410 Works

Data from: Phylogeographic analysis suggests two origins for the riparian azalea Rhododendron indicum (L.) Sweet

Watanabe Yoichi, Izumi Kawamata, Yu Matsuki, Yoshihisa Suyama, Koichi Uehara & Motomi Ito
180123_SNPs_datatoDryad.zip

Raw data used in: Variations in effects of ectosymbiotic microbes on the growth rates among different species and genotypes of Daphnia fed different algal diets

Xuan Zhang, Hajime Ohtsuki, Wataru Makino, Yasuhiko Kato, Hajime Watanabe & Jotaro Urabe
Several recent studies have shown that ectosymbiotic bacterial microbiota, including gut microbes, affect the growth and reproduction of Daphnia, a key organism in lake ecosystems. However, these studies examined specific species, such as the model organism, D. magna, and used green algae as food. It is unclear if symbiotic bacteria affect fitness in other Daphnia species common in lakes and ponds in Japan. In this study, we examined the growth rates of sterilized individuals of...

Raw data used in A unified framework for herbivore-to-producer biomass ratio reveals the relative influence of four ecological factor

Jotaro Urabe, Takehiro Kazama, Masato Yamamichi, Kotaro Tokita, Xuwang Yin, Izumi Katano, Hideyuki Doi, Takehito YOSHIDA & Nelson Hairston
The biomass ratio of herbivores to primary producers reflects the structure of a community. Four primary factors have been proposed to affect this ratio, including production rate, defense traits and nutrient contents of producers, and predation by carnivores. However, identifying the joint effects of these factors across natural communities has been elusive, in part because of the lack of a framework for examining their effects simultaneously. Here, we develop a framework based on Lotka-Volterra equations...

Refugia during the last glacial period and the origin of the disjunct distribution of the insular plant Microtropis japonica (Celastraceae)

Takayuki Yamada, Goro Kokubugata, Shinji Fujii, Chien-Fan Chen, Akira Asakawa, Takuro Ito & Masayuki Maki
Aim: While many phylogeographical studies have focused on continental refugia, the function of islands as refugia has been long overlooked. In this study, we examined the biogeographic history of Microtropis japonica and its insular distribution to elucidate the hidden status of islands on the range expansion of plants. Location: Two disjunct island areas of Japan (the Izu and Ryukyu Islands) and their adjacent areas (the Japanese mainlands Honshu and Kyushu, and Taiwan). Taxon: Microtropis japonica...

Data from: Disentangling the drivers of invasion spread in a vector-borne tree disease

Yutaka Osada, Takehisa Yamakita, Etsuko Shoda-Kagaya, Andrew M. Liebhold & Takehiko Yamanaka
1. Pine wilt disease (PWD) invaded southern Japan in the early 1900’s and has gradually expanded its range to northern Honshu (Japanese mainland). The disease is caused by a pathogenic North American nematode, which is transmitted by native pine sawyer beetles. Recently the disease has invaded other portions of East Asia and Europe where extensive mortality of host pines is anticipated to resemble historical patterns seen in Japan. 2. There is a critical need to...

Data from: Estimating range expansion of wildlife in heterogeneous landscapes: a spatially explicit state-space matrix model coupled with an improved numerical integration technique

Yutaka Osada, Takeo Kuriyama, Masahiko Asada, Hiroyuki Yokomizo & Tadashi Miyashita
Dispersal as well as population growth is a key demographic process that determines population dynamics. However, determining the effects of environmental covariates on dispersal from spatial-temporal abundance proxy data is challenging owing to the complexity of model specification for directional dispersal permeability and the extremely high computational loads for numerical integration. In this paper, we present a case study estimating how environmental covariates affect the dispersal of Japanese sika deer by developing a spatially explicit...

Data from: Integrated evidence reveals a new species in the ancient blue coral genus Heliopora (Octocorallia)

Zoe T. Richards, Nina Yasuda, Taisei Kikuchi, Taryn Foster, Chika Mitsuyuki, Michael Stat, Yoshihisa Suyama & Nerida G. Wilson
Maintaining the accretion potential and three dimensional structure of coral reefs is a priority but reef-building scleractinian corals are highly threatened and retreating. Hence future reefs are predicted to be dominated by non-constructional taxa. Since the Late Triassic however, other non-scleractinian anthozoans such as Heliopora have contributed to tropical and subtropical reef-building. Heliopora is an ancient and highly conserved reef building octocoral genus within the monospecific Family Helioporidae, represented by a single extant species –...

Data generated and analyzed in the work entitled: Signs of the plastid: Enzymes involved in plastid-localized metabolic pathways in a eugregarine species

Yuji Inagaki, Euki Yazaki, Ryosuke Miyata, Yasuhiko Chikami, Ryo Harada, Takashi Kawakubo, Goro Tanifuji, Takuro Nakayama, Kensuke Yahata & Tetsuo Hashimoto
The data were generated and analyzed in the manuscript entitled "Signs of the plastid: Enzymes involved in plastid-localized metabolic pathways in a eugregarine species". This work is currently accepted to be published in Parasitology International. As of April 17, 2021, we have no detail about the manuscript (e.g., issue, volume, page number, DOI number). We generated the transcriptome data from the apicomplexan parasites/symbionts isolated from three terrestrial arthropods, namely the centipede Scolopocryptops rubiginosus and two...

Molecular characterization and function analysis of the rice OsDUF1664 family

Lin Zhang, Dejia Hou, Chunliu Li, Xiaohong Li, Jiangbo Fan, Yilun Dong, Jianqing Zhu, Zhengjian Huang, Zhengjun Xu & Lihua Li
The functions of a large number of genes, including gene families with domains of unknown functions (DUF), still remain unclear. In this study, we analyzed four members of OsDUF1664 (OsDUF1664.1-OsDUF1664.4) in rice Nipponbare. By phylogenetic analysis, DUF1664 members in rice and Arabidopsis were classified into three major groups (I, II, III). Under drought conditions, the expression level of OsDUF1664.3 in rice was significantly elevated. Overexpression of OsDUF1664.3 in Escherichia coli led to a significant enhancement...

3D printing of fracture networks

Anna Suzuki
Conventional experiments using real rock samples have trouble in observing rock structures and controlling fracture properties. Taking advantage of 3D printing technologies, we made a complex fracture network by using a 3D printer. Hydraulic properties, such as porosity and permeability were similar with the theoretical values. A tracer response curve from the flow experiment were compared with numerical simulations.

Long non-coding RNA NEAT1 promotes steatosis via enhancement of estrogen receptor alpha-mediated AQP7 expression in HepG2 cells

Xiaohua Fu, Jing Zhu, Lin Zhang & Jing Shu
Hepatic steatosis is one of the most important features of the pathogenesis for non-alcoholic fatty liver disease. Fat deposition in liver cells can influence hepatic lipogenesis along with other metabolic pathways and further lead to the irreversible liver cirrhosis and injury. However, the underlying mechanism of steatosis remains largely unexplored. Our previous study revealed that AQP7 played an important role in liver steatosis. In this study, we determined that the transcriptional level of AQP7 was...

Long non-coding RNA NEAT1 promotes steatosis via enhancement of estrogen receptor alpha-mediated AQP7 expression in HepG2 cells

Xiaohua Fu, Jing Zhu, Lin Zhang & Jing Shu
Hepatic steatosis is one of the most important features of the pathogenesis for non-alcoholic fatty liver disease. Fat deposition in liver cells can influence hepatic lipogenesis along with other metabolic pathways and further lead to the irreversible liver cirrhosis and injury. However, the underlying mechanism of steatosis remains largely unexplored. Our previous study revealed that AQP7 played an important role in liver steatosis. In this study, we determined that the transcriptional level of AQP7 was...

Microsatellite data from: Multiple colonizations and genetic differentiation from the mainland populations in insular populations of the perennial herb Solidago virgaurea complex (Asteraceae) on recently formed nearshore oceanic islands

Takuma Kimura, Takayuki Yamada, Shota Sakaguchi, Motomi Ito & Masayuki Maki
Aim: Although the evolution of island endemic plants has long been investigated, the majority of such studies have focused on species with remarkable levels of morphological variation and on islands substantially far from the mainland. Except for a few examples such as the Canary Islands, endemic plants on nearshore oceanic islands have received less attention. In this study, we examined the Solidago virgaurea complex on the Japanese mainland Honshu and the adjacent Izu Islands to...

Species divergence and repeated ancient hybridization in a Sulawesian lake system

Kazunori Yamahira, Ixchel Mandagi, Ryo Kakioka, Javier Montenegro, Hirozumi Kobayashi, Kawilarang Masengi, Nobuyuki Inomata, Atsushi Nagano, Atsushi Toyoda, Satoshi Ansai, Masatoshi Matsunami, Ryosuke Kimura, Jun Kitano & Junko Kusumi
An increasing volume of empirical studies demonstrated that hybridization between distant lineages may have promoted speciation in various taxa. However, the timing, extent, and direction of introgressive hybridization remain unknown in many cases. Here, we report a possible case in which repeated hybridization promoted divergence of Oryzias ricefishes (Adrianichthyidae) on Sulawesi, an island of Wallacea. Four Oryzias species are endemic to the Malili Lake system in central Sulawesi, which is composed of five tectonic lakes;...

Anolis isolepis CDS

Shunsuke Kanamori, Luis M. Díaz, Antonio Cádiz, Katsushi Yamaguchi, Shuji Shigenobu & Masakado Kawata
Anolis isolepis CDS predicted using BRAKER2.

10x barcode fastq of Anolis allogus used for Supernova de novo assembly

Shunsuke Kanamori, Luis M. Díaz, Antonio Cádiz, Katsushi Yamaguchi, Shuji Shigenobu & Masakado Kawata
10x barcode fastq of Anolis allogus used for Supernova de novo assembly. Paired-end short read data for Supernova de novo assembly were deposited in the DDBJ Short Read Archive database under BioProject accession number PRJDB13431.

Anolis homolechis peptide sequences

Shunsuke Kanamori, Luis M. Díaz, Antonio Cádiz, Katsushi Yamaguchi, Shuji Shigenobu & Masakado Kawata
Anolis homolechis peptide sequences predicted using BRAKER2.

Anolis isolepis peptide sequences

Shunsuke Kanamori, Luis M. Díaz, Antonio Cádiz, Katsushi Yamaguchi, Shuji Shigenobu & Masakado Kawata
Anolis isolepis peptide sequences predicted using BRAKER2.

Anolis allisoni draft genome (repeat-softmasked)

Shunsuke Kanamori, Luis M. Díaz, Antonio Cádiz, Katsushi Yamaguchi, Shuji Shigenobu & Masakado Kawata
Repeatitive elements annotated by RepeatMasker were softmasked.

Anolis allisoni peptide sequences

Shunsuke Kanamori, Luis M. Díaz, Antonio Cádiz, Katsushi Yamaguchi, Shuji Shigenobu & Masakado Kawata
Anolis allisoni peptide sequences predicted using BRAKER2.

10x barcode fastq of Anolis allogus used for Supernova de novo assembly

Shunsuke Kanamori, Luis M. Díaz, Antonio Cádiz, Katsushi Yamaguchi, Shuji Shigenobu & Masakado Kawata
10x barcode fastq of Anolis allogus used for Supernova de novo assembly. Paired-end short read data for Supernova de novo assembly were deposited in the DDBJ Short Read Archive database under BioProject accession number PRJDB13431.

10x barcode fastq of Anolis homolechis used for Supernova de novo assembly

Shunsuke Kanamori, Luis M. Díaz, Antonio Cádiz, Katsushi Yamaguchi, Shuji Shigenobu & Masakado Kawata
10x barcode fastq of Anolis homolechis used for Supernova de novo assembly. Paired-end short read data for Supernova de novo assembly were deposited in the DDBJ Short Read Archive database under BioProject accession number PRJDB13431.

Anolis porcatus draft genome (repeat-softmasked)

Shunsuke Kanamori, Luis M. Díaz, Antonio Cádiz, Katsushi Yamaguchi, Shuji Shigenobu & Masakado Kawata
Repeatitive elements annotated by RepeatMasker were softmasked.

Anolis porcatus gene annotation

Shunsuke Kanamori, Luis M. Díaz, Antonio Cádiz, Katsushi Yamaguchi, Shuji Shigenobu & Masakado Kawata
The result of gene annotation for Anolis porcatus genome using BRAKER2.

Anolis sagrei peptide sequences

Shunsuke Kanamori, Luis M. Díaz, Antonio Cádiz, Katsushi Yamaguchi, Shuji Shigenobu & Masakado Kawata
Anolis sagrei peptide sequences predicted using BRAKER2.

Registration Year

  • 2023
    20
  • 2022
    271
  • 2021
    28
  • 2020
    23
  • 2019
    14
  • 2018
    12
  • 2017
    8
  • 2016
    15
  • 2015
    10
  • 2014
    3

Resource Types

  • Dataset
    230
  • Text
    77
  • Collection
    65
  • Image
    26
  • Audiovisual
    10
  • Other
    2

Affiliations

  • Tohoku University
    410
  • National Institute for Basic Biology
    72
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    58
  • Capital Medical University
    53
  • University of Melbourne
    52
  • Shanghai Jiao Tong University
    47
  • Chinese Academy of Sciences
    46
  • Southern Medical University
    44
  • Washington University in St. Louis
    43
  • Nanjing Medical University
    42