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ContScout: sensitive detection and removal of contamination from annotated genomes

Author

Listed:
  • Balázs Bálint

    (HUN-REN Biological Research Centre, Szeged)

  • Zsolt Merényi

    (HUN-REN Biological Research Centre, Szeged)

  • Botond Hegedüs

    (HUN-REN Biological Research Centre, Szeged)

  • Igor V. Grigoriev

    (Lawrence Berkeley National Laboratory
    University of California Berkeley)

  • Zhihao Hou

    (HUN-REN Biological Research Centre, Szeged
    University of Szeged)

  • Csenge Földi

    (HUN-REN Biological Research Centre, Szeged
    University of Szeged)

  • László G. Nagy

    (HUN-REN Biological Research Centre, Szeged)

Abstract

Contamination of genomes is an increasingly recognized problem affecting several downstream applications, from comparative evolutionary genomics to metagenomics. Here we introduce ContScout, a precise tool for eliminating foreign sequences from annotated genomes. It achieves high specificity and sensitivity on synthetic benchmark data even when the contaminant is a closely related species, outperforms competing tools, and can distinguish horizontal gene transfer from contamination. A screen of 844 eukaryotic genomes for contamination identified bacteria as the most common source, followed by fungi and plants. Furthermore, we show that contaminants in ancestral genome reconstructions lead to erroneous early origins of genes and inflate gene loss rates, leading to a false notion of complex ancestral genomes. Taken together, we offer here a tool for sensitive removal of foreign proteins, identify and remove contaminants from diverse eukaryotic genomes and evaluate their impact on phylogenomic analyses.

Suggested Citation

  • Balázs Bálint & Zsolt Merényi & Botond Hegedüs & Igor V. Grigoriev & Zhihao Hou & Csenge Földi & László G. Nagy, 2024. "ContScout: sensitive detection and removal of contamination from annotated genomes," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-45024-5
    DOI: 10.1038/s41467-024-45024-5
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    References listed on IDEAS

    as
    1. László G. Nagy & Robin A. Ohm & Gábor M. Kovács & Dimitrios Floudas & Robert Riley & Attila Gácser & Mátyás Sipiczki & John M. Davis & Sharon L. Doty & G Sybren de Hoog & B. Franz Lang & Joseph W. Spa, 2014. "Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts," Nature Communications, Nature, vol. 5(1), pages 1-8, December.
    2. Xueyan Li & Dingding Fan & Wei Zhang & Guichun Liu & Lu Zhang & Li Zhao & Xiaodong Fang & Lei Chen & Yang Dong & Yuan Chen & Yun Ding & Ruoping Zhao & Mingji Feng & Yabing Zhu & Yue Feng & Xuanting Ji, 2015. "Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies," Nature Communications, Nature, vol. 6(1), pages 1-10, November.
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