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Bacillus subtilis is central to Asian fermented soybean foods, including Japanese natto. To explore the genomic boundaries of B. subtilis var. natto , we conducted a comparative pangenome analysis of 42 strains, including the core natto clade (n = 26) and its closest relatives. Our analysis revealed a striking evolutionary paradox centered on a single strain isolated from Indian bekang. Core-genome phylogenetic analysis places this bekang strain clearly outside the tight natto clade, with a Nepalese kinema strain being its closest systematic neighbor. In stark contrast, quantitative analysis of accessory gene profiles revealed this single bekang strain is the functional nearest neighbor to the natto clade, sharing a highly conserved accessory gene repertoire. This shared profile defines a \"natto-type\" adaptive strategy (the \"broad-sense natto group,\" n = 27), separating it from other related strains. Analysis of this group-specific repertoire revealed an enrichment of transcriptional regulators and metabolic enzymes. This finding provides a compelling case study (n = 1) of polygenic adaptation, suggesting complex evolutionary pathways, such as horizontal gene transfer or selective retention, can drive rapid adaptation across disparate lineages.

Some Pyropia species, such as nori ( P . yezoensis ), are important marine crops. We conducted a phylogenetic analysis of 39 samples of Pyropia species grown in Japan using organellar genome sequences. A comparison of the chloroplast DNA sequences with those from China showed a clear genetic separation between Japanese and Chinese P . yezoensis . Conversely, comparing the mitochondrial DNA sequences did not separate Japanese and Chinese P . yezoensis . Analysis of organellar genomes showed that the genetic diversity of Japanese P . yezoensis used in this study is lower than that of Chinese wild P . yezoensis . To analyze the genetic relationships between samples of Japanese Pyropia , we used whole-genome resequencing to analyze their nuclear genomes. In the offspring resulting from cross-breeding between P . yezoensis and P . tenera , nearly 90% of the genotypes analyzed by mapping were explained by the presence of different chromosomes originating from two different parental species. Although the genetic diversity of Japanese P . yezoensis is low, analysis of nuclear genomes genetically separated each sample. Samples isolated from the sea were often genetically similar to those being farmed. Study of genetic heterogeneity of samples within a single aquaculture strain of P . yezoensis showed that samples were divided into two groups and the samples with frequent abnormal budding formed a single, genetically similar group. The results of this study will be useful for breeding and the conservation of Pyropia species.

Hepatic steatosis is an early stage in the progression of non-alcoholic fatty liver disease (NAFLD) and can lead to the development of non-alcoholic steatohepatitis (NASH), a major cause of liver-related morbidity and mortality. Identification of dietary components that can alleviate hepatic steatosis is crucial for developing effective therapeutic strategies for NAFLD. Recently, we demonstrated the impact of lipids extracted from the marine red alga Susabinori ( Pyropia yezoensis ) in a murine model of type 2-diabete ( db / db ). We found that Susabinori lipids (SNL), abundant in eicosapentaenoic acid (EPA)-containing polar lipids, protected against obesity-induced hepatic steatosis in db / db mice. To understand the specific genes or biological pathways underlying the effects of SNL, we conducted RNA-Seq analysis of the hepatic transcriptome. By performing comparative analysis of differentially expressed genes between normal mice and db / db mice consuming a control diet, as well as SNL-fed db / db mice, we identified the 15 SNL-dependent up-regulated genes that were down-regulated in db / db mice but up-regulated by SNL feeding. Gene ontology and pathway analysis on these 15 genes demonstrated a significant association with the metabolisms of arachidonic acid (AA) and linoleic acid (LA). Furthermore, we observed alterations in the expression levels of monoacylglycerol lipase ( Magl ) and fatty acid-binding protein 4 ( Fabp4 ) in the SNL-fed db / db mice, both of which are implicated in AA and LA metabolism. Additionally, the livers of SNL-fed db / db mice exhibited reduced levels of AA and LA, but a high accumulation of EPA. In conclusion, the SNL diet might affect the metabolisms of AA and LA, which contribute to the improvement of hepatic steatosis. Our findings provide insights into the molecular mechanisms underlying the beneficial effects of SNL.

Loquat ( Eriobotrya japonica ) have originated in southeastern China and spread as a cultivated plant worldwide. Many of the loquat genetic resources collected internationally are of unknown origin, and their genetic background requires clarification. This study analyzed the genetic diversity of 95 accessions by using Rad-Seq SNP markers. Data analysis broadly classified loquat into three groups: (1) Japanese and Chinese cultivars and some Japanese strains (wild plants that are not used for commercial cultivation), (2) Vietnamese, Israeli, Greek, USA, and Mexican cultivars and strains, and (3) other Japanese strains. Group 2 is cultivated mostly outside of East Asia and was clearly distinct from the other groups, indicating that varieties of unknown origin with genetic backgrounds different from those of Japanese and Chinese cultivars may have been introduced to Mediterranean countries and North America. Because Japanese and Chinese cultivars belong to group 1, the current Japanese cultivars are derived from genetic resources brought from China. Some of group 1 may have been introduced to Japan before excellent varieties were developed in China, while group 3 may have been indigenous to Japan that have not been introduced by human activities, or may have been brought to Japan by human activities from China.

The razor clam Sinonovacula constricta is a commercially important bivalve in Japan. The current distribution of this species in Japan is limited to Ariake Bay, where the fishery stock is declining. It is necessary to understand the genetic population structure of this species in order to restore the fishery stock while preserving the genetic diversity of the clam. Here, we report for the first time the genetic population structure of S. constricta in Ariake Bay, Japan. Paired-end restriction site-associated DNA sequencing (RAD-Seq) analyzed samples of S. constricta collected from seven mudflats located along Ariake Bay. Two different genetic populations exist in Ariake Bay, one inhabiting wild habitats and the other inhabiting the transplanted area of artificial seedlings. Our results suggest that genetic differentiation occurred between these two populations ( F st value = 0.052), and a high level of genetic differentiation is maintained between the two groups. In the future, monitoring the interbreeding status of the two genetically distinct populations and the genetic differentiation within each population is important for conserving the genetic diversity of S. constricta in Japan.

The Japanese pepper (Zanthoxylum piperitum DC.) is an attractive plant that is highly palatable and benefits human health. There are several lineages of pepper plants in Japan. However, the classification of each lineage by analyzing its volatile compounds and studies on the effects of differences in volatile compounds on human flavor perception have not been performed in detail. Herein, we conducted gas chromatography (GC) and GC/mass spectrometry (GC/MS) analysis of volatile compounds and sensory evaluation of flavor by an analytical panel using 10 commercially available dry powdered Japanese pepper products from different regions. GC and GC/MS analysis detected limonene, β-phellandrene, citronellal, and geranyl acetate as the major volatile compounds of Japanese peppers. The composition of volatile compounds showed different characteristics depending on the growing regions, and cluster analysis of composition classified the products into five groups. The sensory evaluation classified the products into four groups, and the results of both classifications were in good agreement. Our results provide an important basis for proposing cooking and utilization methods that take advantage of the unique characteristics of each lineage based on scientific evidence.

Allium macrostemon Bunge, commonly referred to as \"no-biru\" in Japan, is a widespread wild onion species found across the country. Despite being deeply entwined in ancient Japanese culture, it remains an underutilized crop in Japan. Determining the origins of its domestic populations and understanding their genetic composition is crucial to highlighting the plant's historical significance in Japan. This study aims to bridge this knowledge gap by examining the genetic diversity of 47 A. macrostemon samples from various regions in Japan using RAD-Seq. Our analyses distinguished unique population structures, dividing the samples into three distinct groups: A, B, and C. Notably, groups A and B showed clear evidence of bulb propagation, while group C did not. Group C formed four subgroups: C1, C2, C3, and C4. Hybridization between subgroup C1 and either group A, B, or both, resulted in the emergence of subgroups C2, C3, and C4. Thus, groups A, B, and C1 are posited as the ancestral populations. Additionally, our morphological observations indicated distinct differences among these three groups. Our findings also suggest that human migration may have influenced the plant's distribution, hinting at active usage in the past that later waned, causing its current underutilized status.

Cross-breeding between cultivars of Satsuma mandarins is difficult because of the seeds’ polyembryonic characteristics. Even if a seed is obtained by hybridization, the seed contains only one zygotic embryo (hybrid embryo) and many nucellar embryos. Therefore, for efficient cross-breeding, it is necessary to select a zygotic embryo from among the nucellar embryos. To identify the zygotic embryo, we have developed 119 Indel markers that can be clearly detected by simple agarose gel electrophoresis by mining the Indel region from the resequencing analysis of the short reads of Satsuma mandarin against the reference genome of Satsuma mandarin. Additionally, we showed that the genotype determined by these markers can be used as an indicator for the selection of zygotic embryo-derived individuals. In addition, many of the developed Indel markers were found to be used for genotyping Satsuma mandarin as well as other citrus species and relatives. This codominant DNA marker that can be detected by low-cost, simple electrophoresis is expected to be used for the identification of zygotic embryo-derived individuals and for various purposes such as cultivar identification.

Japanese pepper, Zanthoxylum piperitum , is native to Japan and has four well-known lineages (Asakura, Takahara, Budou, and Arima), which are named after their production area or morphology. Restriction-site associated DNA sequencing (RAD-Seq) was used to analyse 93 accessions from various areas, including these four lineages. Single nucleotide variant analysis was used to classify the plants into eight groups: the Asakura and Arima lineages each had two groups, the Takahara and Budou lineages each had one group, and two additional groups were present. In one Asakura group and two Arima groups, the plants were present in agricultural fields and mountains, thus representing the early stage of domestication of the Japanese pepper. The second Asakura lineage group was closely related to plants present in various areas, and this represents the second stage of domestication of this plant because, after early domestication, genetically related lineages with desirable traits spread to the periphery. These results demonstrate that domestication of Japanese pepper is ongoing. In addition, this study shows that spineless plants are polyphyletic, despite the spineless lineage being considered a subspecies of Japanese pepper.

The chloroplast (cp) genome is a widely used tool for exploring plant evolutionary relationships, yet its effectiveness in fully resolving these relationships remains uncertain. Integrating cp genome data with nuclear DNA information offers a more comprehensive view but often requires separate datasets. In response, we employed the same raw read sequencing data to construct cp genome-based trees and nuclear DNA phylogenetic trees using Read2Tree, a cost-efficient method for extracting conserved nuclear gene sequences from raw read data, focusing on the Aurantioideae subfamily, which includes Citrus and its relatives. The resulting nuclear DNA trees were consistent with existing nuclear evolutionary relationships derived from high-throughput sequencing, but diverged from cp genome-based trees. To elucidate the underlying complex evolutionary processes causing these discordances, we implemented an integrative workflow that utilized multiple alignments of each gene generated by Read2Tree, in conjunction with other phylogenomic methods. Our analysis revealed that incomplete lineage sorting predominantly drives these discordances, while introgression and ancient introgression also contribute to topological discrepancies within certain clades. This study underscores the cost-effectiveness of using the same raw sequencing data for both cp and nuclear DNA analyses in understanding plant evolutionary relationships.