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HiTE: a fast and accurate dynamic boundary adjustment approach for full-length transposable element detection and annotation

Author

Listed:
  • Kang Hu

    (Central South University
    Xiangjiang Laboratory
    Central South University)

  • Peng Ni

    (Central South University
    Xiangjiang Laboratory
    Central South University)

  • Minghua Xu

    (Central South University
    Central South University)

  • You Zou

    (Central South University
    Central South University)

  • Jianye Chang

    (Chinese Academy of Agricultural Sciences)

  • Xin Gao

    (King Abdullah University of Science and Technology (KAUST)
    King Abdullah University of Science and Technology (KAUST))

  • Yaohang Li

    (Old Dominion University)

  • Jue Ruan

    (Chinese Academy of Agricultural Sciences)

  • Bin Hu

    (Ministry of Education (Beijing Institute of Technology)
    Beijing Institute of Technology)

  • Jianxin Wang

    (Central South University
    Xiangjiang Laboratory
    Central South University)

Abstract

Recent advancements in genome assembly have greatly improved the prospects for comprehensive annotation of Transposable Elements (TEs). However, existing methods for TE annotation using genome assemblies suffer from limited accuracy and robustness, requiring extensive manual editing. In addition, the currently available gold-standard TE databases are not comprehensive, even for extensively studied species, highlighting the critical need for an automated TE detection method to supplement existing repositories. In this study, we introduce HiTE, a fast and accurate dynamic boundary adjustment approach designed to detect full-length TEs. The experimental results demonstrate that HiTE outperforms RepeatModeler2, the state-of-the-art tool, across various species. Furthermore, HiTE has identified numerous novel transposons with well-defined structures containing protein-coding domains, some of which are directly inserted within crucial genes, leading to direct alterations in gene expression. A Nextflow version of HiTE is also available, with enhanced parallelism, reproducibility, and portability.

Suggested Citation

  • Kang Hu & Peng Ni & Minghua Xu & You Zou & Jianye Chang & Xin Gao & Yaohang Li & Jue Ruan & Bin Hu & Jianxin Wang, 2024. "HiTE: a fast and accurate dynamic boundary adjustment approach for full-length transposable element detection and annotation," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49912-8
    DOI: 10.1038/s41467-024-49912-8
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    References listed on IDEAS

    as
    1. Jianqiang Shen & Juhong Liu & Kabin Xie & Feng Xing & Fang Xiong & Jinghua Xiao & Xianghua Li & Lizhong Xiong, 2017. "Translational repression by a miniature inverted-repeat transposable element in the 3′ untranslated region," Nature Communications, Nature, vol. 8(1), pages 1-10, April.
    2. Parithi Balachandran & Isha A. Walawalkar & Jacob I. Flores & Jacob N. Dayton & Peter A. Audano & Christine R. Beck, 2022. "Transposable element-mediated rearrangements are prevalent in human genomes," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    Full references (including those not matched with items on IDEAS)

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