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Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats

Author

Listed:
  • Ana Paula Zotta Mota

    (Université Côte d’Azur, CNRS)

  • Georgios D. Koutsovoulos

    (Université Côte d’Azur, CNRS)

  • Laetitia Perfus-Barbeoch

    (Université Côte d’Azur, CNRS)

  • Evelin Despot-Slade

    (Ruđer Bošković Institute)

  • Karine Labadie

    (Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay)

  • Jean-Marc Aury

    (Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay)

  • Karine Robbe-Sermesant

    (Université Côte d’Azur, CNRS)

  • Marc Bailly-Bechet

    (Université Côte d’Azur, CNRS)

  • Caroline Belser

    (Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay)

  • Arthur Péré

    (Université Côte d’Azur, CNRS)

  • Corinne Rancurel

    (Université Côte d’Azur, CNRS)

  • Djampa K. Kozlowski

    (Université Côte d’Azur, CNRS
    Université Côte d’Azur, Center of Modeling, Simulation, and Interactions)

  • Rahim Hassanaly-Goulamhoussen

    (Université Côte d’Azur, CNRS)

  • Martine Rocha

    (Université Côte d’Azur, CNRS)

  • Benjamin Noel

    (Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay)

  • Nevenka Meštrović

    (Ruđer Bošković Institute)

  • Patrick Wincker

    (Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay)

  • Etienne G. J. Danchin

    (Université Côte d’Azur, CNRS)

Abstract

Using long-read sequencing, we assembled and unzipped the polyploid genomes of Meloidogyne incognita, M. javanica and M. arenaria, three of the most devastating plant-parasitic nematodes. We found the canonical nematode telomeric repeat to be missing in these and other Meloidogyne genomes. In addition, we find no evidence for the enzyme telomerase or for orthologs of C. elegans telomere-associated proteins, suggesting alternative lengthening of telomeres. Instead, analyzing our assembled genomes, we identify species-specific composite repeats enriched mostly at one extremity of contigs. These repeats are G-rich, oriented, and transcribed, similarly to canonical telomeric repeats. We confirm them as telomeric using fluorescent in situ hybridization. These repeats are mostly found at one single end of chromosomes in these species. The discovery of unusual and specific complex telomeric repeats opens a plethora of perspectives and highlights the evolutionary diversity of telomeres despite their central roles in senescence, aging, and chromosome integrity.

Suggested Citation

  • Ana Paula Zotta Mota & Georgios D. Koutsovoulos & Laetitia Perfus-Barbeoch & Evelin Despot-Slade & Karine Labadie & Jean-Marc Aury & Karine Robbe-Sermesant & Marc Bailly-Bechet & Caroline Belser & Art, 2024. "Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-44914-y
    DOI: 10.1038/s41467-024-44914-y
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    References listed on IDEAS

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    1. Sabrina Dietz & Miguel Vasconcelos Almeida & Emily Nischwitz & Jan Schreier & Nikenza Viceconte & Albert Fradera-Sola & Christian Renz & Alejandro Ceron-Noriega & Helle D. Ulrich & Dennis Kappei & Ren, 2021. "The double-stranded DNA-binding proteins TEBP-1 and TEBP-2 form a telomeric complex with POT-1," Nature Communications, Nature, vol. 12(1), pages 1-20, December.
    2. Ying Chen & Fan Nie & Shang-Qian Xie & Ying-Feng Zheng & Qi Dai & Thomas Bray & Yao-Xin Wang & Jian-Feng Xing & Zhi-Jian Huang & De-Peng Wang & Li-Juan He & Feng Luo & Jian-Xin Wang & Yi-Zhi Liu & Chu, 2021. "Efficient assembly of nanopore reads via highly accurate and intact error correction," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    3. Dadong Dai & Chuanshuai Xie & Yayi Zhou & Dexin Bo & Shurong Zhang & Shengqiang Mao & Yucheng Liao & Simeng Cui & Zhaolu Zhu & Xueyu Wang & Fanling Li & Donghai Peng & Jinshui Zheng & Ming Sun, 2023. "Unzipped chromosome-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
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