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Development of a universal genomic method for the species identification and phylogenetic analysis of parasitic worms

Research Project

Project/Area Number 21H02725
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 49040:Parasitology-related
Research InstitutionUniversity of Miyazaki

Principal Investigator

Maruyama Haruhiko  宮崎大学, 医学部, 教授 (90229625)

Co-Investigator(Kenkyū-buntansha) 菊地 泰生  東京大学, 大学院新領域創成科学研究科, 教授 (20353659)
長安 英治  宮崎大学, 医学部, 准教授 (20524193)
Project Period (FY) 2021-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥17,550,000 (Direct Cost: ¥13,500,000、Indirect Cost: ¥4,050,000)
Fiscal Year 2023: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2022: ¥7,410,000 (Direct Cost: ¥5,700,000、Indirect Cost: ¥1,710,000)
Fiscal Year 2021: ¥8,060,000 (Direct Cost: ¥6,200,000、Indirect Cost: ¥1,860,000)
Keywords系統分類 / 寄生虫 / ゲノム情報 / 糞線虫 / マンソン孤虫 / ゲノム / 系統解析 / 線虫 / 条虫
Outline of Research at the Start

寄生虫が共通して保有する多数の相同遺伝子を用いた、寄生虫の種内グループや種間関係のレベルでの、汎用性が高く信頼性の高い同定・系統解析法を確立する。最初に、概要ゲノムが存在するStrongyloides属線虫とSpirometra属条虫で全ゲノム情報を用いた精密な系統解析を実施する。次いで、門や綱、あるいはもっと高位の分類単位で共通して保有される相同遺伝子の中から、概要ゲノムで得られたのと同等の結果が得られる遺伝子の組み合わせを見出す。単一の属を超えて幅広い寄生虫に適用できる信頼性の高い同定・解析法の確立は、系統解析の質を一気に高め、寄生適応研究の基盤を形作る。

Outline of Final Research Achievements

In the present research project, we determined intra-genetic phylogenetic relationships with sets of coding genes in Caenorhabditis, Strongyloides, and Spirometra worms. In Caenorhabditis nematodes, a phylogenetic tree generated with ribosomal DNA matched well with that generated with 97 single copy genes, covering 49 nominal species. In Strongyloides parasites, we partially sequenced nearly 20 species to find three large clades in the genus. They were identified with a set of coding gene sequences as well as ribosomal DNA sequences. In Spirometra tapeworm, however, we could not clarify the intra-genus phylogeny and the phylogenetic position of a bizarre species, Sparganum proliferum, because of the small number of samples we could analyze. Based on the nematode data, we are going to select sets of genes for the evaluation of species/subspecies identification.

Academic Significance and Societal Importance of the Research Achievements

DNAシーケンサの発達により、現在では少量のサンプルから大量の塩基配列情報を比較的容易に得ることができる。これまで、配列情報に基づいた種の同定にはPCRベースでリボソームITS領域やミトコンドリアcox-1等の数百塩基対程度を用いていたが、未知配列を新種とすべきか亜種とすべきか、あるいは系統的位置づけを決めるには十分なデータ量ではなかった。われわれの研究では未だ後生動物全体に適用できる遺伝子セットを決定するに至っていないが、少なくとも線虫類においては一定数のシングルコピー遺伝子によって正確な系統的位置を決定できる見通しがついた。フィールド研究・希少種の研究に応用できるものと考えられる。

Report

(4 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Annual Research Report
  • 2021 Annual Research Report
  • Research Products

    (27 results)

All 2024 2023 2022 2021 Other

All Int'l Joint Research (10 results) Journal Article (9 results) (of which Int'l Joint Research: 7 results,  Peer Reviewed: 8 results,  Open Access: 6 results) Presentation (8 results) (of which Invited: 2 results)

  • [Int'l Joint Research] University of Bath(英国)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] CIRMF(ガボン)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] Duzce University(トルコ)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] University of Bath(英国)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] Vietnam National Univ of Agriculture(ベトナム)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] University of Medicine 1(ミャンマー)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] Academia Sinica/National Taiwan University(その他の国・地域)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] Central University of Venezuela(ベネズエラ)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] Duzce University(トルコ)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] University of Bath(英国)

    • Related Report
      2021 Annual Research Report
  • [Journal Article] Syntenic relationship of chromosomes in <i>Strongyloides</i> species and <i>Rhabditophanes diutinus</i> based on the chromosome-level genome assemblies2023

    • Author(s)
      Kounosu Asuka、Sun Simo、Maeda Yasunobu、Dayi Mehmet、Yoshida Akemi、Maruyama Haruhiko、Hunt Vicky、Sugimoto Asako、Kikuchi Taisei
    • Journal Title

      Philosophical Transactions of the Royal Society B: Biological Sciences

      Volume: 379 Issue: 1894 Pages: 20220446-20220446

    • DOI

      10.1098/rstb.2022.0446

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Population genetics study of Strongyloides fuelleborni and phylogenetic considerations on primate-infecting species of Strongyloides based on their mitochondrial genome sequences2023

    • Author(s)
      Ko Phoo Pwint、Haraguchi Misaki、Hara Takashi、Hieu Duong Duc、Ito Ayaka、Tanaka Ryusei、Tanaka Mio、Suzumura Takafumi、Ueda Miya、Yoshida Ayako、Maruyama Haruhiko、Nagayasu Eiji
    • Journal Title

      Parasitology International

      Volume: 92 Pages: 102663-102663

    • DOI

      10.1016/j.parint.2022.102663

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Single worm long read sequencing reveals genome diversity in free-living nematodes2023

    • Author(s)
      Lee Yi-Chien、Lee Hsin-Han、Ke Huei-Mien、Liu Yu-Ching、Wang Min-Chen、Tseng Yung-Che、Kikuchi Taisei、Tsai Isheng Jason
    • Journal Title

      bioRxiv

      Volume: -

    • DOI

      10.1101/2023.04.17.537128

    • Related Report
      2022 Annual Research Report
    • Open Access / Int'l Joint Research
  • [Journal Article] The <i>Aphelenchoides</i> genomes reveal substantial horizontal gene transfers in the last common ancestor of free‐living and major plant‐parasitic nematodes2023

    • Author(s)
      Lai Cheng‐Kuo、Lee Yi‐Chien、Ke Huei‐Mien、Lu Min R.、Liu Wei‐An、Lee Hsin‐Han、Liu Yu‐Ching、Yoshiga Toyoshi、Kikuchi Taisei、Chen Peichen J.、Tsai Isheng Jason
    • Journal Title

      Molecular Ecology Resources

      Volume: 23 Issue: 4 Pages: 905-919

    • DOI

      10.1111/1755-0998.13752

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] The compact genome of Caenorhabditis niphades n. sp., isolated from a wood-boring weevil, Niphades variegatus2022

    • Author(s)
      Sun Simo、Kanzaki Natsumi、Dayi Mehmet、Maeda Yasunobu、Yoshida Akemi、Tanaka Ryusei、Kikuchi Taisei
    • Journal Title

      BMC Genomics

      Volume: 23 Issue: 1 Pages: 765-765

    • DOI

      10.1186/s12864-022-09011-8

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Strongyloidiasis in recently arrived captive-bred meerkats imported to Japan2022

    • Author(s)
      Nagayasu Eiji、Takaki Youki、Takami Yoshinori、Yoshida Ayako、Une Yumi、Maruyama Haruhiko
    • Journal Title

      Journal of Exotic Pet Medicine

      Volume: 40 Pages: 10-11

    • DOI

      10.1053/j.jepm.2021.10.002

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] First demonstration of Strongyloides parasite from an imported pet meerkat - Possibly a novel species in the stercoralis/procyonis group2021

    • Author(s)
      Takaki Y, Kadekaru S, Takami Y, Yoshida A, Maruyama H, Une Y, Nagayasu E
    • Journal Title

      Parasitol Int

      Volume: 84 Pages: 102399-102399

    • DOI

      10.1016/j.parint.2021.102399

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Genome of the fatal tapeworm Sparganum proliferum uncovers mechanisms for cryptic life cycle and aberrant larval proliferation2021

    • Author(s)
      Kikuchi Taisei、Dayi Mehmet、Hunt Vicky L.、Ishiwata Kenji、Toyoda Atsushi、Kounosu Asuka、Sun Simo、Maeda Yasunobu、Kondo Yoko、de Noya Belkisyole Alarcon、Noya Oscar、Kojima Somei、Kuramochi Toshiaki、Maruyama Haruhiko
    • Journal Title

      Communications Biology

      Volume: 4 Issue: 1 Pages: 6720-6720

    • DOI

      10.1038/s42003-021-02160-8

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Additional description and genome analyses of Caenorhabditis auriculariae representing the basal lineage of genus Caenorhabditis2021

    • Author(s)
      Dayi M, Kanzaki N, Sun S, Ide T, Tanaka R, Masuya H, Okabe K, Kajimura H, Kikuchi T
    • Journal Title

      Sci Rep

      Volume: 11 Issue: 1 Pages: 6720-6720

    • DOI

      10.1038/s41598-021-85967-z

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] 話題の寄生虫疾患蠕虫編2024

    • Author(s)
      丸山治彦, 田中美緒
    • Organizer
      第35回日本臨床微生物学会総会・学術集会
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] 多数の虫体が検出されたマンソン孤虫症2024

    • Author(s)
      田中 龍聖, 田中 美緒, 山崎 佳那子, 長安 英治, 久保 宜明, 丸山 治彦
    • Organizer
      第93回日本寄生虫学会大会
    • Related Report
      2023 Annual Research Report
  • [Presentation] On the evolutionary scenario of Strongyloides spp. of primates: discovery of a novel member in the stercoralis-procyonis clade in Gabon2024

    • Author(s)
      長安 英治, Makouloutou-Nzassi Patrice, Boundenga Larson, 丸山 治彦
    • Organizer
      第93回日本寄生虫学会大会
    • Related Report
      2023 Annual Research Report
  • [Presentation] 芽殖孤虫とマンソン裂頭条虫のセクレトームと表皮構造2024

    • Author(s)
      木下 権聖, 引間 篤志, 前田 安信, 吉田 朱美, 丸山 治彦, 石渡 賢治, 近 藤 陽子, 菊地 泰生
    • Organizer
      第93回日本寄生虫学会大会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Early phylogenetic separation between amphibian/reptile- and mammalianinfecting species of Strongyloides2023

    • Author(s)
      Eiji Nagayasu, Youki Takaki, Yoshinori Takami, Haruhiko Maruyama
    • Organizer
      第92回日本寄生虫学会大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Secretome analysis of the fatal tapeworm Sparganum proliferum with cryptic life cycle and aberrant larval proliferation2023

    • Author(s)
      [2]Kensei Kinoshita, Yasunobu Maeda, Asuka Kounosu, Yoko Kondo, Kenji Ishiwata, Haruhiko Maruyama, Taisei Kikuchi
    • Organizer
      第92回日本寄生虫学会大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Placement of Strongyloides sp. obtained from Myanmar domestic cats in a sister taxon position to Strongyloides stercoralis based on almost full-length mitochondrial genome data2021

    • Author(s)
      長安 英治, Phoo Pwint Ko, 丸山 治彦
    • Organizer
      第90回日本寄生虫学会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 寄生虫症血清診断の現場からみた食品媒介寄生虫症2021

    • Author(s)
      丸山治彦
    • Organizer
      第70回日本感染症学会東日本地方会学術集会
    • Related Report
      2021 Annual Research Report
    • Invited

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Published: 2021-04-28   Modified: 2025-01-30  

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