An annotated chromosome-level genome for the red-fronted brown lemur (Eulemur rufifrons) sheds light on brown lemur evolution.

The red-fronted brown lemur (Eulemur rufifrons) is an important species to the function of Madagascar's ecosystems, contributing to critical ecological processes such as seed dispersal. Given its ecological, as well as cultural, importance, genomic resources for E. rufifrons are valuable for understanding evolutionary history and informing conservation strategies. In this study, we present an annotated chromosome-level genome assembly for E. rufifrons, generated using PacBio HiFi long reads and Hi-C proximity ligation data, and demonstrate its utility for understanding patterns of divergence among members of the genus Eulemur. The chromosome-level genome size is 2.41 Gb, and it exhibits high-quality metrics including a scaffold N50 of 100.8 Mb and a BUSCO completeness score of 95.3%. Comparative analyses reveal remarkable synteny between our E. rufifrons assembly and the previously published Eulemur mongoz genome, despite an estimated divergence of ∼4 million years. Phylogenetic and network analyses identify pervasive signals of gene flow across Eulemur, with our focal individual showing unexpected genomic affinities to Eulemur rufus, highlighting the need for methods that account for reticulation in phylogenomic studies. Overall, this genome for E. rufifrons provides a valuable resource for exploring lemur evolutionary history, genomic divergence, and patterns of hybridization. Future research should leverage chromosome-level assemblies to investigate gene flow, adaptive introgression, and regions under selection, advancing our understanding of lemur diversity and informing conservation strategies for these imperiled primates.