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Interestingly, complete ASE genes showed higher gene body CHG methylation than partial ( I P i = 0.05) and non-ASE genes and partial ASE genes showed lower CG methylation than others ( I P i = 3.8 e-08, Figure 1g), suggesting that DNA methylation alterations between alleles from different haplotypes are frequently accompanied with ASEs. Since the cassava genome is highly heterozygous, DNA methylome of the haplotype-collapsed genome misses many features of the methylome. Keywords: haplotype-resolved; DNA methylation; cassava EN haplotype-resolved DNA methylation cassava 247 249 3 01/31/23 20230201 NES 230201 Cytosine DNA methylation is involved in transposable element (TE) silencing, imprinting and X-chromosome inactivation. [Extracted from the article]

Summary: Rice cultivars from japonica and indica lineage possess differential resistance against blast fungus as a result of genetic divergence. Whether different rice cultivars also show distinct metabolomic changes in response to P. oryzae, and their role in host resistance, are poorly understood. Here, we examine the responses of six different rice cultivars from japonica and indica lineage challenged with P. oryzae. Both susceptible and resistant rice cultivars expressed several metabolites exclusively during P. oryzae infection, including the saponin Bayogenin 3‐O‐cellobioside. Bayogenin 3‐O‐cellobioside level in infected rice directly correlated with their resistant attributes. These findings reveal, for the first time to our knowledge that besides oat, other grass plants including rice produces protective saponins. Our study provides insight into the role of pathogen‐mediated metabolomics reprogramming in host immunity. The correlation between Bayogenin 3‐O‐Cellobioside levels and blast resistance suggests that engineering saponin expression in cereal crops represents attractive and sustainable disease management. [ABSTRACT FROM AUTHOR]

Summary: Secondary metabolites (SMs) are crucial for fungi and vary in function from beneficial antibiotics to pathogenicity factors. To generate diversified SMs that enable different functions, SM‐coding regions rapidly evolve in fungal genomes. However, the driving force and genetic mechanism of fungal SM diversification in the context of host‐pathogen interactions remain largely unknown. Previously, we grouped field populations of the rice blast fungus Magnaporthe oryzae (syn: Pyricularia oryzae) into three major globally distributed clades based on population genomic analyses. Here, we characterize a recent duplication of an avirulent gene‐containing SM cluster, ACE1, in a clonal M. oryzae population (Clade 2). We demonstrate that the ACE1 cluster is specifically duplicated in Clade 2, a dominant clade in indica rice‐growing areas. With long‐read sequencing, we obtained chromosome‐level genome sequences of four Clade 2 isolates, which displayed differences in genomic organization of the ACE1 duplication process. Comparative genomic analyses suggested that the original ACE1 cluster experienced frequent rearrangement in Clade 2 isolates and revealed that the new ACE1 cluster is located in a newly formed and transposable element‐rich region. Taken together, these results highlight the frequent mutation and expansion of an avirulent gene‐containing SM cluster through transposable element‐mediated whole‐cluster duplication in the context of host‐pathogen interactions. [ABSTRACT FROM AUTHOR]

Plants generate multitude of aldehydes under abiotic and biotic stress conditions. Ample demonstrations have shown that rice-derived aldehydes enhance the resistance of rice against the rice-blast fungus Magnaporthe oryzae. However, how the fungal pathogen nullifies the inhibitory effects of host aldehydes to establish compatible interaction remains unknown. Here we identified and evaluated the in vivo transcriptional activities of M. oryzae aldehyde dehydrogenase (ALDH) genes. Transcriptional analysis of M. oryzae ALDH genes revealed that the acetylating enzyme Methylmalonate-Semialdehyde Dehydrogenase (MoMsdh/MoMmsdh) elevated activities during host invasion and colonization of the fungus. We further examined the pathophysiological importance of MoMSDH by deploying integrated functional genetics, and biochemical approaches. MoMSDH deletion mutant Δ Momsdh exhibited germination defect, hyper-branching of germ tube and failed to form appressoria on hydrophobic and hydrophilic surface. The MoMSDH disruption caused accumulation of small branch-chain amino acids, pyridoxine and AMP/cAMP in the Δ Momsdh mutant and altered Spitzenkörper organization in the conidia. We concluded that MoMSDH contribute significantly to the pathogenesis of M. oryzae by regulating the mobilization of Spitzenkörper during germ tube morphogenesis, appressoria formation by acting as metabolic switch regulating small branch-chain amino acids, inositol, pyridoxine and AMP/cAMP homeostasis. [ABSTRACT FROM AUTHOR]