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

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, Arthur Péré, Corinne Rancurel, Djampa K. Kozlowski, Rahim Hassanaly-Goulamhoussen, Martine Rocha, Benjamin Noel, Nevenka Meštrović, Patrick Wincker and Etienne G. J. Danchin ()
Additional contact information
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
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

Nature Communications, 2024, vol. 15, issue 1, 1-18

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-44914-y

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