Preprints

1. 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. bioRxiv. DOI: 10.1101/2024.02.16.580620

2. Barragan AC*¹, Latorre SM*¹, Malmgren A, Harant A, Win J, Sugihara Y, Burbano HA, Kamoun S*², Langner T*² (2024) Multiple horizontal mini-chromosome transfers drive genome evolution of clonal blast fungus lineages. bioRxiv. DOI: 10.1101/2024.02.13.580079 *¹Authors contributed equally, *²Corresponding authors

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 (2023) Activation of plant immunity through conversion of a helper NLR homodimer into a resistosome. bioRxiv. DOI: 10.1101/2023.12.17.572070

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, Derevnina L, Wu C-H (2023) Functional divergence shaped the network architecture of plant immune receptors. bioRxiv. DOI: 10.1101/2023.12.12.571219

5. Natsume S, Yaegashi H, Sugihara Y, Abe A, Shimizu M, Oikawa K, White B, Kudoh A, Terauchi R (2022) Whole genome sequencing of a wild yam species Dioscorea tokoro reveals a genomic region associated with sex. bioRxiv. DOI: 10.1101/2022.06.11.495741

Publications

1. 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 *Corresponding authors

2. 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

3. 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

4. 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(9): e1010792. DOI: 10.1371/journal.ppat.1010792 *Corresponding authors

5. 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

6. 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(27): e2116896119. DOI: 10.1073/pnas.2116896119

7. 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

8. 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 *Authors contributed equally

9. 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(3): 299–312. DOI: 10.1270/jsbbs.20148

10. 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(50): 31987–31992. DOI: 10.1073/pnas.2015830117 *Corresponding authors

Presentations

1. 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

2. 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

3. 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

4. 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