Search

Your search keyword '"Nagano, Atsushi J."' showing total 864 results
Start Over Author "Nagano, Atsushi J."
864 results on '"Nagano, Atsushi J."'

152. Single-Cell RNA Sequencing of Arabidopsis Leaf Tissues Identifies Multiple Specialized Cell Types: Idioblast Myrosin Cells and Potential Glucosinolate-Producing Cells.

Author

Maeda, Taro, Sugano, Shigeo S, Shirakawa, Makoto, Sagara, Mayu, Ito, Toshiro, Kondo, Satoshi, and Nagano, Atsushi J

Subjects
RNA sequencing, ARABIDOPSIS, PLANT defenses, TISSUES, BRASSICALES
Abstract

The glucosinolate–myrosinase defense system (GMDS), characteristic of Brassicales, is involved in plant defense. Previous single-cell transcriptomic analyses have reported the expression profiles of multiple GMDS-related cell types (i.e. myrosinase-rich myrosin idioblasts and multiple types of potential glucosinolate synthetic cells as well as a candidate S-cell for glucosinolate accumulation). However, differences in plant stages and cell-type annotation methods have hindered comparisons among studies. Here, we used the single-cell transcriptome profiles of extended Arabidopsis leaves and verified the distribution of previously used markers to refine the expression profiles of GMDS-associated cell types. Moreover, we performed beta-glucuronidase promoter assays to confirm the histological expression patterns of newly obtained markers for GMDS-associated candidates. As a result, we found a set of new specific reporters for myrosin cells and potential glucosinolate-producing cells. [ABSTRACT FROM AUTHOR]

Published
2023
Full Text
View/download PDF

153. Do colour-morphs of an amphidromous goby represent different species? Taxonomy of Lentipes (Gobiiformes) from Japan and Palawan, Philippines, with phylogenomic approaches

Author

Maeda, Ken, primary, Kobayashi, Hirozumi, additional, Palla, Herminie P., additional, Shinzato, Chuya, additional, Koyanagi, Ryo, additional, Montenegro, Javier, additional, Nagano, Atsushi J., additional, Saeki, Toshifumi, additional, Kunishima, Taiga, additional, Mukai, Takahiko, additional, Tachihara, Katsunori, additional, Laudet, Vincent, additional, Satoh, Noriyuki, additional, and Yamahira, Kazunori, additional

Published
2021
Full Text
View/download PDF

156. Species divergence and repeated ancient hybridization in a Sulawesian lake system

Author

Mandagi, Ixchel F., primary, Kakioka, Ryo, additional, Montenegro, Javier, additional, Kobayashi, Hirozumi, additional, Masengi, Kawilarang W. A., additional, Inomata, Nobuyuki, additional, Nagano, Atsushi J., additional, Toyoda, Atsushi, additional, Ansai, Satoshi, additional, Matsunami, Masatoshi, additional, Kimura, Ryosuke, additional, Kitano, Jun, additional, Kusumi, Junko, additional, and Yamahira, Kazunori, additional

Published
2021
Full Text
View/download PDF

159. Koshihikari X Oryza rufipogon Introgression Line with a High Capacity to Take up Nitrogen to Maintain Growth and Panicle Development under Low Nitrogen Conditions.

Author

Adu, Bright G, Argete, Aizelle Y S, Egawa, Sakiko, Nagano, Atsushi J, Shimizu, Akifumi, Ohmori, Yoshihiro, and Fujiwara, Toru

Subjects
RED rice, WILD rice, GERMPLASM, NITROGEN, PLANT growth, RICE, ORYZA
Abstract

Nitrogen (N) is an important macronutrient for plant growth and development. Currently, N fertilizers are required for the efficient production of modern crops such as rice due to their limited capacity to take up N when present at low concentrations. Wild rice represents a useful genetic resource for improving crop responses to low nutrient stress. Here, we describe the isolation and characterization of an introgression line, KRIL37, that carries a small region of the Oryza rufipogon genome in the Oryza sativa L. cv Koshihikari (KH) background. This line was found to grow better under low N conditions and have similar or lower C/N ratios in aerial portions compared to those in the parental KH cultivar, suggesting that KRIL37 has a higher capacity to take up and assimilate N when present at low concentrations. KRIL37 performance in the field was also better than that of KH cultivated without N and fertilizer (−F). Transcriptome analyses of 3-week-old seedlings based on RNA-sequencing revealed that KH induced a wider suite of genes than the tolerant line KRIL37 in response to low N conditions. Some ammonium transporters and N assimilation genes were found to be induced under low N in KRIL37, but not in KH. Our findings suggest that the superior growth performance of KRIL37 under limited N conditions could be due to the expression of wild alleles influencing N uptake and assimilation. Our study demonstrates the potential to use wild rice genomes to improve modern crops for low nutrient tolerance. [ABSTRACT FROM AUTHOR]

Published
2022
Full Text
View/download PDF

164. Genomic Basis of Transcriptome Dynamics in Rice under Field Conditions

Author

Kashima, Makoto, primary, Sakamoto, Ryota L, additional, Saito, Hiroki, additional, Ohkubo, Satoshi, additional, Tezuka, Ayumi, additional, Deguchi, Ayumi, additional, Hashida, Yoichi, additional, Kurita, Yuko, additional, Iwayama, Koji, additional, Adachi, Shunsuke, additional, and Nagano, Atsushi J, additional

Published
2021
Full Text
View/download PDF

169. Additional file 1 of Mapping of quantitative trait loci underlying a magic trait in ongoing ecological speciation

Author

Takahashi, Tetsumi, Nagano, Atsushi J., and Sota, Teiji

Abstract

Additional file 1: Supplementary Figure S1. A linkage map of Telmatochromis temporalis. Twenty-two linkage groups (LGs) consist of 708 double-digested restriction-site associated DNA (ddRAD) markers that were generated from a hybrid cross between the T. temporalis normal and dwarf morphs. Supplementary Figure S2. Comparison of double-digested restriction-site associated DNA (ddRAD) locus positions between Telmatochromis temporalis and Oreochromis niloticus. Sixteen linkage groups (LGs) that do not contain significant or suggestive quantitative trait locus (QTL) for body size are shown. Question mark indicates markers for which the positions on the O. niloticus LG were not identified. See Fig. 3 for the other LGs with QTL. Supplementary Table S1. Results of blast search for ddRAD loci of Telmatochromis temporalis against an Oreochromis niloticus genome.

Published
2021
Full Text
View/download PDF

170. A spinach genome assembly with remarkable completeness, and its use for rapid identification of candidate genes for agronomic traits

Author

Hirakawa, Hideki, Toyoda, Atsushi, Itoh, Takehiko, Suzuki, Yutaka, Nagano, Atsushi J., Sugiyama, Suguru, Onodera, Yasuyuki, Hirakawa, Hideki, Toyoda, Atsushi, Itoh, Takehiko, Suzuki, Yutaka, Nagano, Atsushi J., Sugiyama, Suguru, and Onodera, Yasuyuki

Abstract

Spinach (Spinacia oleracea) is grown as a nutritious leafy vegetable worldwide. To accelerate spinach breeding efficiency, a high-quality reference genome sequence with great completeness and continuity is needed as a basic infrastructure. Here, we used long-read and linked-read technologies to construct a de novo spinach genome assembly, designated SOL_r1.1, which was comprised of 287 scaffolds (total size: 935.7 Mb; N-50 = 11.3Mb) with a low proportion of undetermined nucleotides (Ns= 0.34%) and with high gene completeness (BUSCO complete 96.9%). A genome-wide survey of resistance gene analogues identified 695 genes encoding nucleotide-binding site domains, receptor-like protein kinases, receptor-like proteins and transmembrane-coiled coil domains. Based on a high-density double-digest restriction-site associated DNA sequencing-based linkage map, the genome assembly was anchored to six pseudomolecules representing similar to 73.5% of the whole genome assembly. In addition, we used SOL_r1.1 to identify quantitative trait loci for bolting timing and fruit/seed shape, which harbour biologically plausible candidate genes, such as homologues of the FLOWERING LOCUS T and EPIDERMAL PATTERNING FACTOR-LIKE genes. The new genome assembly, SOL_r1.1, will serve as a useful resource for identifying loci associated with important agronomic traits and for developing molecular markers for spinach breeding/selection programs.

Published
2021

171. H3K27me3 demethylases alter HSP22 and HSP17.6C expression in response to recurring heat in Arabidopsis

Author

90767899, Yamaguchi, Nobutoshi, Matsubara, Satoshi, Yoshimizu, Kaori, Seki, Motohide, Hamada, Kouta, Kamitani, Mari, Kurita, Yuko, Nomura, Yasuyuki, Nagashima, Kota, Inagaki, Soichi, Suzuki, Takamasa, Gan, Eng-Seng, To, Taiko, Kakutani, Tetsuji, Nagano, Atsushi J., Satake, Akiko, 90517096, Ito, Toshiro, 90767899, Yamaguchi, Nobutoshi, Matsubara, Satoshi, Yoshimizu, Kaori, Seki, Motohide, Hamada, Kouta, Kamitani, Mari, Kurita, Yuko, Nomura, Yasuyuki, Nagashima, Kota, Inagaki, Soichi, Suzuki, Takamasa, Gan, Eng-Seng, To, Taiko, Kakutani, Tetsuji, Nagano, Atsushi J., Satake, Akiko, 90517096, and Ito, Toshiro

Abstract

Acclimation to high temperature increases plants’ tolerance of subsequent lethal high temperatures. Although epigenetic regulation of plant gene expression is well studied, how plants maintain a memory of environmental changes over time remains unclear. Here, we show that JUMONJI (JMJ) proteins, demethylases involved in histone H3 lysine 27 trimethylation (H3K27me3), are necessary for Arabidopsis thaliana heat acclimation. Acclimation induces sustained H3K27me3 demethylation at HEAT SHOCK PROTEIN22 (HSP22) and HSP17.6C loci by JMJs, poising the HSP genes for subsequent activation. Upon sensing heat after a 3-day interval, JMJs directly reactivate these HSP genes. Finally, jmj mutants fail to maintain heat memory under fluctuating field temperature conditions. Our findings of an epigenetic memory mechanism involving histone demethylases may have implications for environmental adaptation of field plants.

Published
2021

172. Using a two-stage convolutional neural network to rapidly identify tiny herbivorous beetles in the field

Author

Takimoto, Hironori; https://orcid.org/0000-0002-8795-7109, Sato, Yasuhiro; https://orcid.org/0000-0002-6466-723X, Nagano, Atsushi J; https://orcid.org/0000-0001-7891-5049, Shimizu, Kentaro K; https://orcid.org/0000-0002-6483-1781, Kanagawa, Akihiro, Takimoto, Hironori; https://orcid.org/0000-0002-8795-7109, Sato, Yasuhiro; https://orcid.org/0000-0002-6466-723X, Nagano, Atsushi J; https://orcid.org/0000-0001-7891-5049, Shimizu, Kentaro K; https://orcid.org/0000-0002-6483-1781, and Kanagawa, Akihiro

Abstract

Recently, deep convolutional neural networks (CNN) have been adopted to help non-experts identify insect species from field images. However, the application of these methods on the rapid identification of tiny congeneric species moving across heterogeneous background remains difficult. To improve rapid and automatic identification in the field, we customized an existing CNN-based method for a field video involving two Phyllotreta beetles. We first performed data augmentation using transformations, syntheses, and random erasing of the original images. We then proposed a two-stage method for the detection and identification of small insects based on CNN, where YOLOv4 and EfficientNet were used as a detector and a classifier, respectively. Evaluation of the model revealed that one-step object detection by YOLOv4 alone was not precise (Precision = 0.55) when classifying two species of flea beetles and background objects. In contrast, the two-step CNNs improved the precision (Precision = 0.89) with moderate accuracy (F-measure = 0.55) and acceptable speed (ca. 5 frames per second for full HD images) of detection and identification of insect species in the field. Although real-time identification of tiny insects remains a challenge in the field, our method aids in improving small object detection on a heterogeneous background.

Published
2021

173. Neighbor GWAS: incorporating neighbor genotypic identity into genome-wide association studies of field herbivory

Author

Sato, Yasuhiro; https://orcid.org/0000-0002-6466-723X, Yamamoto, Eiji, Shimizu, Kentaro K; https://orcid.org/0000-0002-6483-1781, Nagano, Atsushi J; https://orcid.org/0000-0001-7891-5049, Sato, Yasuhiro; https://orcid.org/0000-0002-6466-723X, Yamamoto, Eiji, Shimizu, Kentaro K; https://orcid.org/0000-0002-6483-1781, and Nagano, Atsushi J; https://orcid.org/0000-0001-7891-5049

Abstract

An increasing number of field studies have shown that the phenotype of an individual plant depends not only on its genotype but also on those of neighboring plants; however, this fact is not taken into consideration in genome-wide association studies (GWAS). Based on the Ising model of ferromagnetism, we incorporated neighbor genotypic identity into a regression model, named "Neighbor GWAS". Our simulations showed that the effective range of neighbor effects could be estimated using an observed phenotype when the proportion of phenotypic variation explained (PVE) by neighbor effects peaked. The spatial scale of the first nearest neighbors gave the maximum power to detect the causal variants responsible for neighbor effects, unless their effective range was too broad. However, if the effective range of the neighbor effects was broad and minor allele frequencies were low, there was collinearity between the self and neighbor effects. To suppress the false positive detection of neighbor effects, the fixed effect and variance components involved in the neighbor effects should be tested in comparison with a standard GWAS model. We applied neighbor GWAS to field herbivory data from 199 accessions of Arabidopsis thaliana and found that neighbor effects explained 8% more of the PVE of the observed damage than standard GWAS. The neighbor GWAS method provides a novel tool that could facilitate the analysis of complex traits in spatially structured environments and is available as an R package at CRAN ( https://cran.rproject.org/package=rNeighborGWAS ).

Published
2021

176. Geographic and subsequent biotic isolations led to a diversity anomaly of section Heterotropa (genus Asarum : Aristolochiaceae) in insular versus continental regions of the Sino‐Japanese Floristic Region

Author

Takahashi, Daiki, primary, Sakaguchi, Shota, additional, Feng, Yu, additional, Isagi, Yuji, additional, Qiu, Ying‐Xiong, additional, Li, Pan, additional, Lu, Rui‐Sen, additional, Lu, Chang‐Tse, additional, Chung, Shih‐Wen, additional, Lin, Yang‐Shan, additional, Chen, Yun‐Chao, additional, Nagano, Atsushi J., additional, Kawaguchi, Lina, additional, Setoguchi, Hiroaki, additional, and Vanderpoorten, Alain, additional

Published
2021
Full Text
View/download PDF

177. Mapping of Quantitative Trait Loci Controlling Egg-Quality and -Production Traits in Japanese Quail (Coturnix japonica) Using Restriction-Site Associated DNA Sequencing

Author

Haqani, Mohammad Ibrahim, primary, Nomura, Shigeru, additional, Nakano, Michiharu, additional, Goto, Tatsuhiko, additional, Nagano, Atsushi J., additional, Takenouchi, Atsushi, additional, Nakamura, Yoshiaki, additional, Ishikawa, Akira, additional, and Tsudzuki, Masaoki, additional

Published
2021
Full Text
View/download PDF

178. Speciation along a latitudinal gradient: The origin of the Neotropical cycad sister pair Dioon sonorense–D. vovidesii (Zamiaceae)

Author

Gutiérrez‐Ortega, José Said, primary, Molina‐Freaner, Francisco, additional, Martínez, José F., additional, Pérez‐Farrera, Miguel Angel, additional, Vovides, Andrew P., additional, Hernández‐López, Antonio, additional, Tezuka, Ayumi, additional, Nagano, Atsushi J., additional, Watano, Yasuyuki, additional, Takahashi, Yuma, additional, Murakami, Masashi, additional, and Kajita, Tadashi, additional

Published
2021
Full Text
View/download PDF

181. Additional file 2 of Multiple waves of freshwater colonization of the three-spined stickleback in the Japanese Archipelago

Author

Kakioka, Ryo, Mori, Seiichi, Kokita, Tomoyuki, Hosoki, Takuya K., Nagano, Atsushi J., Asano Ishikawa, Kume, Manabu, Toyoda, Atsushi, and Kitano, Jun

Abstract

Additional file 2: Fig. S2. Scatter plots of principal components of genetic differentiation in the Japanese populations based on 813 SNPs. The contributions of each principal component are shown in the parentheses.

Published
2020
Full Text
View/download PDF

182. Figure S3 Genome-wide sliding window analysis of da and π. from Genome-wide patterns of divergence and introgression after secondary contact between Pungitius sticklebacks

Author

Yamasaki, Yo Y., Kakioka, Ryo, Takahashi, Hiroshi, Toyoda, Atsushi, Nagano, Atsushi J., Machida, Yoshiyasu, Møller, Peter R., and Kitano, Jun

Abstract

Speciation is a continuous process. Although it is known that differential adaptation can initiate divergence even in the face of gene flow, we know relatively little about the mechanisms driving complete reproductive isolation and the genomic patterns of divergence and introgression at the later stages of speciation. Sticklebacks contain many pairs of sympatric species differing in levels of reproductive isolation and divergence history. Nevertheless, most previous studies have focused on young species pairs. Here, we investigated two sympatric stickleback species, Pungitius pungitius and P. sinensis, whose habitats overlap in eastern Hokkaido; these species show hybrid male sterility, suggesting that they may be at a late stage of speciation. Our demographic analysis using whole-genome sequence data showed that these species split 1.73 Ma and came into secondary contact 37 200 years ago after a period of allopatry. This long period of allopatry might have promoted the evolution of intrinsic incompatibility. Although we detected on-going gene flow and signatures of introgression, overall genomic divergence was high, with considerable heterogeneity across the genome. The heterogeneity was significantly associated with variation in recombination rate. This sympatric pair provides new avenues to investigate the late stages of the stickleback speciation continuum.This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.

Published
2020
Full Text
View/download PDF

183. Additional file 3 of Multiple waves of freshwater colonization of the three-spined stickleback in the Japanese Archipelago

Author

Kakioka, Ryo, Mori, Seiichi, Kokita, Tomoyuki, Hosoki, Takuya K., Nagano, Atsushi J., Asano Ishikawa, Kume, Manabu, Toyoda, Atsushi, and Kitano, Jun

Abstract

Additional file 3: Fig. S3. Time-calibrated species trees of representative populations of Gasterosteus aculeatus and G. nipponicus inferred with SNAPP based on 2022 SNPs. Results of three independent runs are shown. The trees recorded in a run are overlaid by the maximum clade credibility tree. Posterior probabilities of each node are shown. Each bar indicates the 95% highest posterior density interval of the node height. (A, B, and C) Calibrated with root divergence at 680 ka BP. (D, E, and F) Calibrated with root divergence at 1.38 Ma BP. Individuals from Japanese freshwater populations of G. aculeatus are highlighted in blue.

Published
2020
Full Text
View/download PDF

184. Additional file 7 of Multiple waves of freshwater colonization of the three-spined stickleback in the Japanese Archipelago

Author

Kakioka, Ryo, Mori, Seiichi, Kokita, Tomoyuki, Hosoki, Takuya K., Nagano, Atsushi J., Asano Ishikawa, Kume, Manabu, Toyoda, Atsushi, and Kitano, Jun

Abstract

Additional file 7: Fig. S5. (A) Bar plots showing the results of the population structure analyses of East Pacific samples based on 3790 SNPs with ADMIXTURE (K = 2–4). Individuals are represented as vertical bars with different colours being proportional to the genotypes belonging to each genetic cluster. (B) Cross-validation errors for each K from the ADMIXTURE analyses of the East Pacific populations.

Published
2020
Full Text
View/download PDF

185. Supplementary materials and methods from Genome-wide patterns of divergence and introgression after secondary contact between Pungitius sticklebacks

Author

Yamasaki, Yo Y., Kakioka, Ryo, Takahashi, Hiroshi, Toyoda, Atsushi, Nagano, Atsushi J., Machida, Yoshiyasu, Møller, Peter R., and Kitano, Jun

Abstract

Speciation is a continuous process. Although it is known that differential adaptation can initiate divergence even in the face of gene flow, we know relatively little about the mechanisms driving complete reproductive isolation and the genomic patterns of divergence and introgression at the later stages of speciation. Sticklebacks contain many pairs of sympatric species differing in levels of reproductive isolation and divergence history. Nevertheless, most previous studies have focused on young species pairs. Here, we investigated two sympatric stickleback species, Pungitius pungitius and P. sinensis, whose habitats overlap in eastern Hokkaido; these species show hybrid male sterility, suggesting that they may be at a late stage of speciation. Our demographic analysis using whole-genome sequence data showed that these species split 1.73 Ma and came into secondary contact 37 200 years ago after a period of allopatry. This long period of allopatry might have promoted the evolution of intrinsic incompatibility. Although we detected on-going gene flow and signatures of introgression, overall genomic divergence was high, with considerable heterogeneity across the genome. The heterogeneity was significantly associated with variation in recombination rate. This sympatric pair provides new avenues to investigate the late stages of the stickleback speciation continuum.This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.

Published
2020
Full Text
View/download PDF

195. Effects of Observed Incubation Behavior on Egg Production in Laying Hens of a Commercial Chicken Breed and Detection of Single-Nucleotide Polymorphisms Associated with the Incubation Behavior.

Author

Yuichiro Yonetani, Nagano, Atsushi J., Hideki Ueno, and Tomoko Amano

Subjects
*HENS, *AGRICULTURAL egg production, *POULTRY breeding, *SINGLE nucleotide polymorphisms, *CHICKEN breeds, *GENOME-wide association studies, *POULTRY
Abstract

Upon contact with laid eggs, avians initiate incubation behavior and stop laying additional eggs. This phenomenon suggests that the productivity of laying hens in free-range facilities may decrease because of frequent contact with laid eggs. Here, we examined whether hens of a commercial breed exhibit incubation behavior in a free-range facility and whether egg productivity subsequently decreases. One-hour observations were performed twice weekly for 3 weeks, during which 9 of 129 hens (7.0%) exhibited incubation behavior (i.e., sitting on eggs) in the free-range facility and were defined as incubating hens. During 4 d of continuous behavioral observation, incubating and non-incubating hens laid the same number of eggs statistically (4.6 and 3.6, on average, respectively); however, incubating hens spent significantly more time on average incubating the eggs (2071.9 min) than did the non-incubating hens (20.9 min; P＜0.05), indicating a clear behavioral difference. Subsequently, the incubation behavior and egg productivity of incubating hens and a Silkie Fowl breed hen, which is known to exhibit typical incubation behavior and cessation of laying, were continuously compared for 27 d. The average minutes spent incubating eggs during the observation period increased in both the incubating hens and Silkie Fowl hen and the total time was almost the same (18,088.5 and 23,092 min, respectively). However, the Silkie Fowl hen stopped laying on day 17 after laying 17 eggs, whereas the incubating hens continued laying throughout the observation period. Incubating hens laid an average of 24.5 eggs, indicating that some hens (at least those of the commercial breed used in our study) can continue laying while exhibiting incubation behavior. A single-nucleotide polymorphism associated with incubation behavior was detected on chromosome 4 through genome-wide association analysis. [ABSTRACT FROM AUTHOR]

Published
2022
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results