Unzipped assemblies of polyploid root-knot nematode genomes reveal new kinds of unilateral composite telomeric repeats

Abstract Telomeres play central roles in senescence, aging and chromosome integrity. Using ONT long read sequencing we have assembled the genomes of Meloidogyne incognita , M. javanica and M. arenaria , the three most devastating plant-parasitic nematodes at unparalleled contiguity. The telomeric repeat (TTAGGC)n, evolutionarily conserved in nematodes, was not found in these genomes. Furthermore, no evidence for a telomerase enzyme or for orthologs of C. elegans telomere-associated proteins could be found. Instead, we identified species-specific composite repeats mostly present at one end of contigs. These repeats were G-rich, oriented and transcribed, similarly to known telomeric repeats. Using FISH we confirmed these repeats were present at one single end of M. incognita chromosomes. The discovery of a new kind of telomeric repeat in these species highlights the evolutionary diversity of chromosome protection systems despite their central roles and opens new perspectives towards the development of more specific control methods against these pests.