Deciphering the molecular basis of incompatibility between a novel speciation gene pair in nematode species hybrids

Reproductive barriers, particularly hybrid incompatibility (HI), which is characterized by reduced fitness such as lethality or sterility, effectively impede gene flow between closely related species or within populations, thereby playing a crucial role in speciation. A thorough understanding of HI mechanisms not only deepens our knowledge of the speciation process but also offers significant benefits to human society. Identifying the specific genes involved in HI is challenging because these genes often evolve rapidly, and their detrimental effects typically arise only in hybrids as "by-products" through
negative epistatic interactions between at least two genes, as explained by the Bateson-Dobzhansky-Muller (DM) model. Progress in pinpointing these genes and characterizing their molecular interactions has been significantly hindered by the lack of advanced genetic mapping strategies and suitable model systems.
Our laboratory has employed the nematode species pair Caenorhabditis briggsae and C. nigoni, both closely related to the model organism C. elegans, to study HI. We have developed versatile resources using cutting-edge technologies, which have allowed us to recently identified the first nematode DM incompatible gene pair, Cni-neib-1 and Cbrshls-1. Cni-neib-1, part of a recently evolved C. nigoni-specific F-box gene family, specifically deactivates an essential C. briggsae gene, Cbr-shls-1, but not its C. nigoni ortholog, Cni-shls-1. This provides unprecedented insight into how a rapidly evolving
gene, involved in protein degradation, from one species can induce hybrid lethality, possibly through mistargeting an essential gene in another. However, the precise mechanism by which Cni-neib-1 specifically depletes Cbr-shls-1 activity to induce embryonic lethality remains elusive, and the evolutionary history of Cni-neib-1 and its gene family in C. nigoni is largely unknown.
To address these questions, we propose to first assess interactions between CniNEIB-1 and Cbr-SHLS-1/Cni-SHLS-1 through various protein-protein interaction assays. Next, we will pinpoint key amino acid changes that affect the differential
degradation of the two SHLS-1 proteins by Cni-NEIB-1. Third, we will profile the expression of Cni-NEIB-1 to gain a detailed understanding of how it induces hybrid embryonic lethality. Fourth, by examining the polymorphism of the Cni-neib-1 gene family across C. nigoni wild isolates, we will investigate the evolutionary dynamics of the F-box gene family. Finally, we will evaluate the potential application of Cni-neib-1 as a negative selection marker in C. briggsae.
This proposed research will significantly enhance our understanding of the molecular basis of HI gene interactions that cause detrimental effects, offering invaluable insights into the functioning of negative epistatic interactions in hybrids.