Genome-wide analysis of the cpp gene family in Musca domestica L. (Diptera: Muscidae)

Musca domestica L. is a ubiquitous synanthropic insect species and a recognized mechanical vector of various pathogens. Despite its public health significance and ecological adaptability, the molecular mechanisms underlying its physiological resilience remain poorly understood. Cysteine-rich Polycomb-like Proteins (CPPs), a conserved family of transcription factors first identified in plants, are increasingly recognized for their roles in regulating cell cycle progression, developmental transitions, and responses to environmental stress across eukaryotic taxa. In this study, we conducted the first comprehensive genome-wide identification and analysis of the CPP gene family in M. domestica, alongside a comparative analysis across 16 additional dipteran species of medical, ecological, and model organism relevance. Using a combination of bioinformatics approaches, we identified 21 CPP genes and analyzed their structural organization, conserved motifs, biophysical properties, subcellular localization, and phylogenetic relationships. Our results reveal two major evolutionary clusters within the family, distinguished by the number of CXC domains, and suggest functional divergence among paralogous members. Most CPP proteins exhibited nuclear localization signals and hydrophilic properties, consistent with their presumed regulatory functions. In M. domestica, protein–protein interaction predictions further highlight the potential involvement of CPPs in gene regulatory networks associated with stress tolerance and developmental control. These findings establish a foundational reference for functional genomics studies on CPP genes in dipterans and open new avenues for exploring transcriptional regulation mechanisms in insect adaptation and vector biology.