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.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.


  1. 1.

    , , , & Genomics of the fungal kingdom: insights into eukaryotic biology. Genome Res. 15, 1620–1631 (2005).

  2. 2.

    & A multilocus gene genealogy concordant with host preference indicates segregation of new species, Magnaporthe oryzae from M. grisea. Mycologia 94, 683–693 (2002).

  3. 3.

    , & Agrobacterium tumefaciens-mediated transformation of the plant pathogenic fungus, Magnaporthe grisea. Mol. Cells 12, 407–411 (2001).

  4. 4.

    et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387–391 (2002).

  5. 5.

    et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901–906 (1999).

  6. 6.

    & The Arabidopsis genome: a foundation for plant research. Genome Res. 15, 1632–1642 (2005).

  7. 7.

    et al. Rice mutant resources for gene discovery. Plant Mol. Biol. 54, 325–334 (2004).

  8. 8.

    Flying through the genome: a comprehensive study of functional genomics using RNAi in Drosophila. Trends Endocrinol. Metab. 15, 243–247 (2004).

  9. 9.

    et al. Genome-wide RNAi analysis of Caenorhabditis elegans fat regulatory genes. Nature 421, 268–272 (2003).

  10. 10.

    et al. A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 428, 431–437 (2004).

  11. 11.

    On the trail of a cereal killer: Exploring the biology of Magnaporthe grisea. Annu. Rev. Microbiol. 57, 177–202 (2003).

  12. 12.

    & Medical Mycology (Lea and Febiger, Philadelphia, 1992).

  13. 13.

    et al. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434, 980–986 (2005).

  14. 14.

    et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296, 79–92 (2002).

  15. 15.

    et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296, 92–100 (2002).

  16. 16.

    , & T-DNA as an insertional mutagen in Arabidopsis. Plant Cell 11, 2283–2290 (1999).

  17. 17.

    & Pathogenicity genes of phytopathogenic fungi. Mol. Plant Pathol. 2, 241–255 (2001).

  18. 18.

    & Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking. Genomics 25, 674–681 (1995).

  19. 19.

    , & Trehalose synthesis and metabolism are required at different stages of plant infection by Magnaporthe grisea. EMBO J. 22, 225–235 (2003).

  20. 20.

    , & Inactivation of the mitogen-activated protein kinase Mps1 from the rice blast fungus prevents penetration of host cells but allows activation of plant defense responses. Proc. Natl. Acad. Sci. USA 95, 12713–12718 (1998).

  21. 21.

    , , , & Peroxisomal carnitine acetyl transferase is required for elaboration of penetration hyphae during plant infection by Magnaporthe grisea. Mol. Microbiol. 61, 46–60 (2006).

  22. 22.

    & Dominant active Rac and dominant negative Rac revert the dominant active Ras phenotype in Colletotrichum trifolii by distinct signalling pathways. Mol. Microbiol. 51, 1493–1507 (2004).

  23. 23.

    , , & ERD2, a yeast gene required for the receptor-mediated retrieval of luminal ER proteins from the secretory pathway. Cell 61, 1349–1357 (1990).

  24. 24.

    et al. Characterization of the amyR gene encoding a transcriptional activator for the amylase genes in Aspergillus nidulans. Curr. Genet. 39, 10–15 (2001).

  25. 25.

    & Dominant mutations in a gene encoding a putative protein kinase (BCK1) bypass the requirement for a Saccharomyces cerevisiae protein kinase C homolog. Mol. Cell. Biol. 12, 172–182 (1992).

  26. 26.

    et al. 'PACLIMS': a component LIM system for high-throughput functional genomic analysis. BMC Bioinformatics 10.1186/1471–2105–6-94 (2005).

  27. 27.

    , , , & MuTrack: a genome analysis system for large-scale mutagenesis in the mouse. BMC Bioinformatics 10.1186/1471–2105–5-11 (2004).

  28. 28.

    & Transformation: a tool for studying fungal pathogens of plants. Cell. Mol. Life Sci. 58, 2043–2052 (2001).

  29. 29.

    & Extraction of DNA from milligram amount of fresh, herbarium, and mummified plant tissue. Plant Mol. Biol. 5, 69–76 (1985).

  30. 30.

    et al. Double-joint PCR: a PCR-based molecular tool for gene manipulations in filamentous fungi. Fungal Genet. Biol. 41, 973–981 (2004).

Download references


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. (

Author information

Author notes

    • Sook-Young Park
    •  & Bongsoo Park

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


  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


  1. Search for Junhyun Jeon in:

  2. Search for Sook-Young Park in:

  3. Search for Myoung-Hwan Chi in:

  4. Search for Jaehyuk Choi in:

  5. Search for Jongsun Park in:

  6. Search for Hee-Sool Rho in:

  7. Search for Soonok Kim in:

  8. Search for Jaeduk Goh in:

  9. Search for Sungyong Yoo in:

  10. Search for Jinhee Choi in:

  11. Search for Ju-Young Park in:

  12. Search for Mihwa Yi in:

  13. Search for Seonyoung Yang in:

  14. Search for Min-Jung Kwon in:

  15. Search for Seong-Sook Han in:

  16. Search for Byeong Ryun Kim in:

  17. Search for Chang Hyun Khang in:

  18. Search for Bongsoo Park in:

  19. Search for Se-Eun Lim in:

  20. Search for Kyongyong Jung in:

  21. Search for Sunghyung Kong in:

  22. Search for Maruthachalam Karunakaran in:

  23. Search for Hong-Sik Oh in:

  24. Search for Hyojeong Kim in:

  25. Search for Seryun Kim in:

  26. Search for Jaejin Park in:

  27. Search for Soyoung Kang in:

  28. Search for Woo-Bong Choi in:

  29. Search for Seogchan Kang in:

  30. Search for Yong-Hwan Lee in:


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

About this article

Publication history





Further reading