Multiple losses of ecdysone receptor genes in nematodes: an alternative evolutionary scenario of molting regulation

Molting is a hallmark feature of ecdysozoans, including arthropods, tardigrades, and nematodes. Ecdysone hormones play a crucial role in regulating the molting process of different ecdysozoan taxa. Interestingly, despite this highly conserved function of ecdysone, the model nematode Caenorhabditis elegans has lost the ecdysone receptor (ECR) genes and their molting appears to be ecdysone-independent. The loss of ecr has only been reported in Caenorhabditis within ecdysozoans, and the evolutionary background behind this loss has remained enigmatic. Here, we show that loss of ecr is not exceptional in Caenorhabditis, but has occurred at least three times in Rhabditina and Tylenchina nematodes. Our genome-wide analysis of 160 nematode species revealed multiple losses of ecr and its typical heterodimer partner usp during nematode evolution. Furthermore, using transcriptomic, pharmacological, and in silico/ in vivo protein interaction analyses, we identified two factors that potentially underlie and buffer the loss of ECR gene/function: (1) molting regulation by an alternative nuclear receptor HR3 (NHR-23) and (2) a lineage-specific expansion of nuclear receptors in the ecr-deficient taxa. Taken together, this study shows how key regulators of ecdysozoan molting can be altered during evolution. We propose a novel scenario for the evolution of molting regulation in nematodes.