本文へスキップ


Background

National Institute for Environmental Studies(NIES)preserves cells of endemic species of Japan. However, due to restrictions by the Convention on International Trade in Endangered Species of Wild Fauna and Flora, it is difficult to conduct genome analysis by overseas research institutions, so we must conduct genome analysis at NIES and publish genomic data.

On the other hand, when a wildlife is influenced at the genetic level at the time of a disaster such as the Fukushima Daiichi nuclear accident accompanying the Great East Japan Earthquake, it is essential to obtain the whole genome information of indicator species as an index for comparison.

In the Harmonization with Nature Research (HNR) Program, one of the Issue-Oriented Research Programs of NIES, we will conduct detailed analysis of distribution of organisms and survey of food chain by meta-genome analysis method in Lake Kasumigaura and on Ogasawara islands. In order to produce more practical results, the presence of highly accurate DNA barcode data for species discrimination is required.

In addition, various environmental genomics research such as whole genome analysis, metagenomic analysis, and gene expression analysis, targeting a wide range of organisms from microorganisms to humans are being conducted. Consolidating the provision of infrastructure and analysis support is desired from researchers who want to speed up and expand their research.

Objectives

The purpose of this project is as follows.

Draft analysis of the whole genome will be conducted and announced for organisms with high scarcity, organisms causing environmental problems, and indicator organisms widely distributed in the country.
We will acquire DNA barcodes of organisms distributed in areas subject to environmental research such as Lake Kasumigaura and Ogasawara islands and promote HNR program by analyzing environmental DNA diversity.
Support for genome-related research at NIES such as metagenomic analysis for environmental microorganisms, draft genome analysis of useful bacterial strains, and construction and update of bioinformatics pipelines for experimental animals and humans will be conducted.

Regarding whole genome analysis, we are aiming to announce more than 10 kinds of the draft sequence of whole genome of endangered species over the 5 years. In addition, we are targeting 500 kinds of DNA barcode acquisition over 5 years.

Research summary




Several kinds of draft whole genome will be sequenced every year. These data will include domestic endangered species stored in Time capsule building and Microbial Culture Collection Building. We will sequence the genome of indicator organisms related to environmental problems. Forty kinds of DNA barcodes will be acquired and resistered to the public database.

Support of HNR Program

Collaborating with researchers of the HNR Program, we will acquire 4,000 DNA barcodes (about 300 species) of organisms collected in Lake Kasumigaura and the Ogasawara Islands. they will publish in the international database or in our database. Based on the barcode information, species will be identified to the DNAs obtained from environment and biological samples. These results will be provided to the HNR program and will be used for food network analysis and estimation of wildlife distribution.

Support of genome-related research in NIES

As a core organization of genome science research at NIES, we will provide infrastructure and receive the request of analyses such as metagenomic analysis for environmental microorganisms, draft genome analysis of useful bacterial strains, and gene expression analysis conducted by NIES researchers. In addition, we will construct a genome analysis pipeline for laboratory animals and humans, and respond to individual consultations on analysis methods. In addition, we will manage the server used in the genome analysis pipeline and update the software.


Research overview of 2016

Draft genome information &Acquisition and disclosure of DNA barcodes

We sequenced the whole genome of two endangered avian species (Lagopus muta, Ketupa blakistoni), six species of algae, seven species of agro-bacteria, and one species of mite. They are under registration on international database. We acquired the DNA barcodes of 40 environmental microorganisms stored in Microbial Culture Collection Building and published them in the international database.

Promotion of HNR Program

About 108 kinds of DNA barcodes were acquired for organisms collected in Lake Kasumigaura and they are under registration on an international database.

Support of genome-related research in NIES

We sequenced partial genomes of 11 species of insects, 3 kinds of crustaceans, 2 kinds of fish, 3 kinds of mammalians, and 1 species of avian. They will be used for the construction of DNA markers. We also supported 4 RNAseq analyses conducted by the collaborators of NIES.



Project Members
NAKAJIMA Nobuyoshi(Center for Environmental Biology and Ecosystem Studies) YAMAGUCHI Haruyo(Center for Environmental Biology and Ecosystem Studies)
KAWASHIMA Takaharu(Center for Environmental Biology and Ecosystem Studies) ONUMA Manabu(Center for Environmental Biology and Ecosystem Studies)
KONDO Natsuko(Center for Environmental Biology and Ecosystem Studies) UDAGAWA Osamu(Center for Health and Environmental Risk Research)
ANDO Haruko(Center for Environmental Biology and Ecosystem Studies) SUZUKI Takehiro(Center for Health and Environmental Risk Research)
TAMAOKI Masanori(Fukushima Branch/Center for Environmental Biology and Ecosystem Studies) OKAMURA Kazuyuki(Center for Health and Environmental Risk Research)
YAMAMURA Shigeki(Center for Regional Environmental Research)

Contact address

Environmental Genomics Office NAKAJIMA Nobuyoshi
 TEL:029-850-2490
 Mail:naka-320 (Please attach "@ nies.go.jp" to the end)


Related link

Time Capsule Program for Environmental Specimens