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Shell museomics: Experimental study to utilize museum collections

Research Project

Project/Area Number 19K21646
Research Category

Grant-in-Aid for Challenging Research (Exploratory)

Allocation TypeMulti-year Fund
Review Section Medium-sized Section 3:History, archaeology, museology, and related fields
Research InstitutionThe University of Tokyo

Principal Investigator

Sasaki Takenori  東京大学, 総合研究博物館, 准教授 (70313195)

Co-Investigator(Kenkyū-buntansha) スティアマルガ デフィン  和歌山工業高等専門学校, 生物応用化学科, 准教授 (50625259)
川島 武士  国立遺伝学研究所, 情報研究系, 助教 (10378531)
藤田 敏彦  独立行政法人国立科学博物館, 動物研究部, 部長 (70222263)
西秋 良宏  東京大学, 総合研究博物館, 教授 (70256197)
Project Period (FY) 2019-06-28 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000)
Fiscal Year 2021: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Fiscal Year 2020: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2019: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Keywords博物館 / 貝殻 / DNA / 博物館標本 / DNA抽出 / ミューゼオミクス / 博物館学 / 分類学
Outline of Research at the Start

本研究の目的は、実験的研究を通じて、博物館に収蔵された標本の新しい活用法を模索するものである。具体的には、(1)貝殻からDNAを抽出する実験、(2)次世代シーケンサを用いて博物館の標本からDNA抽出を効率的に行うための実験、(3)様々な年代、保存状態の標本を対象としたDNAの適正な保存条件の検討を行う。本研究では、微細構造、殻層ごとに実験を行う点が特に重要である。そして、以上の結果をもとに、標本を大規模に破壊することなく博物館の古い標本からDNA情報を取得するための技術を高める。

Outline of Final Research Achievements

The purpose of this study is to investigate methods to utilize museum specimens by extracting DNA from shells in museum collections. Due to their high species and morphological diversity, shells are often the subject of collections, and a vast number of specimens are stored in museums in various regions. We conducted experiments in a variety of taxa with the intention of using them for molecular phylogenetic analysis. The results of this study indicate that DNA can be extracted from shells of any species, but the extraction efficiency depends on the method. The question of why DNA can be preserved in shells is a topic for the future.

Academic Significance and Societal Importance of the Research Achievements

DNA用のサンプルの保存には冷凍が理想的であるが、大量の標本を非常に長期に亘って博物館で冷凍収蔵することは現実的ではない。もし乾燥標本もDNA研究に使用することができれば、幅広い分野で博物館標本を活用できるものと期待される。

Report

(4 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Research-status Report
  • 2019 Research-status Report

Research Products

(14 results)

All 2022 2021 2020 2019

All Journal Article (11 results) (of which Int'l Joint Research: 5 results,  Peer Reviewed: 10 results,  Open Access: 9 results) Presentation (3 results)

  • [Journal Article] Molecular phylogeny of Nipponacmea (Patellogastropoda: Lottiidae) from Japan: Reevaluation of species taxonomy and morphological diagnosis.2022

    • Author(s)
      Teruya, S., Setiamarga, D. H. E., Nakano, T., and Sasaki, T.
    • Journal Title

      ZooKeys

      Volume: 1087 Pages: 163-198

    • DOI

      10.3897/zookeys.1087.78193

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Complete mitochondrial genome of the Pacific limpet Cellana nigrolineata (Gastropoda: Patellogastropoda) determined by shotgun sequencing using the Illumina NGS platform.2021

    • Author(s)
      Nakashima, S., Shimizu, M., Hirota, K., Hiruta, S. F., Nakaji, N., Fujita, T., Sasaki, T. and Setiamarga, D. H. E.
    • Journal Title

      Mitochondrial DNA Part B

      Volume: 6 Pages: 1857-1859

    • DOI

      10.1080/23802359.2021.1934579

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A new species of the intertidal limpet Eoacmaea (Patellogastropoda: Eoacmaeidae) from Yonaguni Island, Japan and Taiwan2021

    • Author(s)
      Nakano, T., Sasaki, T., Kosuge, T. and Chan, B. K.K.
    • Journal Title

      Zoological Studies

      Volume: 80: 68 Pages: 1-12

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Hydrophilic shell matrix proteins of Nautilus pompilius and the identification of a core set of conchiferan domains2021

    • Author(s)
      Setiamarga, D. H. E., Hirota, K., Yoshida, M., Takeda, Y., Kito, K., Shimizu, K., Isowa, Y., Ikeo, K., Sasaki, T. and Endo, K.
    • Journal Title

      Genes

      Volume: 12:1925 Pages: 1-16

    • DOI

      10.3390/genes12121925

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Population genetic structure of the pen shell Atrina pectinata sensu lato (Bivalvia: Pinnidae) throughout East Asia2021

    • Author(s)
      Hashimoto, K., Yamada K., Sekino, M., Kobayashi, M., Sasaki, T., Fujinami, Y., Yamamoto, M., Choi, K. and Henmi, Y.
    • Journal Title

      Regional Studies in Marine Science

      Volume: 48: 102024 Pages: 1-12

    • DOI

      10.1016/j.rsma.2021.102024

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Phylogeography and shell morphology of the pelagic snail Limacina helicina in the Okhotsk Sea and western North Pacific2021

    • Author(s)
      Shimizu, K., K. Noshita, K. Kimoto & T. Sasaki
    • Journal Title

      Marine Biodiversity

      Volume: 51 Pages: 22-22

    • DOI

      10.1007/s12526-021-01166-z

    • Related Report
      2021 Annual Research Report 2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] The full mitochondrial genome sequence of the greater argonaut Argonauta argo (Cephalopoda, Argonautoidea) and its phylogenetic position in Octopodiformes2021

    • Author(s)
      Kazuki Hirota, Masa-aki Yoshida, Takehiko Itoh, Atsushi Toyoda, Davin H. E. Setiamarga
    • Journal Title

      Mitochondrial DNA Part B : Resources

      Volume: 6 Pages: 1451-1453

    • DOI

      10.1080/23802359.2021.1911710

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The first complete mitochondrial genome of the Northern Pacific deep-sea goniasterid sea star Ceramaster japonicus (Sladen, 1889) determined using NGS-based shotgun sequencing2021

    • Author(s)
      Yamamoto Masaki、Hiruta Shimpei F.、Arai Mikihito、Shimizu Moe、Mah Christopher L.、Fujita Toshihiko、Setiamarga Davin H. E.
    • Journal Title

      Mitochondrial DNA Part B

      Volume: 6 Pages: 1406-1408

    • DOI

      10.1080/23802359.2021.1911706

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Full genome sequence of a Bacillus safensis strain IDN1 isolated from commercially available natto in Indonesia2021

    • Author(s)
      Yoshida MA, Uomi M, Ikai T, Ilado T, Waturangi D, Ekaputri JJ, Setiamarga DHE
    • Journal Title

      Microbiology Resource Announcements

      Volume: 10

    • DOI

      10.1128/mra.00180-21

    • Related Report
      2021 Annual Research Report
  • [Journal Article] Molecular Species Delimitation of the Genus Reishia (Mollusca: Gastropoda) along the Coasts of China and Korea2020

    • Author(s)
      Zhao Dan、Kong Ling-feng、Sasaki Takenori、Li Qi
    • Journal Title

      Zoological Science

      Volume: 37 Issue: 4 Pages: 382-382

    • DOI

      10.2108/zs190153

    • NAID

      40022331101

    • ISSN
      0289-0003
    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] DNA Barcoding study of shelled Gastropods in the intertidal rocky coasts of Central Wakayama Prefecture, Japan, using two gene markers2019

    • Author(s)
      Setiamarga DHE, Nakaji N, Iwamoto S, Teruya S, Sasaki T
    • Journal Title

      International Journal of GEOMATE

      Volume: 17 Pages: 9-16

    • DOI

      10.21660/2019.62.4521

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] カサガイ類のタイプ標本2021

    • Author(s)
      佐々木猛智・中野智之
    • Organizer
      日本貝類学会令和3 年度大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 海棲動物液浸標本の博物館保存科学:アサリの液浸標本の生 化学的組成変化を例に2020

    • Author(s)
      西本真琴,大原珠海,山本真生,佐々木猛智,Davin H. E. SETIAMARGA
    • Organizer
      第28回 海洋工学シンポジウム
    • Related Report
      2019 Research-status Report
  • [Presentation] 中島理子,中路 渚,Do Van Tu,佐々木猛智,Davin H. E. SETIAMARGA2020

    • Author(s)
      ミトコンドリア由来12S-rRNA遺伝子を用いた有殻腹足類の博物館標本のDNAバーコーディング
    • Organizer
      第28回 海洋工学シンポジウム
    • Related Report
      2019 Research-status Report

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Published: 2019-07-04   Modified: 2023-01-30  

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