotypes. Genetic similarity was significantly greater (P < 0.001) within years than between years, although the difference was small. Our data suggest that M. grisea populations in Korea have been mostly dominated by a single clonal lineage. We cannot conclude from these data that selection by the host population has been a major force in the evolution of M. grisea in Korea.

Brown leaf spot disease caused by Alternaria spp. is among the most common diseases of potato crops. Typical brown spot symptoms were observed in commercial potato-cultivation areas of northern Korea from June to August 2020–2021. In total, 68 isolates were collected, and based on sequence analysis of the internal transcribed spacer (ITS) region, the collected isolates were identified as Alternaria spp. (80.9%). Phylogenetic analysis revealed that a majority of these isolates clustered within a clade that included A. alternata. Additionally, the ITS region and rpb2 yielded the most informative sequences for the identification of A. alternata. Pathogenicity tests confirmed that the collected pathogens elicited symptoms identical to those observed in the field. In pathogenicity tests performed on seven commercial cultivars, the pathogens exhibited strong virulence in both wound and non-wound inoculations. Among the cultivars tested, Arirang-1ho, Arirang-2ho, and Golden Ball were resistant to the pathogens. Furthermore, among the fungicides tested in vitro, mancozeb and difenoconazole were found to be effective for inhibiting mycelial growth. In summary, our findings suggest that A. alternata plays a critical role in leaf disease in potato-growing regions and emphasise the necessity of continuous monitoring and management to protect against this disease in Korea.

Acetylation of histone H3 lysine 56 (H3K56) by the fungal-specific histone acetyltransferase Rtt109 plays important roles in maintaining genome integrity and surviving DNA damage. Here, we investigated the implications of Rtt109-mediated response to DNA damage on development and pathogenesis of the rice blast fungus Magnaporthe oryzae (anamorph: Pyricularia oryzae). The ortholog of Rtt109 in M. oryzae (MoRtt109) was found via sequence homology and its functionality was confirmed by phenotypic complementation of the Saccharomyces cerevisiae Rtt109 deletion strain. Targeted deletion of MoRtt109 resulted in a significant reduction in acetylation of H3K56 and rendered the fungus defective in hyphal growth and asexual reproduction. Furthermore, the deletion mutant displayed hypersensitivity to genotoxic agents, confirming the conserved importance of Rtt109 in genome integrity maintenance and genotoxic stress tolerance. Elevated expression of DNA repair genes and the results of the comet assay were consistent with constitutive endogenous DNA damage. Although the conidia produced from the mutant were not impaired in germination and appressorium morphogenesis, the mutant was significantly less pathogenic on rice leaves. Transcriptomic analysis provided insight into the factors underlying phenotypic defects that are associated with deficiency of H3K56 acetylation. Overall, our results indicate that MoRtt109 is a conserved histone acetyltransferase that affects proliferation and asexual fecundity of M. oryzae through maintenance of genome integrity and response to DNA damage.

In August 2020, anthracnose-like symptoms was observed on pear fruit (Pyrus pyrifolia  P. communis) cultivated at 0.2 ha by the National Institute of Horticultural and Herbal Science Pear Research Institute at the Rural Development Administration (Naju, Jeonnam Province in Korea). Symptoms were observed only on fruit (112 days after full bloom (DAFB)), and disease incidences was at least 90%. Initial black specks developed into larger brown or black lesions on fruit after 3 days. Later, sunken lesions with orange conidial masses were observed. Finally, infected fruit dropped prematurely. To isolate and identify the pathogen, small pieces (5  5 mm) from the margin of lesions on fruit were surface sterilized by immersing in 70% ethanol for 1 minute, washed three times with sterile water, dried, and placed on water agar amended with 100 ppm streptomycin, then incubated in the dark at 25°C. Hyphae emerging from the three independent tissues were subcultured on Potato Dextrose Agar (PDA), resulting in three independent isolates (CP-1, CP-2, CP-3) after single spore isolation. Colonies were pale gray on PDA, but the colony edges were white. Conidia were transparent, cylindrical with rounded ends, and 13.8 to 20.1 μm  4.8 to 6.2 μm (avg. 18.3 μm  5.4 μm, n = 100) in size. Appressoria were dark brown, globose or subcylindrical, and 6.3 to 9.5 μm  5.2 to 6.9 μm in size (8.1  6.1 μm, n = 100). The morphological characteristics were similar to the descriptions of C. gloeosporioides species complex (Weir et al. 2012). Sequences of ITS (MT921589-91), GAPDH (MT921987-89), CAL (MT921990-92), ACT (MT921993-95), CHS-1 (MT921996-98), TUB2 (921999-01), and ApMAT (MT922002-04) sequences from CP-1, CP-2, and CP-3 matched with C. fruiticola strain BRIP 62871 (100%; MK298285), HXQT-2 (100%; MN52588), HXQT-2 (100%; MN52839), HXQT-2 (99.65; MN525801), ICKP18B4 (99.34%; LC494275), HB5 (100%; MH985245), and GQHZJ23 (100%; MN338294), respectively. Concatenated gene sequences were used for a phylogenetic analysis based on the maximum likelihood method. The reference gene accessions and other information are presented in Weir et al. (2012). The analysis placed the isolates within a clade comprising C. fructicola. Pathogenicity of CP-1 was tested using 120 healthy pear fruits. The fruit surfaces were sterilized with 70% ethyl alcohol for 2 min and washed twice with sterilized water. Three 120 DAFB fruits were inoculated with 10 l of a conidial suspension (1×106 conidia/ml) with and without wounding. Another three control fruits were inoculated with sterile distilled with and without wounding. The inoculated fruit were placed in a plastic box to maintain high humidity and incubated in the dark at 25°C. Symptoms were observed on both wounded fruits after 3 days post inoculation (dpi) and 5 dpi on the unwounded fruits. No symptoms were observed in the control on both the wounded fruits. Pathogenicity tests was performed in duplicate. The pathogen was re-isolated from symptomatic tissues (100%) on treatments on both the wounded and unwounded fruits, but not control. The identity of the both re-isolated pathogen from the wounded and unwounded fruits was confirmed via analysis of seven genes and morphological characteristics, thus fulfilling Koch's postulates. Although C. fructicola has been reported on apples and peaches in Korea (Kim et al. 2018; Lee et al. 2020), this is the first report of anthracnose caused by C. fructicola on pear fruit in Korea, highlighting the need for systematically investigating the diversity and incidence of pear anthracnose in Korea. This study will contribute to the development of control strategies for anthracnose disease on pear fruit in Korea.