Biomedical subjects

Ofer Rog

Publications and source records attributed to Ofer Rog.

3 recordsLinked to original sources

PubMed2026

T2T genomes of Caenorhabditis nigoni and Caenorhabditis briggsae reveal divergence in satellite DNA abundance.

The two closely related nematode species, Caenorhabditis nigoni and Caenorhabditis briggsae, are commonly used to study the evolution of reproductive modes in animals, with the self-fertile C. briggsae and outcrossing C. nigoni sharing a common ancestor ∼3.5 million years ago. Earlier genomic analyses revealed that selfing Caenorhabditis species have smaller genomes and proposed that at least some gene loss in C. briggsae is adaptive. However, the incomplete C. nigoni reference genome has limited most comparative analyses to genic regions. Here, we leverage long-read sequencing to generate and annotate telomere-to-telomere (T2T) assemblies for the C. nigoni strain JU1422 and the C. briggsae strain AF16. This new 139 Mb C. nigoni genome resolves 57 gaps and 149 unassigned scaffolds from the previous genome assembly. A major driver of the size difference with the 107 Mb T2T C. briggsae genome is the abundance of satellite DNA, which accounts for 12.8 Mb (9.2%) in C. nigoni and only 3.2 Mb (3.0%) in C. briggsae Notably, the C. nigoni X Chromosome is 13.4 Mb larger than in the previous assembly, making it 60% larger than the C. briggsae X Chromosome compared with 18%-26% difference for the autosomes. We also document a surprising degree of plasticity in the ribosomal DNA, with the C. nigoni X Chromosome harboring a second 45S rDNA array that is absent in C. briggsae The hitherto undocumented divergence in the abundance of repetitive DNA elements makes the new genomes an invaluable resource for genomic analysis.

Journal Article↗

PubMed2026

T2T genomes of Caenorhabditis nigoni and Caenorhabditis briggsae reveals extensive loss of satellite DNA associated with self-fertilization.

The two closely related Caenorhabditis nematode species, C. nigoni and C. briggsae , are commonly used to study the evolution of reproductive modes in animals, with the self-fertile C. briggsae and outcrossing C. nigoni sharing a common ancestor ∼3.5 million years ago. Earlier genomic analyses of these species revealed genome shrinkage associated with selfing and proposed that at least some gene loss can be adaptive. However, the incomplete C. nigoni reference genome limited most comparative analyses to genic regions. Here, we leveraged long-read sequencing to generate a telomere-to-telomere (T2T) assembly for the C. nigoni strain JU1422 and the C. briggsae strain AF16. This new 139Mb C. nigoni genome resolved 57 gaps and 149 unassigned scaffolds from the previous genome assembly. Comparison with the 107Mb T2T C. briggsae genome reveals that the major driver of genome content differences are deletions to satellite DNA arrays, reflecting a loss of 9.6Mb. Interestingly, many of the differences are on the C. nigoni X chromosome, which is >13Mb larger than in the previous assembly. The transition to selfing was thus accompanied by a 37% reduction in the size of the sex chromosome compared to 16-21% shrinkage of the autosomes. We also document a surprising degree of plasticity in the ribosomal DNA, with the X chromosome harboring a second 45S rDNA array that is absent in C. briggsae . Our analysis reveals that obligatory outcrossing may play a major role in the maintenance of satellite DNA arrays.

Journal Article↗

PubMed2024

Diffusion within the synaptonemal complex can account for signal transduction along meiotic chromosomes.

Meiotic chromosomes efficiently transduce information along their length to regulate the distribution of genetic exchanges (crossovers). However, the mode of signal transduction remains unknown. A conserved protein interface called the synaptonemal complex forms between the parental chromosomes. The synaptonemal complex exhibits liquid-like behaviors, suggesting that the diffusion of signaling molecules along its length could coordinate crossover formation. Here, we directly test the feasibility of such a mechanism by tracking a component of the synaptonemal complex (SYP-3) and a conserved regulator of exchanges (ZHP-3) in live Caenorhabditis elegans gonads. While we find that both proteins diffuse within the synaptonemal complex, ZHP-3 diffuses 4- and 9-fold faster than SYP-3 before and after crossover designation, respectively. We use these measurements to parameterize a physical model for signal transduction. We find that ZHP-3, but not SYP-3, can explore the lengths of chromosomes on the time scale of crossover designation, consistent with a role in the spatial regulation of exchanges. Given the conservation of ZHP-3 paralogues across eukaryotes, we propose that diffusion along the synaptonemal complex may be a conserved mechanism of meiotic regulation. More broadly, our work explores how diffusion compartmentalized by condensates could regulate crucial chromosomal functions.

Synaptonemal Complex↗