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Abstract

Rapid translation of genome sequences into meaningful biological information hinges on the integration of multiple experimental and informatics methods into a cohesive platform. Despite the explosion in the number of genome sequences available1, such a platform does not exist for filamentous fungi. Here we present the development and application of a functional genomics and informatics platform for a model plant pathogenic fungus, Magnaporthe oryzae2. In total, we produced 21,070 mutants through large-scale insertional mutagenesis using Agrobacterium tumefaciens–mediated transformation3. We used a high-throughput phenotype screening pipeline to detect disruption of seven phenotypes encompassing the fungal life cycle and identified the mutated gene and the nature of mutation for each mutant. Comparative analysis of phenotypes and genotypes of the mutants uncovered 202 new pathogenicity loci. Our findings demonstrate the effectiveness of our platform and provide new insights on the molecular basis of fungal pathogenesis. Our approach promises comprehensive functional genomics in filamentous fungi and beyond.

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Acknowledgements

We are grateful to K. Lee and N.J. Talbot for their comments and suggestions on the manuscript. This research was partially supported by a grant from the Biogreen21 project funded by the Rural Development Administration, by grants from the Crop Functional Genomics Center (CG1421) and the Microbial Genomics and Applications Center (0462-20060021) of the 21st Century Frontier Research Program funded by the Ministry of Science and Technology, and by Korean Research Foundation Grant (KRF-2004-005-F00013) to Y.H.L. Requests for materials should be addressed to Y.H.L. (yonglee@snu.ac.kr).

Author information

Author notes

    • Sook-Young Park
    •  & Bongsoo Park

    Current address: Department of Plant Pathology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

Affiliations

  1. Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, and Center for Agricultural Biomaterials, Seoul National University, Seoul 151-921, Korea.

    • Junhyun Jeon
    • , Sook-Young Park
    • , Myoung-Hwan Chi
    • , Jaehyuk Choi
    • , Jongsun Park
    • , Hee-Sool Rho
    • , Soonok Kim
    • , Jaeduk Goh
    • , Sungyong Yoo
    • , Jinhee Choi
    • , Ju-Young Park
    • , Mihwa Yi
    • , Seonyoung Yang
    • , Min-Jung Kwon
    • , Bongsoo Park
    • , Se-Eun Lim
    • , Kyongyong Jung
    • , Sunghyung Kong
    • , Maruthachalam Karunakaran
    • , Hong-Sik Oh
    • , Hyojeong Kim
    • , Seryun Kim
    • , Jaejin Park
    • , Soyoung Kang
    •  & Yong-Hwan Lee
  2. National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Korea.

    • Seong-Sook Han
    •  & Byeong Ryun Kim
  3. Department of Plant Pathology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

    • Chang Hyun Khang
    •  & Seogchan Kang
  4. Department of Biotechnology and Bioengineering, Dongeui University, Busan 614-714, Korea.

    • Woo-Bong Choi

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Contributions

S.-Y.P., M.-H.C., J.J., H.-S.R., S.K., J.G. and S.Y. generated the mutants and performed high-throughput phenotype screening. J.C., J.-Y.P., M.Y., S.Y., S.-E.L. and M.-J.K. assisted in phenotype assessment. J.P., K.J., S.K., S.K., J.P., B.P. and S.K. developed the ATMT database. J.J., M.-H.C., S.Y., J.G., M.K. and W.-B.C. performed targeted knockout of the selected ORFs. S.-S.H. and B.R.K. performed pathogenicity tests on pot-grown rice plants. J.C., J.J., J.G., S.Y. and M.-H.C. performed TAIL PCR and sequence analysis. J.J., C.H.K., H.-S.O., H.K., S.K., S.K. and Y.-H.L. contributed to the writing of this paper. Y.-H.L. designed and directed this study.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Yong-Hwan Lee.

Supplementary information

PDF files

  1. 1.

    Supplementary Table 1

    Summary of high-throughput phenotype screening and selection of mutants.

  2. 2.

    Supplementary Table 2

    Phenotypes and genes affected by T-DNA insertions in ATMT mutants.

  3. 3.

    Supplementary Table 3

    Predicted protein and genome sequence source for 48 fungal species.

  4. 4.

    Supplementary Table 4

    In-depth phenptype analysis and T-DNA-tagged locations of pathogenicity-defective mutations.

  5. 5.

    Supplementary Table 5

    Analysis of the linkage between T-DNA insertion and pathogenicity defects by targeted disruption.

  6. 6.

    Supplementary Methods

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DOI

https://doi.org/10.1038/ng2002

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