Kotikalapudi, M. | bioRxiv Science

bioRxiv2026

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.

genomics↗

bioRxiv2025

Implications of Endogenous Small Regulatory RNAs on Gene Silencing in Mollusks

Mollusks are an abundant group of animals with many economically important members that are phylogenetically distinct from nearly all genetic model organisms. This study provides clade-wide evaluation of sRNA biogenesis pathways, with emphasis on the easter oyster, Crassostrea virginica. Understanding these molecules prescribes RNAi-based gene silencing approaches, benefiting genetic investigation and biotechnology. Similar to other animal groups, mollusks have conserved microRNAs (miRNAs) with some shared with ecdysozoans and deuterostomes; however, there was no evidence of an endogenous small-interfering RNA (siRNA) pathway. These results suggest that long double-stranded RNA (dsRNA)-based RNAi is not appropriate for gene silencing in Mollusks as well as other members of the broader Lophotrochozoan clade. The study also finds an abundance of piwi-interacting RNAs (piRNAs) in both soma and gonads. Differences are also found in piRNA biology. Many invertebrates exhibit somatic piRNAs; however, mollusk piRNAs appear to be restricted to a subset of cells, limiting the potential of piRNA-based RNAi. Further, individual animals also express a unique collection of piRNAs that seem to be only partially determined through inheritance from both parents. Together this work defines the RNAi mechanisms in mollusks, which represent 23% of animals, and provides insights into the phenotypic diversity seen in this group. Significance StatementThis study provides an extensive, clade-wide evaluation of small RNA (sRNA) biogenesis pathways in mollusks. Our findings reveal that, unlike ecdysozoans and deuterostomes, mollusks lack a functional siRNA pathway, which fundamentally changes expectations around RNA interference (RNAi) applications in Mollusca. Instead, we find the expected microRNAs and an assortment of piwi-interacting RNAs (piRNAs). We show that piRNA biology in mollusks is highly cell-type specific and genetically individualized. We further demonstrate that piRNA expression is likely linked to stem-like, quiescent cells, suggesting a critical role in genomic maintenance. This work offers insight into RNAi potential in mollusks, the second largest animal phylum, and has significant implications for both basic biology and applied sciences such as pest control and aquaculture.

evolutionary biology↗