Underground threat: major discovery of parasitic worm chromosomes

Nematodes are a group containing hundreds of thousands of species of worms, including dangerous plant and animal parasites. Among plant parasitic worms, root-knot nematodes are public enemy number 1. Present all over the globe, they destroy over 10% of the world's agricultural production, by attacking the roots of over 4,000 different plants.

Since 2007, a multidisciplinary team of researchers from Université Côte d'Azur, INRAE and CNRS has been decoding and analyzing the genome of these parasitic rootworms. This work, focused on identifying genetic singularities, has recently reached a major new milestone.
In fact, the meticulous analysis of these genomes has shown that root-knot nematode chromosomes begin and end in a way that is completely unprecedented in the living world. Our chromosomes, like those of animals, plants and fungi, are protected at their ends by special regions called telomeres, which act as beacons. Their shortening during cell division causes aging, and their disruption is responsible for many cancers.

Generally speaking, telomeres are composed of a short, highly conserved DNA repeat motif forming complexes with proteins and RNA at the ends of chromosomes. However, those of root-knot nematodes are completely new. The DNA of their telomeres has a complex structure, composed of a unique tangle of repeated motifs, with no similarity to motifs found in other forms of life. Moreover, proteins classically associated with telomeres in other nematode and animal species are also lacking in the genomes of these parasitic worms.

The implications of this discovery are far-reaching. Firstly, it reveals regions at the ends of chromosomes that are unique in their complexity and heterogeneity. These could constitute new telomere structures with no equivalent to date in the living world, raising numerous questions as to their origin, function and implications for genome dynamics and stability. Moreover, this singularity represents a possible weak link to be exploited for more targeted control of these crop-destroying worms. Disrupting telomere function could have an impact on worm survival. And since the DNA sequences of these telomeres are unique to them, precisely targeting them would be unlikely to impact other species.
Before this can be achieved, a great deal of research is still required, in particular to identify the proteins and RNAs interacting at telomere level and decipher how they function.

Implications for other parasitic worms?

Interestingly, their analyses showed that simple DNA motifs and telomere-associated proteins are also found in at least two families of parasitic worms.They are also found in at least 2 families of worms that are parasitic on humans and farm or domestic animals (horses, goats and sheep), responsible in particular for anguillosis and trichinellosis.

Reference

Mota, A.P.Z., Koutsovoulos, G.D., Perfus-Barbeoch, L. et al. Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats. Nat Commun 15, 773 (2024). https://doi.org/10.1038/s41467-024-44914-y

Scientific contact

Etienne Danchin - etienne.danchin@inrae.fr
Institut Sophia Agrobiotech (ISA) research unit
Plant Health and Environment (SPE) Scientific Department
INRAE Provence-Alpes-Côte d'Azur Center