engleski

The strange chromosome ends of root-knot nematodes

Advances in genome sequencing technologies have allowed progressing in the assembly of various nematode genomes several of which now reach or approach chromosome-level resolution. This allows studying genome and chromosome structures at unprecedented scales, including chromosome ends. Using a combination of ONT long reads, Illumina short reads and Hi-C chromatin contact information we have improved genome completeness and contiguity for the root-knot nematodes Meloidogyne incognita, M. javanica and M. arenaria. For instance, previous versions of these genomes were assembled in >10, 000 fragments with N50 values of dozens of kilobases. New genome assemblies now yield hundreds of fragments with N50 values of several megabases. We investigated whether telomere motif repeats could be found at the end of some contigs, thus representing chromosome ends. To our surprise, the canonical (TTAGGC)n telomere motif arrays found at the ends of C. elegans and other nematode chromosomes were not found at contig ends in these root-knot nematode genomes. Further search for any 6 to 12-mers repeated at the ends of contigs failed to identify any clear repeated motif. Because no telomeric repeat could be identified, we investigated whether the telomerase enzyme, responsible for the addition of telomere repeats at chromosome ends was present in these genomes. Consistent with the absence of telomere repeat neither the telomerase enzyme nor telomerase reverse transcriptase domain were present. A search on 63 nematode proteomes showed the telomerase domain was otherwise widely conserved across the nematode tree of life. Besides the genus Meloidogyne in which the telomerase was completely absent (despite 10 species searched) this domain was also not found in Pristionchus and Strongyloides species. Interestingly, the telomerase domain was found in Pratylenchus, suggesting a loss specific to the Meloidogyne genus among Tylenchomorpha. A more comprehensive search for enriched degenerated motifs at the extremities of contigs, allowed identifying a ca. 300bp complex motif repeated in arrays at ca. 50 contig ends. This motif is conserved and repeated at contig ends in at least all clade I root-knot nematodes surveyed so far. We designed probes and performed fluorescent in situ hybridization in M. incognita cells and confirmed this complex motif was present at one end of most chromosomes. These findings suggest unusual and complex chromosome ends in the root-knot nematodes.

Nematodes ; Meloidogyne ; Genome assembly ; Telomeres

Održano i kratko izlaganje - Poster flash presentation (Etienne G.J. Danchin).