Biology subjects

Nagano, Y.

Publications and source records attributed to Nagano, Y..

16 recordsLinked to original sources

bioRxiv2026

The automated eukaryotic pangenome pipeline EukPan reveals accessory genome differentiation beyond core-gene phylogeny in Aspergillus oryzae

Pangenome analysis reveals recurrent gene-content variation beyond a single reference genome, but its application to eukaryotes is constrained by inconsistent gene annotation. ANNEVO predicts gene models from genome FASTA assemblies without RNA-seq data. We developed EukPan, an automated post-annotation pipeline that standardizes GFF/GTF files, selects representative isoforms, constructs proteomes, infers orthogroups, builds a concatenated single-copy core-protein alignment, and summarizes shared accessory orthogroups while excluding orthogroups detected in only one genome. Applied with ANNEVO to 123 Aspergillus oryzae genomes, EukPan identified 11,245 core and 4,407 shared accessory orthogroups. The core-protein phylogeny broadly recovered the reported A-H classification, whereas accessory-genome analyses clearly separated the 33 group-A strains from the other 90 strains. Directional analysis identified 62 group-A-associated and 158 group-A-depleted orthogroups, with major facilitator superfamily (MFS) transporter and fungal Zn2Cys6 transcription-factor domains prominent in the depleted set. Among 93 orthogroups present in all non-A strains and absent from all group-A strains, 59 mapped to 10 segments of RIB40, the standard A. oryzae reference genome and a non-A (group-F) strain. EukPan therefore enables reproducible, coordinated core- and accessory-pangenome analysis from eukaryotic genome assemblies.

genomics↗

bioRxiv2025

Diversity of vector-dispersed microbes peaks at a landscape-defined intermediate rate of dispersal

Dispersal rate has long been considered a primary determinant of species diversity in ecological communities. However, this knowledge is mostly built on studies of organisms that disperse actively by themselves or passively via physical forces. For organisms that disperse passively via other organisms, the landscape matrix that affects their vectors should indirectly shape the diversity of the vectored, but this relationship remains poorly understood. We investigated landscape-dispersal-diversity relationships in nectar-inhabiting bacteria that disperse via flower-visiting insects. Field observation and experiments revealed that bacterial diversity and abundance peaked at an intermediate frequency of insect visits, which was in turn determined by the surrounding landscape characteristics observed at the 200-m radius scale. Based on this finding, we discuss the possibility that species diversity tends to be maximized at an intermediate dispersal rate, especially when habitat patches of vectored organisms constitute consumable resources for their vectors.

ecology↗

bioRxiv2025

Conserved accessory genes link phylogenetically distinct Bacillus subtilis from Japanese and Indian fermented soyfoods

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 strainbeing 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.

genomics↗

bioRxiv2024

Intra- and inter-chain contacts determine TCR specificity: applying protein co-evolution methods to TCRαβ pairing

The six complementarity determining regions (CDRs) of the T cell receptor (TCR) form multiple contacts with cognate peptide and major histocompatibility complex, thus determining antigen specificity. However, the contacts between the CDRs themselves are less understood. We perform a systematic study of all available TCR structures, and identify consistent patterns of intra- and inter-chain CDR contacts. We further show that the sequences of paired TCR and TCR{beta} are not independent within sets of antigen-specific TCRs, for most epitopes. We quantify this sequence restriction using a mutual information framework. Co-evolution models can achieve some de novo prediction of TCR/TCR{beta} pairing, without using a training set of known pairs. The conserved pattern of CDR amino acid contacts, and the mutual sequence constraints between antigen-specific sets of T cell receptor and {beta} chains could play an important role in shaping the antigen-specific T cell repertoire.

immunology↗

bioRxiv2024

Structure-activity relationships and crucial mechanisms of the coumarin family as germination inhibitors

Coumarin is produced by various land plants, such as cherry trees, and is known to exhibit a wide range of physiological activities. Notably, one of its primary functions is the inhibition of seed germination. However, the structural basis underlying coumarins germination-inhibitory effect remains poorly understood. In this study, we analyzed the structure-activity relationships of coumarin analogs in two plant species, white clover and Arabidopsis, and demonstrated that the benzene ring and ester bond within the coumarin skeleton constitute the minimal structural requirements for germination inhibition. The inhibitory effects of dihydrocoumarin, which lacks the double bond in the coumarin skeleton, varied among plant species, while those of various other modified coumarin analogs also differed across species. In both plant species, coumarin consistently proved to be one of the most potent inhibitors. Furthermore, the observation that dihydrocoumarin exhibited a strong germination inhibitory effect only in white clover suggests that certain coumarin analogs may act in a species-specific manner. Additionally, the mechanism of coumarin-mediated germination inhibition remains largely unclear. Using RNA-Seq analysis on Arabidopsis seeds, we uncovered a novel and critically important mechanism whereby coumarin suppresses the expression of genes encoding expansins, proteins that are responsible for loosening plant cell walls. This study is significant for understanding how coumarin contributes to plant competition in nature.

plant biology↗

bioRxiv2024

Identification of new resistance QTL regions in loquat cultivar Champagne against Pseudomonas syringae pv. eriobotryae group C

Loquat canker, caused by Pseudomonas syringae pv. eriobotryae, is a bacterial disease that infects loquat (Eriobotrya japonica) and has been reported in several countries. Three pathotypes, A, B, and C, have been reported in Japan. The loquat cultivar Champagne is resistant to the loquat canker group C and possesses a qualitative trait governed by a recessive homozygous pse-c gene located on Linkage Group 3 (LG3), and quantitative traits located at unidentified loci. In this study, we identified novel quantitative trait loci (QTL) regions for resistance to group C in this cultivar. A seedling population with Tanaka (Pse-c/Pse-c) crossed with Champagne (pse-c/pse-c) was tested. The genetic map of Champagne includes a total of 1,016 SNP markers mapped across 17 LGs, covering a total distance of 1,301 cM and an average marker density of 1.4 cM/locus. In addition to minor potential QTLs, the major QTL for resistance to loquat canker group C was detected in the upper region of LG14, with the QTL contributing 6.9% to the disease index. The results of this study open new possibilities for resistance breeding against this disease. Highlights.A total of 1,016 SNP markers were mapped on a linkage map consisting of 17 linkage groups with a total distance of 1,301 cM. QTL analysis revealed a novel resistance QTL region in Champagne against loquat canker group C in the upper part of the LG14. The identified QTLs in this study provide new possibilities for resistance breeding in loquat.

plant biology↗

bioRxiv2024

Cost-Effective Approaches to Elucidate Intergeneric Relationships of Plants: Utilizing Multiple Conserved Nuclear Genes and Whole Chloroplast Genomes

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.

genomics↗

bioRxiv2023

tidytcells: standardizer for TCR/MHC nomenclature

T cell receptors (TCRs) underpin the diversity and specificity of T cell activity. As such, TCR repertoire data is valuable both as an adaptive immune biomarker, and as a way to identify candidate therapeutic TCRs. Analysis of TCR repertoires relies heavily on computational analysis, and therefore it is of vital importance that the data is standardized and computer-readable. However in practice, the usage of different abbreviations and non-standard nomenclature in different datasets makes this data pre-processing non-trivial. tidytcells is a lightweight, platform-independent Python package that provides easy-to-use standardization tools specifically designed for TCR nomenclature. The software is open-sourced under the MIT license and is available to install from the Python Package Index (PyPI).

immunology↗

bioRxiv2022

Diversity in DNA sequence, structure, and heterozygosity of nuclear rRNA gene region in Neopyropia yezoensis

DNA sequence reads of Neopyropia yezoensis (susabi-nori), its relative N. tenera (asakusa-nori), and their hybrids available in the sequence read archive produced assembled sequences of the nuclear rRNA gene region for 82 samples. Analysis of the assembled sequences revealed structural differences in the region of nuclear rRNA genes, with 17 forms depending on the presence or absence of introns and their lengths. The samples were divided into three groups based on differences in DNA sequences: Japanese N. yezoensis, Chinese N. yezoensis, and N. tenera/hybrids of N. tenera and N. yezoensis that exist in both countries. Despite genetic differentiation, the Japanese and Chinese N. yezoensis exhibit common structural forms. One sample of Chinese N. yezoensis presented almost 1:1 heterozygosity, whereas five other samples of Chinese N. yezoensis showed non-1:1 heterozygosity. In the latter case, neither the ratio of alleles nor the ratio of the number of introns was 1:1, suggesting the existence of an ongoing mechanism to eliminate the nuclear rRNA gene region on one of the homologous chromosomes in N. yezoensis.

plant biology↗

bioRxiv2021

Dissecting the clonality of I1 plasmids using ORF-based binarized structure network analysis of plasmids (OSNAp)

Phylogenetic relationship of 97 I1 plasmids harboring blaCTX-M genes encoding extended-spectrum beta-lactamase (ESBL) was analyzed using the ORF-based binarized structure network analysis of plasmids (OSNAp). The majority of plasmids carrying blaCTX-M-1 or blaCTX-M-8, ESBL genes primarily associated with domestic animals, were clonal. On the other hand, plasmids carrying blaCTX-M-14 or blaCTX-M-15, identified from both humans and domestic animals, were diverse in their contents. The findings suggest that circulation of I1 plasmids among humans and animals may contribute to their diversity.

microbiology↗

bioRxiv2020

Elucidation of Japanese pepper (Zanthoxylum piperitum De Candolle) domestication using RAD-Seq

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.

plant biology↗

bioRxiv2020

Massive occurrence of benthic plastic debris at the abyssal seafloor beneath the Kuroshio Extension, the North West Pacific

The deep-sea is considered to be an ultimate sink for marine plastic debris. The abyssal (3500-6500 m) covers the bulk of the deep ocean floor yet little is known about the extent of plastic debris on the abyssal seafloor. We undertook a quantitative assessment of debris presents on the abyssal seafloor (5700-5800 m depth) beneath the Kuroshio Extension current system in the Northwest Pacific, which is one of the major transit points for massive amounts of debris sourced from Asia that are entering the North Pacific Ocean. The dominant type of debris was single-use plastics-mainly bags and food packaging. The density of plastic debris (average 4561 items km-2) in the abyssal zone was the highest recorded for an abyssal plain, suggesting that the deep-sea basin of the Northwest Pacific is a significant reservoir of plastic debris.

ecology↗

bioRxiv2020

Genetic diversity and population structure of razor clam Sinonovacula constricta in Ariake Bay, Japan, revealed using RAD-Seq SNP markers.

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 (Fst 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.

zoology↗

bioRxiv2020

Genomic diversity of 39 Pyropia species grown in Japan

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.

genomics↗

bioRxiv2020

Production of a tributyltin-binding protein 2 knockout mutant strain of Japanese medaka, Oryzias latipes

Tributyltin-binding proteins (TBT-bps), members of the lipocalin family, bind TBT in fish blood and are presumed to contribute to detoxification of TBT. Recent studies have shown that many fish species have TBT-bp genes, and that these genes are induced by stresses such as exposure to chemicals or fish pathogenic bacteria. However, the function of TBT-bps, and the mechanisms of their induction and detoxification activity are still unclear. Here, towards elucidating the functions of TBT-bp2, we produced a TBT-bp2 knockout (TBT-bp2-/-) strain of Japanese medaka, Oryzias latipes, by using the CRISPR/Cas9 system. Gene expression of the mutated TBT-bp2 was reduced, and the cDNA sequencing and predicted protein structure suggested possible loss of function. However, the fish could be grown under normal conditions. Exposure of the TBT-bp2-/- strain of medaka to various stresses in future experiments is expected to contribute to our understanding of this novel detoxification system in aquatic organisms.

pharmacology and toxicology↗

bioRxiv2019

Bacterial diversity in deep-sea sediments under influence of asphalt seep at the Sao Paulo Plateau

Here we investigated the diversity of bacterial communities from deep-sea surface sediments under influence of asphalt seeps at the Sao Paulo Plateau using next-generation sequencing (NGS) method. Sampling was performed at North Sao Paulo Plateau using the human occupied vehicle Shinkai 6500 and her support vessel Yokosuka. The microbial diversity was studied at two surficial sediment layers (0-1 and 1-4 cm) of five samples collected in cores in water depths ranging from 2,456-2,728 m. Bacterial communities were studied through sequencing of 16S rRNA gene on the Ion Torrent platform and clustered in operational taxonomic units. We observed high diversity of bacterial sediment communities as previously described by other studies. When we considered community composition, the most abundant classes were Alphaprotebacteria (27.7%), Acidimicrobiia (20%), Gammaproteobacteria (11.3%) and Deltaproteobacteria (6.6%). Most abundant OTUs at family level were from two uncultured bacteria from Actinomarinales (5.95%) and Kiloniellaceae (3.17%). The unexpected high abundance of Alphaproteobacteria and Acidimicrobiia in our deep-sea microbial communities may be related to the presence of asphalt seep at North Sao Paulo Plateau, since these bacterial classes contain bacteria that possess the capability of metabolizing hydrocarbon compounds.

microbiology↗