Shusei Sato

• Tohoku University

Plant trait databases play a crucial role in understanding ecological and evolutionary processes yet remain insufficient due to geographical and data availability limitations. To address this limitation, we developed a novel large-scale text extraction approach using a large language model (LLM) to transform descriptions of Floras into structured t...

Bradyrhizobium sp. strain SUTN9-2 demonstrates cell enlargement, increased DNA content, and efficient nitrogen fixation in response to rice (Oryza sativa) extract. This response is attributed to the interaction between the plant’s cationic antimicrobial peptides (CAMPs) and the Bradyrhizobium BacA-like transporter (BclA), similar to bacteroid in le...

Symbiotic nitrogen fixation is a highly coordinated process involving legume plants and nitrogen-fixing bacteria known as rhizobia. In this study, we investigated a novel Fix⁻ mutant of the model legume Lotus japonicus that develops root nodules with endosymbiotic rhizobia but fails in nitrogen fixation. Map-based cloning identified the causal gene...

Cannabis sativa L. has a variety of uses, including fiber production, food, oil, and medicine. In response to environmental concerns regarding chemical fertilizers, Bacillus velezensis S141 was examined as a plant-growth-promoting bacterium (PGPB) for cannabis. This study evaluated the effects of S141 on cannabis growth and utilized transcriptomic...

The symbiotic relationship between legumes and rhizobia is known to be influenced by specific rhizobial type III effectors (T3Es) in certain cases. In this study, we present evidence that the symbiosis between Vigna radiata and Bradyrhizobium elkanii USDA61 is controlled by a T3E called NopP2, and this interaction is highly dependent on the genetic...

The genetic makeup of natural plant populations often allows them to persist for many years without succumbing to disease. Transferring such properties to crops could increase resilience and reduce reliance on chemical pesticides . However, the population genomics of plant-microbiome interactions remain poorly understood. Here, we use Lotus japonic...

Although microbial inoculation may be effective for sustainable crop production, detrimental aspects have been argued because of the potential of inoculated microorganisms to behave as invaders and negatively affect the microbial ecosystem. We herein compared the impact of rhizobial inoculation on the soil bacterial community with that of agricultu...

Mung bean (Vigna radiata L.), a vital legume in Asia with significant nutritional benefits, is highly susceptible to Cercospora leaf spot (CLS) caused by Cercospora canescens, leading to significant yield losses. As an alternative to chemical fungicides, bio-priming with rhizobacteria can enhance plant resistance. This study explores the potential...

The symbiotic interaction between leguminous and Bradyrhizobium sp. SUTN9-2 mainly relies on the nodulation process through Nod factors (NFs), while the type IV secretion system (T4SS) acts as an alternative pathway in this symbiosis. Two copies of T4SS (T4SS1 and T4SS2) are located on the chromosome of SUTN9-2. ΔT4SS1 reduces both nodule number an...

The biological interactions between plants and their root microbiomes are essential for plant growth, and even though plant genotype (G), soil microbiome (M), and growth conditions (environment; E) are the core factors shaping root microbiome, their relationships remain unclear. In this study, we investigated the effects of G, M, and E and their in...

N2O is an important greenhouse gas influencing global warming, and agricultural land is the predominant (anthropogenic) source of N2O emissions. Here, we report the high N2O-reducing activity of Bradyrhizobium ottawaense, suggesting the potential for efficiently mitigating N2O emission from agricultural lands. Among the 15 B. ottawaense isolates ex...

N 2 O is the major greenhouse gases influencing global warming, and agricultural land is the predominant (anthropogenic) source of N 2 O emissions. Here, we report the high N 2 O-reducing activity of Bradyrhizobium ottawaense , suggesting the potential for efficiently mitigating N 2 O emission from agricultural lands. Among the 15 B. ottawaense iso...

Grafting is widely used as a method to increase stress tolerance in good fruiting lines of Solanaceae plants. However, little is known about how grafting, affects epigenetic modifications and leads to stress tolerance, especially within the same line. Here, we studied the effects of self-grafting in tomato plants on histone and DNA modifications an...

Many plant species have succeeded in colonizing a wide range of diverse climates through local adaptation, but the underlying molecular genetics remain obscure. We previously found that winter survival was a direct target of selection during colonization of Japan by the perennial legume Lotus japonicus and identified associated candidate genes. Her...

Onions are one of the most widely cultivated vegetables worldwide; however, the development and utilization of molecular markers have been limited because of the large genome of this plant. We present a genome-wide marker design workflow for onions and its application in a high-throughput genotyping method based on target amplicon sequencing. The e...

As soybean cultivars are adapted to a relatively narrow range of latitude, the effects of climate changes are estimated to be severe. To address this issue, it is important to improve our understanding of the effects of climate change by applying the simulation model including both genetic and environmental factors with their interactions (GxE). To...

Grafting is a method used in agriculture to improve crop production and tolerance to biotic and abiotic stress. This technique is widely used in tomato, Solanum lycopersicum L.; however, the effects of grafting on changes in gene expression associated with stress tolerance in shoot apical meristem cells are still under-discovered. To clarify the ef...

Transposable elements (TEs) constitute a large proportion of genomes of multicellular eukaryotes including flowering plants. TEs are normally maintained in a silenced state and their transpositions rarely occur. Hybridization between distant species has been regarded as a “shock” that stimulates genome re‐organization, including TE mobilization. Ho...

Methane-oxidizing bacteria (methanotrophs) play an ecological role in methane and nitrogen fluxes because they are capable of nitrogen fixation and methane oxidation, as indicated by genomic and cultivation-dependent studies. However, the chemical relationships between methanotrophy and diazotrophy and aerobic and anaerobic reactions, respectively,...

Many plant species have succeeded in colonizing a wide range of diverse climates through local adaptation, but the underlying molecular genetics remain obscure. We previously found that winter survival was a direct target of selection during colonization of Japan by the perennial legume Lotus japonicus and identified associated candidate genes. Her...

Biological interactions between plants and their root microbiomes are pivotal for plant growth. Even though the plant genotype [G], soil microbiome [C], and growth conditions (environment) [E] are core factors shaping the root microbiome, their relationships remain unclear. We disentangled the effects of G, C, E, and their interactions on the Lotus...

In legume-rhizobia symbiosis, partner recognition and the initiation of symbiosis processes require the mutual exchange of chemical signals. Chemicals, generally (iso)flavonoids, in the root exudates of the host plant induce the expression of nod genes in rhizobia, and, thus, are called nod gene inducers. The expression of nod genes leads to the pr...

Raphanus has undergone a lengthy evolutionary process and has rich diversity. However, the inter- and intraspecific phylogenetic relationships and genetic diversity of this genus are not well understood. Through SSR-sequencing and multi-analysis of 939 wild, semi-wild and cultivated accessions, we discovered that the European wild radish (EWR) popu...

Increased plant phosphorus uptake and growth as a result of inoculation with arbuscular mycorrhizal (AM) fungi is observed less often under field conditions than in pot experiments. Interaction between introduced and indigenous AM fungi is one of the reasons for ineffectiveness of inoculation in the field. We aimed to distinguish the effect of intr...

Onion is an important vegetable crop with an estimated genome size of 16 Gb. We describe the de novo assembly and ab initio annotation of the genome of a doubled haploid onion line DHCU066619, which resulted in a final assembly of 14.9 Gb with an N50 of 464 Kb. Of this, 2.4 Gb was ordered into eight pseudomolecules using four genetic linkage maps....

Symbiosis between organisms influences their evolution via adaptive changes in genome architectures. Immunity of soybean carrying the Rj2 allele is triggered by NopP (type III secretion system [T3SS]-dependent effector), encoded by symbiosis island A (SymA) in B. diazoefficiens USDA122. This immunity was overcome by many mutants with large SymA del...

Background Genomic information for Allium cepa L. is limited as it is heterozygous and its genome is very large. To elucidate potential SNP markers obtained by NGS, we used a complete set of A. fistulosum L.- A. cepa monosomic addition lines (MALs) and doubled haploids (DHs). These were the parental lines of an A. cepa mapping population for transc...

Legume plants form a root-nodule symbiosis with rhizobia. This symbiosis establishment generally relies on rhizobium-produced Nod factors (NFs) and their perception by leguminous receptors (NFRs) that trigger nodulation. However, certain rhizobia hijack leguminous nodulation signalling via their type III secretion system, which functions in pathoge...

Lotus japonicus is a model legume, that accumulates 8-hydroxyflavonol derivatives such as gossypetin (8-hydroxyquercetin) 3-O-glycoside, which confer the yellow color to its petals. An enzyme, flavonoid 8-hydroxylase (LjF8H), is assumed to be involved in the biosynthesis, but the specific gene is yet to be identified. The LjF8H cDNA was isolated as...

Background Genomic information for Allium cepa L. is limited as it is heterozygous and its genome is very large. To elucidate potential SNP markers obtained by NGS, we used a complete set of A. fistulosum L.-A. cepa monosomic addition lines (MALs) and doubled haploids (DHs). These were the parental lines of an A. cepa mapping population for transcr...

Organogenesis of legume root nodules begins with the nodulation factor‐dependent stimulation of compatible root cells to initiate divisions, signifying an early nodule primordium formation event. This is followed by cellular differentiation, including cell expansion and vascular bundle formation, and we previously showed that Lotus japonicus NF‐YA1...

Progress in conventional breeding methods for taro (Colocasia esculenta L. Schott) via crossing has been limited, and suitable genetic materials for the development of new cultivars are scarce as most commercial taro cultivars are either non-flowering or rarely flowering triploids. In an attempt to advance taro breeding, we performed mutational bre...

Aim: Lotus japonicus is a herbaceous perennial legume that has been used extensively as a genetically tractable model system for deciphering the molecular genetics of symbiotic nitrogen fixation. Our aim is to improve the L. japonicus reference genome sequence, which has so far been based on Sanger and Illumina sequencing reads from the L. japonic...

Aim Lotus japonicus is a herbaceous perennial legume that has been used extensively as a genetically tractable model system for deciphering the molecular genetics of symbiotic nitrogen fixation. Our aim is to improve the L. japonicus reference genome sequence, which has so far been based on Sanger and Illumina sequencing reads from the L. japonicus...

Root hair cells form the primary interface of plants with the soil environment, playing key roles in nutrient uptake and plant defense. In addition, they are typically the first cells infected by nitrogen-fixing soil bacteria during the root nodule symbiosis. Here we report a role for the Cellulose Synthase-Like D1 ( CSLD1 ) gene in root hair devel...

Bradyrhizobium elkanii, a rhizobium with a relatively wide host range, possesses a functional type III secretion system (T3SS) that is involved in symbiotic incompatibility against Rj4-genotype soybean (Glycine max) and some accessions of mung bean (Vigna radiata). To expand our knowledge on the T3SS-mediated partner selection mechanism in the symb...

Salinization of the soils is one of the most prominent problems threatening global food security. Root microbiome engineering using biofertilizers provides a sustainable way to increase agricultural productivity. Halophytes, which are extremely salt-tolerant plants, can tolerate up to 1300 mM NaCl. Members of the halophytic root microbiome now prov...

Colonization of new habitats is expected to require genetic adaptations to overcome environmental challenges. Here, we use full genome re-sequencing and extensive common garden experiments to investigate demographic and selective processes associated with colonization of Japan by Lotus japonicus over the past ~20,000 years. Based on patterns of gen...

Leguminous plants establish endosymbiotic associations with rhizobia and form root nodules in which the rhizobia fix atmospheric nitrogen. The host plant and intracellular rhizobia strictly control this symbiotic nitrogen fixation. We recently reported a Lotus japonicus Fix ⁻ mutant, apn1 ( aspartic peptidase nodule-induced 1 ), that impairs symbio...

Cultivated soybean (Glycine max) carrying the Rj2 allele restricts nodulation with specific Bradyrhizobium strains via host immunity, mediated by rhizobial type III secretory protein NopP and the host resistance protein Rj2. Here we found that the single isoleucine residue I490 in Rj2 is required for induction of symbiotic incompatibility. Furtherm...

Germplasm enhancement and breeding is difficult for garlic (Allium sativum L.) as it can only be vegetatively propagated. Hence, mutation induction is still the most effective way to create new varieties. Calli from two Chinese commercial garlic varieties, Zhoumou (ZM) and Yongnian (YN), were treated with different dosages (1, 3, 5 and 7 Gy) of gam...

Germplasm enhancement and breeding is difficult for garlic (Allium sativum L.) as it can only be vegetatively propagated. Hence, mutation induction is still the most effective way to create new varieties. Calli from two Chinese commercial garlic varieties, Zhoumou (ZM) and Yongnian (YN), were treated with different dosages (1, 3, 5 and 7 Gy) of gam...

The southern root-knot nematode, Meloidogyne incognita, is a pest that decreases yield and the quality of sweetpotato [Ipomoea batatas (L.) Lam.]. There is a demand to produce resistant cultivars and develop DNA markers to select this trait. However, sweetpotato is hexaploid, highly heterozygous, and has an enormous genome (∼3 Gb), which makes gene...

Arbuscular mycorrhizal fungi (AMF) are a group of soil microorganisms that establish symbioses with most land plant species. “Root trap culture” generally has been used for isolating a single regenerated spore in order to establish a monospecific, native AMF line. Roots may be co-colonized with multiple AMF species; however, only a small portion of...

Nucleoporins are components of the nuclear pore complexes, channels that regulate the transport of macromolecules between the nucleus and cytoplasm. The nucleoporin GLE1 (GLFG lethal1) functions in the export of messenger RNAs containing poly(A) tails from the nucleus into the cytoplasm. Here we investigated a mutant of the model legume Lotus japon...

Here, we report a comprehensive analysis of the widely targeted metabolome and transcriptome profiles of Allium fistulosum L. (FF) with the single extra chromosome of shallot [A. cepa L. Aggregatum group (AA)] to clarify the novel gene functions in flavonoid biosynthesis. An exhaustive metabolome analysis was performed using the selected reaction m...

Arbuscular mycorrhizal (AM) fungi are important members of the root microbiome and may be used as biofertilizers for sustainable agriculture. To elucidate the impact of AM fungal inoculation on indigenous root microbial communities, we used high-throughput sequencing and an analytical pipeline providing fixed operational taxonomic units (OTUs) as a...

Colonization of new habitats is expected to require genetic adaptations to overcome environmental challenges. Here we use full genome re-sequencing and extensive common garden experiments to investigate demographic and selective processes associated with the recent colonization of Japan by Lotus japonicus. We carefully track the colonization proces...

Background: Cucumbers (Cucumis sativus) are known for their plasticity in sex expression. DNA methylation status determines gene activity but is susceptible to environmental condition changes. Thus, DNA methylation-based epigenetic regulation may at least partially account for the instability of cucumber sex expression. Do temperature and photoper...

The cucumber (Cucumis sativus) is characterized by its diversity and seasonal plasticity in sexual type. A long day length condition significantly decreased the cucumber female flower ratio by 17.7%-52.9%, and the effect of photoperiod treatment is more significant under low temperature than under high temperature. Transcriptome analysis indicates...

Morphogens provide positional information and their concentration is key to the organized development of multicellular organisms. Nitrogen-fixing root nodules are unique organs induced by Nod factor-producing bacteria. Localized production of Nod factors establishes a developmental field within the root where plant cells are reprogrammed to form in...

Structural genomic resources of Allium plants have been less developed because Allium species have a relatively large genome size. In this background, there have been few reports of construction of BAC libraries of Allium species. Nevertheless, the BAC clones of Allium cepa (bulb onion) developed as a partial library can be used for not only molecu...

Genotype-specific incompatibility in legume-rhizobium symbiosis has been suggested to be controlled by effector-triggered immunity underlying pathogenic host-bacteria interactions. However, the rhizobial determinant interacting with the host resistance protein (e.g., Rj2) and the molecular mechanism of symbiotic incompatibility remain unclear. Usin...

A quarter of a century has passed since Lotus japonicus was proposed as a model legume because of its suitability for molecular genetic studies. Since then, a comprehensive set of genetic resources and tools has been developed, including recombinant inbred lines, a collection of wild accessions, published mutant lines, a large collection of mutant...

Inoculation with arbuscular mycorrhizal fungi (AMF) can increase the growth of host plants, especially under condition of low phosphate (P) availability. Although this effect is shown relatively easily in simplified systems such as pot experiments, it is often hard to show in the field because of complicating factors such as competition with indige...

We report here the complete sequences of the main genome (4.8 Mb) and seven plasmids of the semifilamentous, nonheterocystous cyanobacterium Pseudanabaena sp. ABRG5-3, a strain isolated from a pond in Japan. These data are expected to enhance our understanding of the Pseudanabaena subclade near the root of cyanobacterial diversity.

[This corrects the article DOI: 10.1371/journal.pone.0181784.].

Jatropha curcas L. has attracted worldwide recognitions in recent years, because its seed oil is suitable to substitute for fossil fuels, and it can grow in semi-arid lands. It has been traditionally planted in tropical and subtropical regions, but recent mass cultivation as a biofuel crop is still severally restricted by its low seed production, s...

The establishment of a root nodule symbiosis between a leguminous plant and a rhizobium requires complex molecular interactions between the two partners. Compatible interactions lead to the formation of nitrogen-fixing nodules, however, some legumes exhibit incompatibility with specific rhizobial strains and restrict nodulation by the strains. Brad...

Glucosinolates (GSLs) and their hydrolysis products present in Brassicales play important roles in plants against herbivores and pathogens as well as in the protection of human health. To elucidate the molecular mechanisms underlying the formation of species-specific GSLs and their hydrolysed products in Raphanus sativus L., we performed a comparat...

The nitrogen-fixing symbiosis of legumes and Rhizobium bacteria is established by complex interactions between the two symbiotic partners. Legume Fix– mutants form apparently normal nodules with endosymbiotic rhizobia but fail to induce rhizobial nitrogen fixation. These mutants are useful for identifying the legume genes involved in the interactio...

The draft genome sequence of a wild rose (Rosa multiflora Thunb.) was determined using Illumina MiSeq and HiSeq platforms. The total length of the scaffolds was 739,637,845 bp, consisting of 83,189 scaffolds, which was close to the 711 Mbp length estimated by k-mer analysis. N50 length of the scaffolds was 90,830 bp, and extent of the longest was 1...

Jatropha curcas L. (Jatropha), a shrub species of the family Euphorbiaceae, has been recognized as a promising biofuel plant for reducing greenhouse gas emissions. However, recent attempts at commercial cultivation in Africa and Asia have failed because of low productivity. It is important to elucidate genetic diversity and relationship in worldwid...

Jatropha curcas L. (Jatropha), a shrub species of the family Euphorbiaceae, has been recognized as a promising biofuel plant for reducing greenhouse gas emissions. However, recent attempts at commercial cultivation in Africa and Asia have failed because of low productivity. It is important to elucidate genetic diversity and relationship in worldwid...

The genus Allium is a rich source of steroidal saponins, and its medicinal properties have been attributed to these bioactive compounds. The saponin compounds with diverse structures play a pivotal role in Allium’s defense mechanism. Despite numerous studies on the occurrence and chemical structure of steroidal saponins, their biosynthetic pathway...

Total number of up- and down-regulated genes in the root, bulb and leaf of Allium cepa Aggregatum group (AA) and Monosomic Addition Lines (MALs = FF1A, FF2A, FF3A, FF4A, FF5A, FF6A, FF7A and FF8A) in compare to A. fistulosum (FF) as control. (PDF)

AM scatter plots of the root differential gene expression of Allium cepa Aggregatum group (AA) and monosomic addition lines (MALs = FF1A, FF2A, FF3A, FF4A, FF5A, FF6A, FF7A, and FF8A) in comparison with A. fistulosum (FF) as control. Log2 fold change of AA/FF and MALs/FF on the y-axis and average count of RPKM (Reads Per Kilobase of exon per Millio...

Venn diagram showing the distribution of common up-regulated and down-regulated genes of Allium cepa Aggregatum group (AA) and monosomic addition lines (MALs = FF1A, FF2A, FF3A, FF4A, FF5A, FF6A, FF7A and FF8A) in the Leaf (A), bulb (B) and root (C). (PDF)

13C NMR spectroscopic data of the aglycone and sugar moieties of the Alliospiroside A isolated from the root of Allium fistulosum with extra chromosome 2A from A. cepa Aggregatum group. (PDF)

AM scatter plots of the leaf differential gene expression of Allium cepa Aggregatum group (AA) and monosomic addition lines (MALs = FF1A, FF2A, FF3A, FF4A, FF5A, FF6A, FF7A, and FF8A) in comparison with A. fistulosum (FF) as control. Log2 fold change of AA/FF and MALs/FF on the y-axis and average count of RPKM (Reads Per Kilobase of exon per Millio...

AM scatter plots of the bulb differential gene expression of Allium cepa Aggregatum group (AA) and monosomic addition lines (MALs = FF1A, FF2A, FF3A, FF4A, FF5A, FF6A, FF7A, and FF8A) in comparison with A. fistulosum (FF) as control. Log2 fold change of AA/FF and MALs/FF on the y-axis and average count of RPKM (Reads Per Kilobase of exon per Millio...

Cucumber (Cucumis sativus L.) is characterized by its diverse and flexible sexual types. Here, we evaluated the effect of low temperature (LT) exposure on cucumber femaleness under short-day conditions. Shoot apices were subjected to whole-genome bisulfate sequencing (WGBS), mRNA-seq, and sRNA-seq. The results showed that temperature had a substant...