Yu Sugihara
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Preprints

  1. Pai H, Sakai T, Posbeyikian A, Frijters R, Sugihara Y, Contreras MP, Kourelis J, Adachi H, Kamoun S, Toghani A (2025). A hierarchical immune receptor network in lettuce reveals contrasting patterns of evolution in sensor and helper NLRs. bioRxiv. DOI:10.1101/2025.02.25.639832
  2. Kudoh A, Natsume S, Sugihara Y, Kato H, Abe A, Oikawa K, Shimizu M, Itoh K, Tsujimura M, Takano Y, Sakai T, Adachi H, Ohta A, Ohtsu M, Ishizaki T, Terachi T, Terauchi R (2025). Whole-genome sequencing reveals the molecular basis of sex determination in the dioecious wild yam (Dioscorea tokoro). bioRxiv. DOI:10.1101/2025.04.28.650915
  3. Fujisaki K, Abe Y, Sugihara Y, Nemoto K, Ito K, Kanzaki E, Ishikawa K, Iwai M, Utsushi H, Saitoh H, Takagi H, Takeda T, Abe A, Zheng S, Bialas A, Banfield MJ, Kamoun S, Terauchi R (2024). Binding of a pathogen effector to rice Exo70 proteins tethered to the NOI/RIN4 integrated domain of the NLR receptor Pii2 confers immunity against fungi. bioRxiv. DOI:10.1101/239400

Publications

* Corresponding authors、+ Authors contributed equally

  1. Toghani A, Frijters R, Bozkurt TO, Terauchi R, Kamoun S*, Sugihara Y* (2025). Can AI modeling of protein structures distinguish between sensor and helper NLR immune receptors?. New Phytologist, 248: 17–23. DOI:10.1111/nph.70391
  2. Sugihara Y, Kourelis J, Contreras MP, Pai H, Harant A, Selvaraj M, Toghani A, Martinez-Anaya C*, Kamoun S* (2025). Helper NLR immune protein NRC3 evolved to evade inhibition by a cyst nematode virulence effector. PLOS Genetics, 21: e1011653. DOI:10.1371/journal.pgen.1011653
  3. Selvaraj M, Toghani A, Pai H, Sugihara Y, Kourelis J, Yuen ELH, Ibrahim T, Zhao H, Xie R, Maqbool A, Concepcion JCD la, Banfield MJ, Derevnina L, Petre B, Lawson DM, Bozkurt TO, Wu C-H, Kamoun S*, Contreras MP* (2024). Activation of plant immunity through conversion of a helper NLR homodimer into a resistosome. PLOS Biology, 22: e3002868. DOI:10.1371/journal.pbio.3002868
  4. Huang C-Y, Huang Y-S, Sugihara Y, Wang H-Y, Huang L-T, Lopez-Agudelo JC, Chen Y-F, Lin K-Y, Chiang B-J, Toghani A, Kourelis J, Wang C-H, Derevnina L, Wu C-H (2024). Subfunctionalization of NRC3 altered the genetic structure of the Nicotiana NRC network. PLOS Genetics, 20: e1011402. DOI:10.1371/journal.pgen.1011402
  5. Sugimura Y, Oikawa K, Sugihara Y, Utsushi H, Kanzaki E, Ito K, Ogasawara Y, Fujioka T, Takagi H, Shimizu M, Shimono H, Terauchi R, Abe A (2024). Impact of rice GENERAL REGULATORY FACTOR14h (GF14h) on low-temperature seed germination and its application to breeding. PLOS Genetics, 20: e1011369. DOI: 10.1371/journal.pgen.1011369
  6. Barragan AC*+, Latorre SM+, Malmgren A, Harant A, Win J, Sugihara Y, Burbano HA, Kamoun S*, Langner T* (2024). Multiple horizontal mini-chromosome transfers drive genome evolution of clonal blast fungus lineages. Molecular Biology and Evolution, 41: msae164. DOI: 10.1093/molbev/msae164
  7. Sugihara Y, Abe Y, Takagi H, Abe A, Shimizu M, Ito K, Kanzaki E, Oikawa K, Kourelis J, Langner T, Win J, Białas A, Lüdke D, Contreras MP, Chuma I, Saitoh H, Kobayashi M, Zheng S, Tosa Y, Banfield MJ, Kamoun S*, Terauchi R*, Fujisaki K* (2023). Disentangling the complex gene interaction networks between rice and the blast fungus identifies a new pathogen effector. PLOS Biology, 21:e3001945. DOI: 10.1371/journal.pbio.3001945
  8. Nishiyama C, Sekiguchi S, Sugihara Y, Nishikawa M, Makita N, Segawa T, Terasaki M, Takagi H, Koyanagi T (2023). Phylogenomic analysis in Latilactobacillus sakei by using polymorphisms detected by next-generation sequencing. Bioscience of Microbiota, Food and Health, advpub: 2022–017. DOI: 10.12938/bmfh.2022-017
  9. Saiga S, Tada M, Segawa T, Sugihara Y, Nishikawa M, Makita N, Sakamoto M, Tanaka K, Wada T, Takagi H (2023). NGS-based genome wide association study helps to develop co-dominant marker for the physical map-based locus of PFRU controlling flowering in cultivated octoploid strawberry. Euphytica, 219:6. DOI: 10.1007/s10681-022-03132-7
  10. Takeda T*, Takahashi M, Shimizu M, Sugihara Y, Saitoh H, Fujisaki K, Ishikawa K, Utsushi H, Kanzaki E, Sakamoto Y, Abe A, Terauchi R* (2022). Rice apoplastic CBM1-interacting protein counters blast pathogen invasion by binding conserved carbohydrate binding module 1 motif of fungal proteins. PLOS Pathogens, 18: e1010792. DOI: 10.1371/journal.ppat.1010792
  11. Natsume S, Sugihara Y, Kudoh A, Oikawa K, Shimizu M, Ishikawa Y, Nishihara M, Abe A, Innan H, Terauchi R (2022). Genome Analysis Revives a Forgotten Hybrid Crop Edo-dokoro in the Genus Dioscorea. Plant and Cell Physiology, pcac109. DOI: 10.1093/pcp/pcac109
  12. Shimizu M, Hirabuchi A, Sugihara Y, Abe A, Takeda T, Kobayashi M, Hiraka Y, Kanzaki E, Oikawa K, Saitoh H, Langner T, Banfield MJ, Kamoun S, Terauchi R (2022). A genetically linked pair of NLR immune receptors show contrasting patterns of evolution. Proceedings of the National Academy of Sciences, 119: e2116896119. DOI: 10.1073/pnas.2116896119
  13. Sugihara Y, Young L, Yaegashi H, Natsume S, Shea DJ, Takagi H, Booker H, Innan H, Terauchi R, Abe A (2022). High-performance pipeline for MutMap and QTL-seq. PeerJ, 10: e13170. DOI: 10.7717/peerj.13170
  14. Sugihara Y+, Kudoh A+, Tamiru-Oli M, Takagi H, Natsume S, Shimizu M, Abe A, Asiedu R, Asfaw A, Adebola P, Terauchi R (2021). Population genomics of yams: evolution and domestication of Dioscorea species. In: Population Genomics. Springer, Cham. DOI: 10.1007/13836_2021_94
  15. Segawa T, Nishiyama C, Tamiru-Oli M, Sugihara Y, Abe A, Sone H, Itoh N, Asukai M, Uemura A, Oikawa K, Utsushi H, Ikegami-Katayama A, Imamura T, Mori M, Terauchi R, Takagi H (2021). Sat-BSA: an NGS-based method using local de novo assembly of long reads for rapid identification of genomic structural variations associated with agronomic traits. Breeding Science, 71: 299–312. DOI: 10.1270/jsbbs.20148
  16. Sugihara Y, Darkwa K, Yaegashi H, Natsume S, Shimizu M, Abe A, Hirabuchi A, Ito K, Oikawa K, Tamiru-Oli M, Ohta A, Matsumoto R, Agre P, De Koeyer D, Pachakkil B, Yamanaka S, Muranaka S, Takagi H, White B, Asiedu R, Innan H, Asfaw A*, Adebola P*, Terauchi R* (2020). Genome analyses reveal the hybrid origin of the staple food crop white Guinea yam (Dioscorea rotundata). Proceedings of the National Academy of Sciences, 17: 31987–31992. DOI: 10.1073/pnas.2015830117

Presentations

  1. Sugihara Y, Toghani A, Frijters R, Bozkurt TO, Terauchi R, Kamoun S. Can AI modelling of protein structures distinguish between sensor and helper NLR immune receptors? 2025 IS-MPMI. Cologne, Germany. July 2025.
  2. Sugihara Y, Kourelis J, Contreras MP, Pai H, Selvaraj M, Toghani A, Martinez-Anaya C, Kamoun S. Helper NLR immune protein NRC3 evolved to evade inhibition by a cyst nematode virulence effector. The 26th Annual Meeting of Society for Evolutionary Studies, Japan. Kanagawa, Japan. Aug. 2024.
  3. Sugihara Y, Białas A, Langner T, Barragan AC, Kourelis J, Abe Y, Fujisaki K, Banfield MJ, Terauchi R, Kamoun S. The NLR immune receptor Pik-1 evolved to respond to fungal effectors of the AVR-Mgk family early in the evolution of Oryza and prior to rice domestication. 2023 IS-MPMI. Rhode Island, PA. July 2023.
  4. Sugihara Y. Genetics approach using whole genome sequencing to rapidly identify the genomic loci involved in biological traits of rice blast fungus. 12th Japan-US Seminar in Plant Pathology. Zoom workshop. October 2020.
  5. Sugihara Y, Natsume S, Abe A, Shimizu M, Obidiegwu J, Terauchi R. Population genomics of Dioscorea tokoro, a wild yam species. Plant and Animal Genome (PAG) XXVII Conference. San Diego, CA. January 2019.
  6. Sugihara Y, Abe A, Shimizu M, Yaegashi H, Natsume S, Obidiegwu J, Terauchi R. Application of population genomics and GWAS to Dioscorea rotundata (white Guinea yams) for identifying loci controlling agronomically important traits. Plant and Animal Genome (PAG) XXVII Conference. San Diego, CA. January 2019.