Long read genome assemblies of polyploid root-knot nematodes revealed unusual and specific chromosome ends

Long read genome assemblies of polyploid root-knot nematodes.

Long read genome assemblies of polyploid root-knot nematodes revealed unusual and specific chromosome ends

06 October 2023

Sophia Antipolis - INRAE PACA - A010

As part of the ISA scientific event to be held on Friday, October 06, 2023 at 11 a.m. in room A010, Ana Zotta Mota, a post-doctoral fellow in the GAME team, will present some of her work.

Abstract :

Assembling the genomes of polyploid hybrid species is a challenge, due to variable degrees of divergence between the sub-genome copies. To resolve the complex genomes of species from the genus Meloidogyne, we used Oxford Nanopore long read sequencing technology. We were able to sequence and assemble the whole genomes of three of the most devastating plant-parasitic nematodes. This allowed resolving and assembling highly repetitive regions of the M. incognita, M. arenaria and M. javanica genomes for the first time. Thanks to this new assembly, we could investigate how chromosomes start and end in these species.

Against all odds, we could find neither the telomerase genes nor the canonical telomeric repeat sequence of C. elegans. Instead, at the end of some assembled contigs, we found a composite G-rich repeat, varying in sequence from one species to another. Similar to known telomeric sequences, the repeat is predicted to form G-quadruplex structures and is stranded. Analysis of RNA-seq data revealed the repeat is transcribed in the three species, similar to TERRA in species with canonical telomeres.

We compared this new repetitive sequence against all nematode species with a sequenced genome, and apart from partial matches in closely related Meloidogyne species, the repeat was absent from the rest of the nematodes. The repeat also shows no similarity with any known transposable element and is more likely to represent satellite DNA.

Using fluorescent in-situ hybridization we confirmed the repeat had a telomeric localization but only at one extremity of most of the chromosomes in M. incognita. The presence of TERRA-like transcripts, the predicted ability of the repeats to form G-quaruplex structures and the absence of similarity with transposable elements suggests an ALT (alternative lengthening of telomeres) mechanism for the multiplication of telomeres in these species.

The discovery of new kinds of telomeric repeats opens many perspectives towards understanding how genome stability and plasticity are controlled in these species

The seminar can also be followed via Zoom at the following link:

Contact: animisa@inrae.fr

Modification date : 05 October 2023 | Publication date : 03 October 2023