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Hybrid de novo genome-reassembly reveals new insights on pathways and pathogenicity determinants in rice blast pathogen Magnaporthe oryzae RMg_Dl.

ABSTRACT: Blast disease incited by Magnaporthe oryzae is a major threat to sustain rice production in all rice growing nations. The pathogen is widely distributed in all rice paddies and displays rapid aerial transmissions, and seed-borne latent infection. In order to understand the genetic variability, host specificity, and molecular basis of the pathogenicity-associated traits, the whole genome of rice infecting Magnaporthe oryzae (Strain RMg_Dl) was sequenced using the Illumina and PacBio (RSII compatible) platforms. The high-throughput hybrid assembly of short and long reads resulted in a total of 375 scaffolds with a genome size of 42.43 Mb. Furthermore, comparative genome analysis revealed 99% average nucleotide identity (ANI) with other oryzae genomes and 83% against M. grisea, and 73% against M. poe genomes. The gene calling identified 10,553 genes with 10,539 protein-coding sequences. Among the detected transposable elements, the LTR/Gypsy and Type LINE showed high occurrence. The InterProScan of predicted protein sequences revealed that 97% protein family (PFAM), 98% superfamily, and 95% CDD were shared among RMg_Dl and reference 70-15 genome, respectively. Additionally, 550 CAZymes with high GH family content/distribution and cell wall degrading enzymes (CWDE) such endoglucanase, beta-glucosidase, and pectate lyase were also deciphered in RMg_Dl. The prevalence of virulence factors determination revealed that 51 different VFs were found in the genome. The biochemical pathway such as starch and sucrose metabolism, mTOR signaling, cAMP signaling, MAPK signaling pathways related genes were identified in the genome. The 49,065 SNPs, 3267 insertions and 3611 deletions were detected, and majority of these varinats were located on downstream and upstream region. Taken together, the generated information will be useful to develop a specific marker for diagnosis, pathogen surveillance and tracking, molecular taxonomy, and species delineation which ultimately leads to device improved management strategies for blast disease.

SUBMITTER: Reddy B

PROVIDER: S-EPMC8616942 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Rice blast disease caused by Magnaporthe oryzae is a devastating disease of cultivated rice worldwide. Infections by this fungus lead to a significant reduction in rice yields and threats to food security. To gain better insight into growth and cell death in M. oryzae during infection, we characterized two predicted M. oryzae metacaspase proteins, MoMca1 and MoMca2. These proteins appear to be functionally redundant and can complement the yeast Yca1 homologue. Biochemical analysis revealed that M. oryzae metacaspases exhibited Ca2+-dependent caspase activity in vitro Deletion of both MoMca1 and MoMca2 in M. oryzae resulted in reduced sporulation, delay in conidial germination, and attenuation of disease severity. In addition, the double ΔMomca1mca2 mutant strain showed increased radial growth in the presence of oxidative stress. Interestingly, the ΔMomca1mca2 strain showed an increased accumulation of insoluble aggregates compared to the wild-type strain during vegetative growth. Our findings suggest that MoMca1 and MoMca2 promote the clearance of insoluble aggregates in M. oryzae, demonstrating the important role these metacaspases have in fungal protein homeostasis. Furthermore, these metacaspase proteins may play additional roles, like in regulating stress responses, that would help maintain the fitness of fungal cells required for host infection.IMPORTANCEMagnaporthe oryzae causes rice blast disease that threatens global food security by resulting in the severe loss of rice production every year. A tightly regulated life cycle allows M. oryzae to disarm the host plant immune system during its biotrophic stage before triggering plant cell death in its necrotrophic stage. The ways M. oryzae navigates its complex life cycle remain unclear. This work characterizes two metacaspase proteins with peptidase activity in M. oryzae that are shown to be involved in the regulation of fungal growth and development prior to infection by potentially helping maintain fungal fitness. This study provides new insights into the role of metacaspase proteins in filamentous fungi by illustrating the delays in M. oryzae morphogenesis in the absence of these proteins. Understanding the mechanisms by which M. oryzae morphology and development promote its devastating pathogenicity may lead to the emergence of proper methods for disease control.

Project description:Rice blast (Magnaporthe oryzae) is a key concern in combating global food insecurity given the disease is responsible for approximately 30% of rice production losses globally-the equivalent of feeding 60 million people. These losses increase the global rice price and reduce consumer welfare and food security. Rice is the staple crop for more than half the world's population so any reduction in rice blast would have substantial beneficial effects on consumer livelihoods. In 2012, researchers in the US began analyzing the feasibility of creating blast-resistant rice through cisgenic breeding. Correspondingly, our study evaluates the changes in producer, consumer, and environmental welfare, if all the rice produced in the Mid-South of the US were blast resistant through a process like cisgenics, using both international trade and environmental assessment modeling. Our results show that US rice producers would gain 69.34 million dollars annually and increase the rice supply to feed an additional one million consumers globally by eliminating blast from production in the Mid-South. These results suggest that blast alleviation could be even more significant in increasing global food security given that the US is a small rice producer by global standards and likely experiences lower losses from blast than other rice-producing countries because of its ongoing investment in production technology and management. Furthermore, results from our detailed life cycle assessment (LCA) show that producing blast-resistant rice has lower environmental (fossil fuel depletion, ecotoxicity, carcinogenics, eutrophication, acidification, global warming potential, and ozone depletion) impacts per unit of rice than non-blast resistant rice production. Our findings suggest that any reduction in blast via breeding will have significantly positive impacts on reducing global food insecurity through increased supply, as well as decreased price and environmental impacts in production.

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Hybrid de novo genome-reassembly reveals new insights on pathways and pathogenicity determinants in rice blast pathogen Magnaporthe oryzae RMg_Dl.

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