Salve, B. G.; H, S.; Vijay, N.

Background Genomic rearrangements, including segmental deletions, duplications, translocations, and inversions of DNA segments, can contribute to gene losses, thereby reshaping genome architecture and potentially resulting in functional consequences. In squamates, karyotypic evolution mainly involves chromosome number reduction through fusions and microchromosome to macrochromosome translocations, although fissions have also contributed to diversification in several lineages. Despite these dynamics, the evolutionary processes and underlying genetic mechanisms driving chromosomal rearrangements and associated gene losses in squamates remain poorly understood. Results In this study, we analysed chromosome/scaffold-level assemblies of 265 squamates, corroborated by short-read, long-read, and transcriptomic data. We found multiple lines of evidence for the absence of 53 genes in the squamate lineage. Notably, increased genomic rearrangement activity appears to be associated with the squamate-specific loss of these genes, including IL34, STAP1, LAPTM5, and TNIP2, which are key regulators of macrophage activation and polarisation. Most of the missing genes were intact in tuatara and other vertebrate species. Furthermore, we find that many of the genes missing from squamates are organised in syntenic clusters and are involved in essential immune functions, raising important questions about whether their absence in squamates reflects true gene loss or simply results from incomplete assemblies. Conclusions Together, our comparative genomic analyses highlight that the loss of crucial genes in squamate lineages has occurred primarily through inter- and intrachromosomal rearrangements, including segmental deletions. These findings offer insights into the evolutionary loss of genes involved in macrophage differentiation and inform the development of novel pharmaceutical approaches for modulating immune responses.