Biology subjects

Sugihara, Y.

Publications and source records attributed to Sugihara, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Convergent recognition of tobamovirus movement proteins by phylogenetically distinct NLR immune receptors

The tobamovirus Tomato brown rugose fruit virus (ToBRFV) has rapidly emerged as a major threat to tomato production worldwide, overcoming the widely deployed Tm-22-mediated resistance and challenging current strategies for tobamovirus disease control. The tomato coiled-coil nucleotide-binding leucine-rich repeat (CC-NLR) immune receptor HREZ confers resistance to ToBRFV. However, the activation mechanism underlying HREZ recognition of ToBRFV remains unclear. Here, we show that HREZ is activated by the movement protein (MP) of ToBRFV and induces hypersensitive cell death. Upon activation, HREZ assembles into a higher-order oligomeric complex, with AlphaFold 3 modelling supporting a pentameric resistosome model. Phylogenetic analysis places HREZ in a CC-NLR lineage distinct from the canonical tobamovirus resistance receptor Tm-22, consistent with convergent evolution of tobamovirus MP recognition. Comparative analysis of eight MPs from the family Virgaviridae reveals that HREZ and Tm-22 have distinct recognition spectra. Four distinct tobamovirus MPs that activate HREZ also promote its assembly into a higher-order oligomeric complex. Together, these findings show how phylogenetically distinct CC-NLRs can converge on the same viral target while retaining distinct recognition breadth and provide a foundation for developing resistance strategies against current and emerging tobamoviruses.

plant biology↗

bioRxiv2026

Evolution of an unstable sex determination system in white Guinea yam (Dioscorea rotundata)

Plants often produce unstable sex phenotypes; however, the underlying evolutionary and molecular mechanisms are unclear. In white Guinea yam (Dioscorea rotundata), the most economically important tuber crop, genetic improvement is critical for food security but remains constrained by dioecy and complex sex phenotypes. White Guinea yam has a ZZ/ZW sex determination system in which ZZ individuals are consistently male, whereas ZW individuals can be female, male, or monoecious. Here we show that chromosome 11 is the sex chromosome, featuring a 1.2-Mb inversion between the Z and W chromosomes. A 170-kb W-specific region carries the microRNA gene dro-MIR432, likely involved in sex switching. The recent emergence of this miRNA-mediated ZZ/ZW system, distinct from the XY/XX system within Dioscorea, underscores the dynamic evolution of plant sex determination.

plant biology↗

bioRxiv2026

A wheat immune receptor pair executes cell death through a helper MLKL

To promote disease resistance, plant nucleotide-binding, leucine-rich repeat (NLR) immune receptors often require paired co-receptors. In many cases, paired NLRs comprise one NLR to perceive effectors (the sensor) and another NLR to execute cell death (the helper). However, NLRs can also pair with sensor kinase fusion protein (KFP) receptors, but whether non-NLR components within such pairs can execute cell death, remains unclear. Here, we investigate the mechanism of an immune receptor pair comprising the wheat NLR Rwt3.6.8 NLR (R3NLR) and an MLKL protein, Rwt3.6.8 associated kinase (R3AK). Using Nicotiana benthamiana transient expression assays we confirmed that both R3NLR and R3AK are required for cell death in response to blast pathogen effectors PWT3, PWT6 or PWT8. Through mutational analysis we show the 4-helical bundle (4HB) domain of R3AK is required to execute cell death and R3AK can be made auto-active by perturbing the kinase catalytic active site. Activation of R3AK is also associated with a shift to a higher oligomeric state. Furthermore, as the NLR R3NLR is not actively involved in the execution of cell death we hypothesise that R3AK acts as a helper. A phylogenetic analysis indicates widespread distribution of this paired configuration in Poales. Together, this study establishes a novel resistance mechanism involving a non-canonical NLR/MLKL system. Significance StatementHere we investigate the mechanism of a novel plant immune receptor pair from wheat, R3NLR/R3AK. A nucleotide-binding, leucine-rich repeat (NLR) receptor and a mixed lineage kinase like (MLKL) protein are both required to mediate resistance to blast pathogen effector proteins PWT3, PWT6 and PWT8. Adopting a mutagenesis approach, we show that the MLKL protein executes cell death through its N-terminal 4-helical bundle domain, and this is associated with a shift to a higher oligomeric state. Mutations of conserved sequence motifs in the NLR support its role as a sensor, although effector interactions have not yet been observed. This study reveals a plant immune receptor pair that functions via a putative NLR sensor paired to a cell death executing MLKL protein.

plant biology↗

bioRxiv2026

AI-guided discovery of atypical protein assemblies

Artificial intelligence (AI) systems such as AlphaFold have transformed structural biology by enabling accurate prediction of protein structures. However, their capacity to uncover new classes of macromolecular assemblies remains largely untapped. We developed the Structural Novelty Index (SNI), a quantitative framework for identifying protein complexes that diverge from canonical architectures. As one implementation of SNI, we developed SNINRC-Hexa, to identify unconventional resistosomes formed by nucleotide-binding, leucine-rich repeat immune receptors (NLRs). We used it to analyze AlphaFold 3 models of 637 non-redundant NRC proteins from 346 genomes representing 85 plant species. This analysis identified candidates with predicted architectures distinct from the canonical hexameric resistosomes of NRC proteins. Biochemical purification and negative-stain transmission electron microscopy of NRC7 orthologs from multiple species supported the SNI prediction and revealed an unexpected undecameric (11-mer) assembly. Our results establish SNI as a scalable approach for discovering atypical protein complexes.

bioinformatics↗

bioRxiv2025

Stepwise and lineage-specific divergence of a major immune co-chaperone complex in leptosporangiate ferns

Protein-protein interactions are essential for proper cellular function and are often under strong evolutionary pressures to maintain their stability and specificity. In plants, a broadly distributed chaperone complex comprised of the RAR1 (REQUIRED FOR MLA12 RESISTANCE 1) and SGT1 (SUPRESSOR OF THE G2 ALLELE OF SKP1) co-chaperones alongside the HSP90 (HEAT SHOCK PROTEIN90) core chaperone are important for immunity. Despite its importance in flowering plants, a deeper understanding of how this complex evolved remains limited. Here, we examine the molecular evolutionary history of the RAR1-SGT1 interaction across land plants. We identified a lineage-specific divergence of the RAR1-SGT1 binding interface in vascular non-seed ferns, which renders orthologs unable to interact outside of their lineage. Further investigation of interface diversity uncovered a single amino acid residue in RAR1 and three corresponding residues in SGT1 that collectively dictate binding specificity. Ancestral state reconstruction supported stepwise evolution of specificity in SGT1 in leptopsporangiate ferns, which was initiated by a promiscuous intermediate state that widened its capacity to bind RAR1 before subsequent mutations locked in specificity. Our data highlight the broad conservation of the RAR1-SGT1 interface and the coevolutionary dynamics that shaped interface maintenance during lineage-specific diversification.

plant biology↗

bioRxiv2025

Whole-genome sequencing reveals the molecular basis of sex determination in the dioecious wild yam Dioscorea tokoro

Dioecious plants, which have distinct male and female individuals, constitute [~]5% of angiosperm species and have emerged frequently and independently from hermaphroditic ancestors. Although recent molecular studies of sex determination have started to reveal the diversity of the genetic systems underlying dioecy, research on the evolution of dioecy is limited, especially in monocots. Here, we describe the molecular basis of sex determination in the monocot Dioscorea tokoro, a dioecious wild yam endemic to East Asia. Chromosome-scale and haplotype-resolved genome assemblies and linkage analysis suggested that this plant has a male heterogametic sex determination (XY) system, with sex determination regions located on chromosome 3. Sequence read coverage analysis of the sex chromosomes revealed X- and Y-specific regions in putative pericentromeric chromosome regions. Within the Y-specific region, we identified two candidate genes that are likely involved in sex determination: BLH9, encoding a homeobox protein, and HSP90, encoding a molecular chaperone. BLH9 has similar functions to AtBLH9 in Arabidopsis thaliana. BLH9 is thought to suppress female organ development, whereas HSP90 might be required for pollen development. These results shed light on the complex evolution of dioecy in plants. Author summarySexual reproduction is a nearly universal, indispensable feature of evolution in eukaryotes. The molecular mechanisms underlying sex determination vary depending on the taxon. However, most information about this process was derived from studies of model organisms and/or domesticated species. To elucidate the diversity and evolution of sex determination, we need to expand the taxonomic breadth of these investigations. Here, we focused on the monocot genus Dioscorea, which contains species with multiple sex-determination systems, suggesting that frequent evolutionary transitions occur between the different sex-determination systems. We investigated the genetics of sex determination in Dioscorea tokoro, a dioecious wild yam endemic to East Asia. Whole-genome assembly and genetic analysis, along with transcriptome analysis, suggested that this species employs a male heterogametic sex determination (XY) system, with two Y-chromosome-specific genes that might be involved in male and female differentiation. These findings enhance our understanding of the complex evolution of dioecy.

plant biology↗

bioRxiv2025

A hierarchical immune receptor network in lettuce reveals contrasting patterns of evolution in sensor and helper NLRs

Nucleotide-binding domain and leucine-rich repeat immune receptors (NLRs) are known for their rapid evolution, even at the intraspecific level, yet the rates of evolution differ significantly across various NLR classes. Within the NRC (NLR Required for Cell Death) network, NLRs operate in complex sensor-helper configurations to confer immunity against a diverse array of pathogens, particularly in Asterids. While helper NLRs are typically conserved and evolve slowly, sensor NLRs tend to evolve more rapidly. However, the functional connections between slow and fast-evolving NLRs remain poorly understood, notably in important crop species. We conducted a comparative analysis of NLRs across 40 Solanales and 29 Asterales genomes to explore NRC network expansion and diversification within the less-studied Asterales order. Our findings reveal that the NRC network has expanded less in Asterales compared to Solanales. We functionally validated a minimal Asterales NRC network with 2 helpers and 9 sensors in common lettuce (Lactuca sativa). Through selection and diversification analysis and structural modeling of NRC helper and sensor subclades in the Lactuca genus, we found varying evolutionary diversification rates between NRC helpers and sensors. We found a correlation between sensor diversification rates and helper dependency, with sensors reliant on a phylogenetically conserved helpers experiencing limited diversification pressure. Our results highlight the lineage- and function-specific evolution of the NRC network, offering insights into the evolutionary pressures shaping plant immune receptor networks.

plant biology↗

bioRxiv2024

Can AI modelling of protein structures distinguish between sensor and helper NLR immune receptors?

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 configurations. Furthermore, funnel-shaped structures--essential for activating immune responses--were reliably predicted in helpers but not in sensors. Applying this method to uncharacterized NLR pairs from rice, we found that AlphaFold 3 can differentiate between putative sensors and helpers even when both proteins lack non-canonical domain annotations. These findings suggest that AlphaFold 3 offers a new approach to categorize NLRs and enhances our understanding of the functional configurations in plant immune systems, even in the absence of non-canonical domain annotations.

plant biology↗

bioRxiv2024

Integrated hepatic ferroptosis gene signature dictates pathogenic features of ferroptosis

Background & AimsFerroptosis, a distinctive form of cell death induced by iron-dependent lipid peroxidation, is implicated in various biological processes, including liver diseases. Establishing an iron overload-induced ferroptosis model and identifying hepatic gene signatures associated with ferroptosis are crucial for understanding its role in liver pathogenesis. MethodsF-box and leucine-rich repeat protein 5 (FBXL5) is a substrate-recognition component of the SCF E3 ligase complex that restricts intracellular iron levels. In this study, we used liver-specific Fbxl5-null mice to establish an iron overload-induced ferroptosis model. Transcriptome analysis identified genes involved in hepatic ferroptosis. Integrating these gene signatures with another ferroptosis model enabled the assessment of ferroptosis-related pathology in murine liver injury models and in 174 patients undergoing liver resection surgery. ResultsIron overload induced severe liver damage in liver-specific Fbxl5-null mice, characterized by elevated liver enzymes, histopathological changes, and lipid peroxidation. Transcriptome analysis revealed a distinct set of genes associated with hepatic ferroptosis response. Generating a gene signature for evaluating ferroptosis enhanced the understanding of ferroptosis-related pathologies in liver diseases. Iron overload exacerbated liver damage in murine ischemia-reperfusion injury models via ferroptosis induction. In human patients, elevated serum iron levels correlated with sustained post-operative liver damage, indicating heightened susceptibility to ferroptosis. ConclusionHere, a murine model of iron overload-induced hepatic ferroptosis was established, and a gene signature indicative of hepatic ferroptosis response in both mice and humans was identified. These findings underscore the role of ferroptosis in liver injury progression and suggest potential therapeutic targets for liver disease intervention. HIGHLIGHTSO_LILiver-specific Fbxl5 knockout mice provide an iron-induced ferroptotic injury model C_LIO_LIIntegrated gene signature of iron- and acetaminophen-induced liver injury dictates ferroptosis C_LIO_LIIron overload aggravates hepatic ischemia-reperfusion injury in mice C_LIO_LIPatients with high iron levels show delayed post-operative liver damage recovery C_LI IMPACT AND IMPLICATIONSOur study elucidated the critical role of iron in liver disease pathogenesis and ischemia-reperfusion injury (IRI). By establishing a murine model of iron overload-induced ferroptosis, we confirmed that iron overload exacerbated hepatic IRI, underscoring the importance of ferroptosis in liver damage. Additionally, the development of an integrated gene signature for hepatic ferroptosis response provides a valuable tool for evaluating ferroptosis in liver diseases. Via analysis of patient data, we also highlighted the clinical relevance of ferroptosis in post-operative liver damage, offering insights into potential therapeutic strategies targeting iron and ferroptosis to improve outcomes in patients with liver diseases.

molecular biology↗

bioRxiv2024

Helper NLR immune protein NRC3 evolved to evade inhibition by a cyst nematode virulence effector

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 species are sensitive to suppression by SS15 and tested hypotheses about adaptive evolution of the binding interface between the SS15 inhibitor and NRC proteins. Whereas all tested orthologs of NRC2 were inhibited by SS15, some natural variants of NRC1 and NRC3 are insensitive to SS15 suppression. Ancestral sequence reconstruction combined with functional assays revealed that NRC3 transitioned from an ancestral suppressed form to an insensitive one over 19 million years ago. Our analyses revealed the evolutionary trajectory of coevolution between a parasite inhibitor and its NLR immune receptor target, identifying key evolutionary transitions in helper NLRs that counteract this inhibition. This work reveals a distinct type of gene-for-gene interaction between parasite or pathogen immunosuppressors and host immune receptors that contrasts with the coevolution between AVR effectors and immune receptors.

plant biology↗

bioRxiv2024

Impact of rice GENERAL REGULATORY FACTOR14h (GF14h) on low-temperature seed germination and its application to breeding

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 REGULATORY FACTOR14h (GF14h) gene, which is expressed during seed germination. The Arroz da Terra GF14h allele encodes functional GF14h, whereas Japanese rice variety Hitomebore harbors a 4-bp deletion in the coding region. Knocking out functional GF14h in a near-isogenic line (NIL) carrying the Arroz da Terra allele decreased LTG, whereas overexpressing functional GF14h in Hitomebore increased LTG, indicating that GF14h is the causal gene behind qLTG11. Analysis of numerous Japanese rice accessions revealed that the functional GF14h allele was lost from popular varieties during modern breeding. We generated a NIL in the Hitomebore background carrying a 172-kb genomic fragment from Arroz da Terra including GF14h. The NIL showed superior LTG compared to Hitomebore, with otherwise comparable agronomic traits. The functional GF14h allele from Arroz da Terra represents a valuable resource for direct seeding in cold regions. Author SummaryRice serves as a fundamental crop sustaining over half of the global population. With the rapid growth of the worlds population, it will become increasingly important to improve rice productivity. On the other hand, the aging of rice farmers in Japan has resulted in a constant labor shortage. To address this, direct seeding, in which seeds are sown directly in rice fields without going through the most labor-intensive part of the rice cultivation process, i.e., seedling production and transplanting, has been recommended. However, prevalent elite rice varieties are known to be unsuitable for direct seeding due to their poor seed germination ability under low-temperature conditions. In this study, we show for the first time that GF14h gene from the Portuguese variety Arroz da Terra improves seed germination at low temperatures (LTG). In addition, a novel cross-bred line was generated by introducing the GF14h-containing genomic segment from Arroz da Terra into Hitomebore, a widely cultivated variety in northern Japan. This line is expected to be used as a pre-breeding material to enhance LTG. This study will provide a genetic basis for LTG and contribute to basic and applied research progress.

plant biology↗

bioRxiv2024

Multiple horizontal mini-chromosome transfers drive genome evolution of clonal blast fungus lineages

Crop disease pandemics are often driven by clonal lineages of plant pathogens that reproduce asexually. How these clonal pathogens continuously adapt to their hosts despite harboring limited genetic variation, and in absence of sexual recombination remains elusive. Here, we reveal multiple instances of horizontal chromosome transfer within pandemic clonal lineages of the blast fungus Magnaporthe (Syn. Pyricularia) oryzae. We identified a horizontally transferred 1.2Mb supernumerary mini-chromosome which is remarkably conserved between M. oryzae isolates from both the rice blast fungus lineage and the lineage infecting Indian goosegrass (Eleusine indica), a wild grass that often grows in the proximity of cultivated cereal crops. Furthermore, we show that this mini-chromosome was horizontally acquired by clonal rice blast isolates through at least nine distinct transfer events over the past three centuries. These findings establish horizontal mini-chromosome transfer as a mechanism facilitating genetic exchange among different host-associated blast fungus lineages. We propose that blast fungus populations infecting wild grasses act as genetic reservoirs that drive genome evolution of pandemic clonal lineages that afflict cereal crops.

evolutionary biology↗

bioRxiv2023

Activation of plant immunity through conversion of a helper NLR homodimer into a resistosome

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 accumulates in vivo as a homodimer that converts into a higher order oligomer upon activation by its upstream virus disease resistance protein Rx. The Cryo-EM structure of NRC2 in its resting state revealed intermolecular interactions that mediate homodimer formation. These dimerization interfaces have diverged between paralogous NRC proteins to insulate critical network nodes and enable redundant immune pathways. Our results expand the molecular mechanisms of NLR activation pointing to transition from homodimers to higher-order oligomeric resistosomes.

plant biology↗

bioRxiv2023

Functional divergence shaped the network architecture of plant immune receptors

In solanaceous plants, several sensor NLRs and their helper NLRs, known as NRC, form a complex network to confer immunity against pathogens. While the sensor NLRs and downstream NRC helpers display diverse genetic compatibility, the evolution and molecular basis of the complex network structure remained elusive. Here we demonstrated that functional divergence of NRC3 variants has shaped the genetic architecture of the NLR network. Natural NRC3 variants form three allelic groups displaying distinct compatibilities with sensor NLRs. Ancestral sequence reconstruction and analyses of natural and chimeric variants identified six key amino acids involved in sensor-helper compatibility, with two residues critical for subfunctionalization. Co-functioning Rpi-blb2 and NRC3 variants showed stronger transient interactions upon effector detection, with NRC3 membrane-associated complexes forming subsequently. Our findings reveal how mutations in helper NLRs, particularly NRC3, have driven the evolution of their transient interactions with sensor NLRs, leading to subfunctionalization and contributing significantly to the complexity of the NRC network in plant immunity. TeaserHelper NLR subfunctionalization alters transient interactions with sensor NLRs, enhancing plant immune system complexity.

plant biology↗

bioRxiv2023

Histopathology-assisted proteogenomics provides foundations for stratification of melanoma metastases

Here we describe the histopathology-driven proteogenomic landscape of 142 treatment-naive metastatic melanoma samples. We identified five proteomic subtypes that integrate the immune and stroma microenvironment components, and associate with clinical and histopathological parameters, providing foundations for an in-depth molecular classification of melanoma. Our study shows that BRAF V600 mutated melanomas display heterogeneous biology, where the presence of an oncogene-induced senescence-like phenotype improves patient survival. Therefore, we propose a mortality-risk-based stratification, which may contribute to a more personalized approach to patient treatment. We also found a strong association between tumor microenvironment composition, disease progression, and patient outcome supported by single-cell omic signatures that point to straightforward histopathological connective tissue-to-tumor ratio assessment for better informed medical decisions. A melanoma-associated signature of single amino acid variants (SAAV) responsible for remodeling the extracellular matrix was uncovered together with SAAV-derived neoantigen candidates as targets of anti-tumor immune responses. Overall, this study offers comprehensive stratifications of melanoma metastases that may help develop tailored strategies for diagnosing and treating the disease.

cancer biology↗

bioRxiv2022

Proteogenomic Characterization Reveals Therapeutic Opportunities Related to Mitochondrial Function in Melanoma

The dynamics of more than 1900 mitochondrial proteins was explored through quantitative proteomics in 151 melanoma-related tissue samples of both surgical and autopsy origin. Dysregulation of mitochondrial pathways in primary tumors, metastases, and peritumoral tissues was correlated with age and survival of patients, as well as with tumor cell proliferation and the BRAF mutation status of the tumors. The outlined proteomic landscape confirmed the central role of a pathologically upregulated mitochondrial translation machinery and oxidative phosphorylation (OXPHOS) in the development, proliferation, and progression of melanomas. Our results from different melanoma cell lines confirmed our findings and we could document that treatments with selected OXPHOS inhibitors and antibiotics successfully impaired tumor cell proliferation. In addition, we provided proteomic evidence on the mechanism-of-action of the different treatments. These observations could contribute to the development of therapeutic approaches targeting the mitochondrial pathology in melanoma. TOC figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/513481v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@11f21e2org.highwire.dtl.DTLVardef@e98c64org.highwire.dtl.DTLVardef@100145forg.highwire.dtl.DTLVardef@399284_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIMitochondrial proteome landscape outlined in 151 melanoma-related samples C_LIO_LIMitochondrial Translation and OXPHOS impact disease severity and survival C_LIO_LIBRAF V600E mutation correlates with upregulation of mitochondrial energy production C_LIO_LITargeting the mitochondrial OXPHOS and ribosomes impairs tumor cell proliferation C_LIO_LITherapeutic opportunities complementary to the standard of care are proposed C_LI In briefMitochondrial proteome profiling of melanomas reveals dysregulation in major metabolic pathways, suggesting a central role of the mitochondria within the development and progression of melanoma. Targeting mitochondrial pathways has the potential to impact the course of the disease, which provides opportunities for complementary drug interventions.

cancer biology↗

bioRxiv2022

Tangled gene-for-gene interactions mediate co-evolution of the rice NLR immune receptor Pik and blast fungus effector proteins

Studies focused solely on single organisms can fail to identify the networks underlying host-pathogen gene-for-gene interactions. Here, we integrate genetic analyses of rice (Oryza sativa, host) and rice blast fungus (Magnaporthe oryzae, pathogen) and uncover a new pathogen recognition specificity of the rice nucleotide-binding domain and leucine-rich repeat protein (NLR) immune receptor Pik, which mediates resistance to M. oryzae expressing the avirulence effector gene AVR-Pik. Rice Piks-1, encoded by an allele of Pik-1, recognizes a previously unidentified effector encoded by the M. oryzae avirulence gene AVR-Mgk1, which is found on a mini-chromosome. AVR-Mgk1 has no sequence similarity to known AVR-Pik effectors, and is prone to deletion from the mini-chromosome mediated by repeated Inago2 retrotransposon sequences. AVR-Mgk1 is detected by Piks-1 and by other Pik-1 alleles known to recognize AVR-Pik effectors; recognition is mediated by AVR-Mgk1 binding to the integrated heavy metal-associated (HMA) domain of Piks-1 and other Pik-1 alleles. Our findings highlight how complex gene-for-gene interaction networks can be disentangled by applying forward genetics approaches simultaneously to the host and pathogen. We demonstrate dynamic co-evolution between an NLR integrated domain and multiple families of effector proteins.

plant biology↗

bioRxiv2022

Whole genome sequencing of a wild yam species Dioscorea tokoro reveals a genomic region associated with sex

Dioscorea tokoro is a wild species distributed in East Asia including Japan. Typical of the genus Dioscorea, D. tokoro is dioecious with male and female flowers borne on separate individuals. To understand its sex determination system and to serve as a model species for population genomics of obligate outcrossing wild species, we set out to determine the whole genome sequence of the species. Here we show 443 Mb genome sequence of D. tokoro distributed over 2,931 contigs that were anchored on 10 linkage groups. Linkage analysis of sex in a segregating F1 family revealed a sex determination locus residing on Pseudochromosome 3 with XY-type male heterogametic sex determination system.

plant biology↗