IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-63889-y.html
   My bibliography  Save this article

TEtrimmer: a tool to automate the manual curation of transposable elements

Author

Listed:
  • Jiangzhao Qian

    (Worringerweg 1
    Worringerweg 3)

  • Hang Xue

    (University of California)

  • Shujun Ou

    (592 Aronoff Laboratory, 318W 12th Avenue)

  • Ludwig Mann

    (Worringerweg 3)

  • Jessica Storer

    (Unit 3179)

  • Lisa Fürtauer

    (Worringerweg 1)

  • Tony Heitkam

    (Worringerweg 3)

  • Mary C. Wildermuth

    (University of California)

  • Stefan Kusch

    (Worringerweg 1
    Wilhelm-Johnen-Straße)

  • Ralph Panstruga

    (Worringerweg 1)

Abstract

Transposable elements (TEs) are repetitive DNA sequences that move within genomes and play important roles in gene regulation and genome evolution. Accurate TE annotation in genomes is crucial for downstream analyses but challenging due to their sequence diversity and frequent fragmentation, including the occurrence of nested copies. We here present TEtrimmer, a tool that automates and replaces key steps of traditional manual curation of TEs. TEtrimmer combines phylogenetic tree analysis with the machine learning method DBSCAN to cluster TE sequences accurately and applies a sliding-window strategy to remove poorly conserved regions of TE-derived multiple sequence alignments. TEtrimmer also provides detailed report plots and features a graphical user interface (GUI) application. Tested on the genomes of six organisms belonging to various kingdoms of eukaryotic life and three simulated genomes, TEtrimmer consistently improved the identification of intact TEs compared to the established tools EDTA and RepeatModeler2.

Suggested Citation

  • Jiangzhao Qian & Hang Xue & Shujun Ou & Ludwig Mann & Jessica Storer & Lisa Fürtauer & Tony Heitkam & Mary C. Wildermuth & Stefan Kusch & Ralph Panstruga, 2025. "TEtrimmer: a tool to automate the manual curation of transposable elements," Nature Communications, Nature, vol. 16(1), pages 1-20, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-63889-y
    DOI: 10.1038/s41467-025-63889-y
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-63889-y
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-025-63889-y?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Bo Xia & Weimin Zhang & Guisheng Zhao & Xinru Zhang & Jiangshan Bai & Ran Brosh & Aleksandra Wudzinska & Emily Huang & Hannah Ashe & Gwen Ellis & Maayan Pour & Yu Zhao & Camila Coelho & Yinan Zhu & Al, 2024. "On the genetic basis of tail-loss evolution in humans and apes," Nature, Nature, vol. 626(8001), pages 1042-1048, February.
    2. Metin Balaban & Niema Moshiri & Uyen Mai & Xingfan Jia & Siavash Mirarab, 2019. "TreeCluster: Clustering biological sequences using phylogenetic trees," PLOS ONE, Public Library of Science, vol. 14(8), pages 1-20, August.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Sung Hee Ko & Pierce Radecki & Frida Belinky & Jinal N. Bhiman & Susan Meiring & Jackie Kleynhans & Daniel Amoako & Vanessa Guerra Canedo & Margaret Lucas & Dikeledi Kekana & Neil Martinson & Limakats, 2024. "Rapid intra-host diversification and evolution of SARS-CoV-2 in advanced HIV infection," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    2. Matteo Ciciani & Michele Demozzi & Eleonora Pedrazzoli & Elisabetta Visentin & Laura Pezzè & Lorenzo Federico Signorini & Aitor Blanco-Miguez & Moreno Zolfo & Francesco Asnicar & Antonio Casini & Anna, 2022. "Automated identification of sequence-tailored Cas9 proteins using massive metagenomic data," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    3. Paul O. Sheridan & Yiyu Meng & Tom A. Williams & Cécile Gubry-Rangin, 2023. "Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    4. Jonas Fuchs & Johanna Kleine & Mathias Schemmerer & Julian Kreibich & Wolfgang Maier & Namuun Battur & Thomas Krannich & Somayyeh Sedaghatjoo & Lena Jaki & Anastasija Maks & Christina Boehm & Carina W, 2025. "varVAMP: degenerate primer design for tiled full genome sequencing and qPCR," Nature Communications, Nature, vol. 16(1), pages 1-19, December.
    5. Mengyu Shang & Yinuo Li & Qiuyu Cao & Jingxuan Ren & Yuqiang Zeng & Jinxin Wang & Rachel V. L. Gonzalez & Xiaohui Zhang, 2025. "A motif preferred adenine base editor with minimal bystander and off-targets editing," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
    6. Ning Zhang & Luuk Harbers & Michele Simonetti & Constantin Diekmann & Quentin Verron & Enrico Berrino & Sara E. Bellomo & Gabriel M. C. Longo & Michael Ratz & Niklas Schultz & Firas Tarish & Peng Su &, 2024. "High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    7. Almorò Scarpa & Riccardo Pianezza & Hannah R. Gellert & Anna Haider & Bernard Y. Kim & Eric C. Lai & Robert Kofler & Sarah Signor, 2025. "Double trouble: two retrotransposons triggered a cascade of invasions in Drosophila species within the last 50 years," Nature Communications, Nature, vol. 16(1), pages 1-16, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-63889-y. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.