Biology subjects

Nozawa, S.

Publications and source records attributed to Nozawa, S..

6 recordsLinked to original sources

bioRxiv2026

The emergence of the rice blast fungus (Pyricularia oryzae) coincides with the evolutionary divergence of rice

Rice blast, caused by Pyricularia oryzae, is one of the most destructive diseases threatening global rice production. Reconstructing the evolutionary history of P. oryzae in the context of the well-documented history of rice dispersal provides a powerful framework for predicting the coevolutionary dynamics of crops and their pathogens. However, the absence of fossil evidence has precluded robust estimation of the pathogen's origin and evolutionary timescale. Here, we inferred genome-wide divergence times for P. oryzae using archaeological constraints derived from the emergence and spread of rice cultivation. Our analyses indicate that P. oryzae originated approximately 18,300 years ago, coincident with the divergence of Oryza sativa L. from its ancestral lineage rather than with rice domestication itself. Calibrating the evolutionary history of the pathogen against this host divergence further indicates that P. oryzae reached the Japanese archipelago 2,590 years ago based on nucleotide sequences and 3,030 years ago based on amino acid sequences, closely matching archaeological estimates for the arrival of rice agriculture in Japan. Contrary to the prevailing view that rice blast emerged with rice domestication approximately 10,000 years ago, our results place the origin of P. oryzae before domestication and link its subsequent spread to the expansion of cultivated rice. These findings redefine the evolutionary history of one of the world's most important crop pathogens and establish a temporal framework for understanding crop-pathogen coevolution over millennial timescales.

evolutionary biology↗

bioRxiv2025

PCR-based specific detection of multiple Nigrospora species causing a banana leaf spot disease

The genus Nigrospora has been identified as the primary causative agent of leaf spot disease in banana plantations in Mindanao, the Philippines. The symptoms caused by Nigrospora species are similar to those of black leaf streak disease (black sigatoka), which has made managing the disease challenging. Furthermore, development of rapid and precise molecular diagnostic methodologies for leaf spot disease has remained elusive. In the present study, a polymerase chain reaction (PCR)-based detection system was developed. The system targets a Nigrospora-specific genomic region, which was identified through comparative analysis of the genus Nigrospora and related genera. The newly designed primer set nigF/nigR specifically detected six pathogenic Nigrospora species associated with banana leaf spot disease (N. chinensis, N. lacticolonia, N. nigrocolonia, N. singularis, N. sphaerica, and N. vesicularifera), while no amplicon was observed for 15 non-Nigrospora species, including Pseudocercospora fijiensis isolated from banana leaves. The results indicate that the primers enable clear differentiation from other genera, including the important pathogen P. fijiensis. The primers also detected diverse Nigrospora isolates (N. banbusae, N. chinensis, N. musae, N. oryzae, N. sphaerica, and N. rubi) obtained from different hosts and regions within Japan, demonstrating broad applicability. Sensitivity testing demonstrated the capacity to detect as minimal as 10 pg of genomic DNA. Additionally, a pathogenic Nigrospora isolate was detected successfully from infected banana tissue. This study presents a novel molecular diagnostic tool for Nigrospora species, offering a rapid, specific, and practical approach, which could enhance evidence-based disease management in epidemiological investigations and banana production systems.

molecular biology↗

bioRxiv2025

Outbreak of leaf spot disease of Cavendish banana caused by Nigrospora spp. in Mindanao Island, Philippines

Banana leaf diseases are a significant threat to Cavendish banana production. In the Philippines, the main disease has been diagnosed as Black sigatoka disease caused by Pseudocercospora fijiensis based on symptoms. However, our study showed that the main pathogen in Mindanao island, the largest banana-producing region in the Philippines, belongs to the genus Nigrospora, contradicting previous assumptions. We clarified the phylogenetic positions of 160 Nigrospora isolates based on molecular phylogenetic analyses using ITS, {beta}-tubulin, and tef1 sequences, and compared their morphology with known species. Molecular phylogenetic and morphological analysis revealed that Nigrospora isolates comprised N. chinensis, N. lacticolonia, N. cf. singularis, N. sphaerica, N. vesicularifera, and a novel species, N. nigrocolonia. Pathogenicity tests on banana leaves confirmed that these species are pathogenic. Species other than N. sphaerica were for the first time reported as pathogens of banana leaf. The results of the fungicide sensitivity test using 14 fungicides, including pyrimethanil, spiroxamine, and tebuconazole, for the Sigatoka disease showed 100% inhibition of all isolates at 100 ppm of active ingredients. However, low-sensitivity isolates were observed for the remaining 11 fungicides. Our findings indicated the need for a comprehensive review of banana leaf disease prevention strategies.

molecular biology↗

bioRxiv2025

ANI-netID: a genome similarity-network based biological identification system

Fungal identification is based on sequence similarity comparisons, with multiple genes often utilized in conjunction, similar to most taxonomic studies. The identification process involves the individual comparison of the similarities of each gene. However, owing to insufficient information, incomplete lineage sorting, gene transfer, hybridization, gene duplication, and loss, different species may match, depending on the DNA region used for comparison. Additionally, identification methods exist that set a uniform similarity threshold value, but they hit multiple species above the threshold. In this study, we introduced ANI-netID, which was developed to address these challenges. ANI-netID is an identification method based on the phylogenetic species concept, where the threshold value is determined by the combination of individuals with the lowest nucleotide similarity within groups (clique groups), such as species and genera. This checks whether the queried individual fall into the same clique group as the reference individual with the highest similarity. ANI-netID solves not only the above-mentioned problems but also indicates that the individual being identified may represent a new lineage, if the individual does not belong to any clique group.

microbiology↗

bioRxiv2020

Hypoxia-tolerant vascular endothelial growth factor-A (VEGF-A) and the genetic variations of VEGFA in Sherpa highlanders

Sherpa highlanders demonstrate extraordinary tolerance to hypoxia at high altitudes, partly by one of the adaptation mechanisms promoting increases of microcirculatory blood flow and capillary density at high altitude for restoring oxygen supply to tissues. Hypoxia stimulates vascular endothelial growth factor (VEGF), which is an important signaling protein involved in hypoxia-stimulated vasculogenesis and angiogenesis. Our present study included 51 Sherpas dwelling in Namche Bazaar village (3440 m) and 76 non-Sherpa lowlanders residing in Kathmandu (1300 m) in Nepal. In these participants, we measured plasma VEGF-A concentrations and genotyped five single-nucleotide polymorphisms (SNPs) of VEGFA: rs699947, rs8333061, rs1570360, and rs2010963 in the 5'-untranslated region (5'-UTR); and rs3025039 in the 3'-UTR. The average circulating VEGF-A level in Sherpas did not respond to hypoxia at the high altitude in 3440 m, remaining equivalent to the level in non-Sherpa lowlanders at low altitude. Allele discriminations for the analyzed SNPs revealed significant genetic divergences of rs699947, rs8333061, and rs2010963 in Sherpa highlanders compared with non-Sherpa lowlanders, East Asians, South Asians, and the global population; however, consistency with the indigenous Tibetan highlanders from the Tibet Plateau. On the other hand, the SNP rs3025039 in the 3'-UTR presented constant preserved genetic variation among global populations. Our findings indicated that the physiological sea-level VEGF-A concentration in Sherpa highlanders at high altitude was probably linked with the significant variations of VEGFA in Sherpas that regulate the gene expression in a manner of tolerance to hypoxia through production of the optimal biological level of VEGF-A at high altitudes. Precise angiogenesis at high altitude contributes to the adaptive levels of capillary density and microcirculation, providing efficient and effective diffusion of oxygen to tissues and representing human adaptation to high-altitude hypoxia environment. Author summarySherpa highlanders demonstrate extraordinary tolerance to hypoxia at high altitudes, partly by one of the adaptation mechanisms promoting increases of microcirculatory blood flow and capillary density at high altitude for restoring oxygen supply to tissues. Vascular endothelial growth factor (VEGF) is mainly stimulated by hypoxia, and is an important signaling protein involved in hypoxia-stimulated vasculogenesis and angiogenesis. Interestingly, we found that the circulating VEGF-A level in Sherpa highlanders did not respond to hypoxia at high altitude. Furthermore, allele discrimination of the single nucleotide polymorphisms (SNPs) of VEGFA revealed significant divergences of rs699947, rs8333061, and rs2010963 within the VEGFA regulation region in Sherpa highlanders compared to the non-Sherpa lowlanders, East Asians, South Asians, and the global population; however, consistency with Tibetan highlanders from the Tibet Plateau. We propose that the hypoxia-tolerant circulating VEGF-A level in Sherpa highlanders is linked with the genetic variations of VEGFA, contributing to human adaptation to high-altitude hypoxic environments.

genetics↗

bioRxiv2019

Exome sequencing of ion-beam-induced mutants facilitates the detection of candidate genes responsible for phenotypes of mutants in rice

Ion beams are physical mutagens used for plant and microbe breeding that cause mutations via a distinct mechanism from those of chemical mutagens or gamma rays. We utilized whole-exome sequencing of rice DNA in order to understand the properties of ion beam-induced mutations in a genome-wide manner. DNA libraries were constructed from selected carbon-ion-beam-induced rice mutants by capturing with a custom probes covering 66.3 M bases of nearly all exons and miRNAs predicted in the genome. A total of 56 mutations, including 24 single nucleotide variations, 23 deletions, and 5 insertions, were detected in five mutant rice lines (two dwarf and three early-heading-date mutants). The mutations were distributed among all 12 chromosomes, and the average mutation frequency in the M1 generation was estimated to be 2.7 x 10-7 per base. Many single base insertions and deletions were associated with homopolymeric repeats, whereas larger deletions up to seven base pairs were observed at polynucleotide repeats in the DNA sequences of the mutation sites. Of the 56 mutations, six were classified as high-impact mutations that caused a frame shift or loss of exons. A gene that was functionally related to the phenotype of the mutant was disrupted by a high-impact mutation in four of the five lines tested, suggesting that whole-exome sequencing of ion-beam-irradiated mutants could facilitate the detection of candidate genes responsible for the mutant phenotypes.

plant biology↗