Ken Naito

Complete genome sequences of tolaasin-detoxifying Mycetocola spp., M. lacteus MAFF 211326, M. saprophilus MAFF 211324, and M. tolaasinivorans MAFF 211325, were determined. The length of the circular chromosomes of these strains was 3.47, 3.52, and 3.49 Mbp, respectively, and a 28,409-bp plasmid was found in M. lacteus MAFF 211326. Genomic comparisons of mushroom-associated, -pathogenic, and environmental strains of Mycetocola spp. showed that the genomic synteny of chromosomes was largely shared among Mycetocola spp. Furthermore, the previously estimated catalytic triad of tolaasin-degrading factor (Tdf) is conserved among the genomes of strains isolated from mushrooms and non-mushroom substrates. Lipopeptides, including tolaasins, are biologically active and involved in various biological interactions. The antagonistic traits of Mycetocola spp. might not be restricted to tolaasin detoxification; therefore, genome information of Mycetocola spp. will facilitate the mining and identification of enzymes that cleave cyclic lipopeptides acting in various biological interactions observed in agricultural and ecological contexts.

Complete genome sequences of tolaasin-detoxifying Mycetocola spp., M. lacteus MAFF 211326, M. saprophilus MAFF 211324, and M. tolaasinivorans MAFF 211325, were determined. The length of the circular chromosomes of these strains was 3.47, 3.52, and 3.49 Mbp, respectively, and a 28,409-bp plasmid was found in M. lacteus MAFF 211326. Genomic comparisons of mushroom-associated, -pathogenic, and environmental strains of Mycetocola spp. showed that the genomic synteny of chromosomes was largely shared among Mycetocola spp. Furthermore, the previously estimated catalytic triad of tolaasin-degrading factor (Tdf) is conserved among the genomes of strains isolated from mushrooms and non-mushroom substrates. Lipopeptides, including tolaasins, are biologically active and involved in various biological interactions. The antagonistic traits of Mycetocola spp. might not be restricted to tolaasin detoxification; therefore, genome information of Mycetocola spp. will facilitate the mining and identification of enzymes that cleave cyclic lipopeptides acting in various biological interactions observed in agricultural and ecological contexts.

The adzuki bean cultivar ‘Erimo-shozu’ has been grown in Hokkaido for around 40 years for its high yield and tolerance to cold. It is susceptible to brown stem rot (BSR), a soilborne disease that reduces yields, but processors value its quality, and new BSR-resistant cultivars have not been able to replace it. We bred the BSR-resistant cultivar ‘Erimo 167’ through repeated backcrossing using DNA markers. ‘Erimo 167’ has the same agronomic traits and quality as ‘Erimo-shozu’ but is resistant to BSR. Genome-wide SNP polymorphism analysis confirmed that the genomes of ‘Erimo 167’ and ‘Erimo-shozu’ were almost identical except for part of chromosome 3 where the BSR-resistance gene is located.

Vigna riukiuensis is one of the most salt-tolerant species within the genus Vigna, yet intraspecific variation in its salt tolerance remains uncharacterized. In this study, we evaluated 61 accessions of V. riukiuensis under 200 mM NaCl using effective quantum yield (Y(II)) as an indicator of salt tolerance. Accessions were classified into five clusters, showing substantial variation that accessions in the tolerant group maintained Y(II) for four weeks whereas those in the sensitive group lost Y(II) in a week. We repeated the Y(II)-based classification for a subset of accessions and the results generally reproduced that of the first evaluation. In addition, we measured Na+ and K+ allocation in roots, stems and leaves and found the pattern of Na+ allocation greatly varied even within the most tolerant accessions whereas the pattern of K+ allocation, not the Na+/K+ ratio, showed a minor correlation with salt tolerance. Interestingly, JP254554 restricted Na+ transport from roots to leaves, but it did not develop Casparian strips even under salt stress. This study provides the first comprehensive assessment of intraspecific variation in V. riukiuensis, identifying promising donor accessions for breeding, and highlighting various unknown mechanisms to be elucidated in the future.

Vigna luteola, a wild legume species, shows remarkable variation in salinity tolerance across its natural habitats, with coastal populations exhibiting high tolerance and riverbank populations being sensitive. This intraspecific variation provides a valuable system for investigating the genetic basis of salt tolerance. A major QTL for salt tolerance was previously identified by crossing salt-tolerant and salt-sensitive accessions, but the responsible genes remain unknown. In this study, grafting experiments between the two accessions revealed that the root plays a primary role in salt tolerance by suppressing Na+ transport to the shoot. We then conducted root transcriptome analysis and identified four candidate genes located within the QTL and highly expressed under salt stress in the tolerant accession: CBL-INTERACTING PROTEIN KINASE 6 (CIPK6), CAFFEOYL SHIKIMATE ESTERASE (CSE), FCS-LIKE ZINC FINGER PROTEIN 13 (FLZ13), and DROUGHT-INDUCED 21 (DI21). Promoter analysis revealed that the CIPK6 promoter contains transcription factor binding motifs unique to the salt-tolerant accession, which may contribute to its high expression under salt stress. These findings suggest that CIPK6 is regulated by cis-regulatory differences and is the most promising candidate for the salt-tolerance QTL. The identified genes in this study provide a foundation for developing salt-tolerant crops in the future.

Single‐copy orthologs are often used to reconstruct phylogenetic trees of life. A set of single‐copy orthologs can be prepared by building a new database including the species/strains of interest and performing a homology search, but these steps are time‐consuming when working with a large number of samples. To address this issue, more efficient and practical approaches are needed. Here, we developed a new pipeline called CUSCO, which reconstructs phylogenetic trees from the genome sequences of desired samples, including polyploid genomes or those without annotation using a reference set of protein sequences. As a benchmark, we compared the CUSCO pipeline with OrthoFinder. The CUSCO pipeline reproduced the same tree topologies that were reconstructed using single‐copy orthologs selected by OrthoFinder in a significantly shorter runtime. The pipeline is implemented with a function to identify a minimal set of marker genes that reconstruct a species tree, which is comparable to the one reconstructed from single‐copy orthologs. We also verified that the minimal set of marker genes identified by CUSCO accurately reproduces the tree topology obtained from the whole genome dataset. Sequencing these marker genes enables rapid and cost‐effective inference of the phylogenetic position of newly sampled species. Now that the genomes can be sequenced easily and inexpensively, the speed and accuracy of CUSCO facilitate large‐scale phylogenomic analyses on a desktop computer. Availability and implementation https://github.com/seikot345/CUSCO/ .

The Ghd7 (Grain number, plant height, and heading date 7) gene integrates red light signals and circadian rhythms to control floral repression under long-day conditions in rice. CRISPR/Cas9 systems were employed to create a series of deletion mutant lines in the upstream regions of Ghd7, covering a 65-kb genomic region from its transcription start site (TSS). These deletions ranged from 2 to 25 kb in size. Three deletion lines, those from 0 to -3 kb (0/-3 K), -20 to -40 kb (-20/-40 K), and -26 to -30 kb (-26/-30 K) from the TSS, resulted in early flowering, similar to Ghd7 knockout lines. The -20/-40 and -26/-30 K lines exhibited a loss of acute Ghd7 morning induction. Night-break experiments consistently supported these findings, suggesting that the key cis-regulatory region for red light responses was located within the 3.7-kb region in -26/-30 K. In seedlings of the 0/-3 K deletion line, which retains the -29 to -86 bp region, Ghd7 showed a diurnal pattern similar to wild type. This suggests that the deleted region in 0/-3 K is dispensable for both circadian rhythms and red-light responses. Further analyses of two deletion lines within the -26/-30 K region allowed us to narrow down the core cis-regulatory elements, responsive to morning-light signals, within a 228-bp segment located at 28-kb upstream of the TSS in Ghd7.

Adzuki is a central legume in East Asian culinary culture, yet its domestication origin remains debated. Using ~700 accessions across Asia, we show that the initial domestication happened three to five thousand years ago in central Japan during the Jomon period, followed by a range expansion into China and secondary hybridization with Chinese wild populations. We mapped, validated, and dated key genes associated with seed coat color evolution ( VaPAP1 for loss of mottled black and VaANR1 for gain of red colors). The frequency increases of variants affecting key domestication syndrome substantially predated the wild-cultigen divergence. Together, our results resolve the conflict between genetic and archaeological evidence about adzuki origins and reconstruct the evolutionary trajectory of archaeobotanically unobservable traits, consistent with a role of early weak selection during domestication.

Vigna luteola , a wild legume species, shows remarkable variation in salinity tolerance across its natural habitats, with coastal populations exhibiting high tolerance and riverbank populations being sensitive. This intraspecific variation provides a valuable system for investigating the genetic basis of salt tolerance. A major QTL for salt tolerance was previously identified by crossing salt-tolerant and salt-sensitive accessions, but the responsible genes remain unknown. In this study, grafting experiments between the two accessions revealed that the root plays a primary role in salt tolerance by suppressing Na⁺ transport to the shoot. We then conducted root transcriptome analysis and identified four candidate genes located within the QTL and highly expressed under salt stress in the tolerant accession: CBL-INTERACTING PROTEIN KINASE 6 (CIPK6) , CAFFEOYL SHIKIMATE ESTERASE (CSE) , FCS-LIKE ZINC FINGER PROTEIN 13 (FLZ13) , and DROUGHT-INDUCED 21 (DI21) . Promoter analysis revealed that the CIPK6 promoter contains transcription factor binding motifs unique to the salt-tolerant accession, which may contribute to its high expression under salt stress. These findings suggest that CIPK6 is regulated by cis -regulatory differences and is the most promising candidate for the salt-tolerance QTL. The identified genes in this study provide a foundation for developing salt-tolerant crops in the future.

Here, we report the complete genome sequences of four strains of Pseudomonas allii (MAFF 301514, MAFF 302050, MAFF 730042, and MAFF 730146) that represent pathogens causing bacterial rot in onion, lettuce, Chinese yam, and tomato, respectively, in Japan.