Kyoto University · Agricultural and Biological Sciences
Professor Yu Sugihara's research lab specializes in plant genomics, functional genetics, and molecular plant pathology, with a focus on understanding the genetic and evolutionary mechanisms underlying disease resistance and crop domestication. The lab employs advanced sequencing technologies and bioinformatics pipelines—such as MutMap and QTL-seq—to identify key genes controlling agronomic traits in economically important crops, particularly yams and solanaceous species. A central theme of the lab’s work is dissecting the molecular mechanisms of nucleotide-binding domain and leucine-rich repeat (NLR) immune receptors, including their activation, oligomerization, and evasion by pathogenic effectors. The lab also investigates the complex evolutionary histories of polyploid and hybrid crop species, especially in the genus *Dioscorea*, to clarify their origins and domestication pathways.
Figures are computed from collected data and may differ slightly.
The new pipelines of MutMap and QTL-seq are written in Python and can be installed via bioconda. The source code and manuals are available online (MutMap: https://github.com/YuSugihara/MutMap, QTL-seq: https://github.com/YuSugihara/QTL-seq).
White Guinea yam (<i>Dioscorea rotundata</i>) is an important staple tuber crop in West Africa. However, its origin remains unclear. In this study, we resequenced 336 accessions of white Guinea yam and compared them with the sequences of wild <i>Dioscorea</i> species using an improved reference genome sequence of <i>D. rotundata</i> In contrast to a previous study suggesting that <i>D. rotundata</i> originated from a subgroup of <i>Dioscorea praehensilis</i>, our results suggest a hybrid origin
Nucleotide-binding domain and leucine-rich repeat (NLR) proteins can engage in complex interactions to detect pathogens and execute a robust immune response via downstream helper NLRs. However, the biochemical mechanisms of helper NLR activation by upstream sensor NLRs remain poorly understood. Here, we show that the coiled-coil helper NLR NRC2 from Nicotiana benthamiana accumulates in vivo as a homodimer that converts into a higher-order oligomer upon activation by its upstream virus disease re
Abstract Yam is a collective name of tuber crops belonging to the genus Dioscorea . Yam is important not only as a staple food crop but also as an integral component of society and culture of the millions of people who depend on it. However, due to its regional importance, yam has long been regarded as an “orphan crop” lacking a due global attention. Although this perception is changing with recent advances in genomics technologies, domestication processes of most yam species are still ambiguous
Abstract Bulked segregant analysis implemented in MutMap and QTL-seq is a powerful and efficient method to identify agronomically important loci. However, the previous pipelines were not user-friendly to install and run. Here, we describe new pipelines for MutMap and QTL-seq. These updated pipelines are approximately 5-8 times faster than the previous pipeline, are easier for novice users to use and can be easily installed through bioconda with all dependencies.
Parasites can counteract host immunity by suppressing nucleotide binding and leucine-rich repeat (NLR) proteins that function as immune receptors. We previously showed that a cyst nematode virulence effector SPRYSEC15 (SS15) binds and inhibits oligomerisation of helper NLR proteins in the expanded NRC1/2/3 clade by preventing intramolecular rearrangements required for NRC oligomerisation into an activated resistosome. Here we examined the degree to which NRC proteins from multiple Solanaceae spe
Nucleotide binding and leucine-rich repeat (NLR) proteins are intracellular immune receptors that occur across all kingdoms of life but are particularly highly diversified in plants (Barragan & Weigel, 2021). In plants, NLRs that carry a coiled-coil (CC) domain at their N termini are the most phylogenetically widespread class. Following pathogen recognition, CC-NLR proteins oligomerize into pentameric or hexameric pore-like complexes (Wang et al., 2019; Förderer et al., 2022; Zhao et al., 2022;
We report a dataset of 66,665 NLR immune receptor sequences extracted using NLRtracker from the proteomes of 124 genomes of plants in the Solanaceae family. These include samples from the following genera: Solanum (108 genomes, 30 species), Physalis (1, 1), Capsicum (7, 3), and Nicotiana (8, 5). This dataset includes NLR protein sequences and their domain annotations. The dataset is made available to the community as an open access resource as part of the OpenPlantNLR initiative.
Direct seeding is employed to circumvent the labor-intensive process of rice (Oryza sativa) transplantation, but this approach requires varieties with vigorous low-temperature germination (LTG) when sown in cold climates. To investigate the genetic basis of LTG, we identified the quantitative trait locus (QTL) qLTG11 from rice variety Arroz da Terra, which shows rapid seed germination at lower temperatures, using QTL-seq. We delineated the candidate region to a 52-kb interval containing GENERAL
ABSTRACT NLR immune receptors can be functionally organized in genetically linked sensor-helper pairs. However, methods to categorize paired NLRs remain limited, primarily relying on the presence of non-canonical domains in some sensor NLRs. Here, we propose that the AI system AlphaFold 3 can classify paired NLR proteins into sensor or helper categories based on predicted structural characteristics. Helper NLRs showed higher AlphaFold 3 confidence scores than sensors when modelled in oligomeric
We report a dataset of 66,665 NLR immune receptor sequences extracted using NLRtracker from the proteomes of 124 genomes of plants in the Solanaceae family. These include samples from the following genera: Solanum (108 genomes, 30 species), Physalis (1, 1), Capsicum (7, 3), and Nicotiana (8, 5). This dataset includes NLR protein sequences and their domain annotations. The dataset is made available to the community as an open access resource as part of the OpenPlantNLR initiative.
Abstract White Guinea yam ( Dioscorea rotundata ) is an important staple tuber crop of West Africa. However, its origin remains unclear. In this study, we re-sequenced 336 accessions of white Guinea yam and compared them with the sequences of the wild Dioscorea species using an improved reference genome sequence of D. rotundata . Our results suggest a hybrid origin of white Guinea yam from crosses between the rainforest wild species D. praehensilis and the savannah-adapted D. abyssinica . We ide
ABSTRACT Parasites can counteract host immunity by suppressing nucleotide binding and leucine-rich repeat (NLR) proteins that function as immune receptors. We previously showed that a cyst nematode virulence effector SPRYSEC15 (SS15) binds and inhibits oligomerisation of helper NLR proteins in the expanded NRC1/2/3 clade by preventing intramolecular rearrangements required for NRC oligomerisation into an activated resistosome. Here we examined the degree to which NRC proteins from multiple Solan
Please refer to the material_and_method.pdf to check how we generated each file. 01_NRCH_cds_23-03-03.fasta FASTA file containing the nucleotide sequences of 2341 NRC helper sequences extracted from 124 Solanaceae NLRome dataset [1] and 20 NRC helper sequences from Adachi et al. 2023 [2]. 02_NRCH_cds_23-03-03.min2400max2800.fasta FASTA file containing the nucleotide sequences of 1753 NRC helper sequences filtered to keep only sequences between 2400 and 2800 bp. 03_NRCH_cds_23-03-03.min2400max280
Please refer to the material_and_method.pdf to check how we generated each file. 01_NRCH_cds_23-03-03.fasta FASTA file containing the nucleotide sequences of 2341 NRC helper sequences extracted from 124 Solanaceae NLRome dataset [1] and 20 NRC helper sequences from Adachi et al. 2023 [2]. 02_NRCH_cds_23-03-03.min2400max2800.fasta FASTA file containing the nucleotide sequences of 1753 NRC helper sequences filtered to keep only sequences between 2400 and 2800 bp. 03_NRCH_cds_23-03-03.min2400max280
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