Genome assembly of Gangetic dolphin ( Platanista gangetica ) reveals signature of regressive evolution

The Gangetic dolphin (Platanista gangetica), an endangered freshwater cetacean endemic to the Indian subcontinent, exhibits distinctive morphological and physiological adaptations to riverine habitats. Here, we present a high-quality draft genome assembly of P. gangetica. The assembled genome is 2.53 Gb in size, with a scaffold N50 of 116.1 Mb and a scaffold L50 of 9. Genome completeness assessed using BUSCO against the mammalia_odb10 dataset indicated a genome completeness of 97.73%. We predicted 27,983 protein-coding genes, and 19,616 were confidently mapped to eggNOG ortholog groups. Phylogenetic reconstruction placed the divergence of P. gangetica from the common bottlenose dolphin (Tursiops truncatus) at approximately 30.9 million years ago. Furthermore, we identified 66 positively selected genes in the P. gangetica genome possibly linked to key traits, including sensory adaptations such as vision loss and enhanced hearing, cardiovascular and metabolic regulation, limb modification, and cognitive function. Demographic inference revealed historical fluctuations in effective population size, with a marked decline during the Last Glacial Maximum (∼20–30 kya), likely driven by climatic shifts and habitat changes. This assembly represents a substantial improvement over previously available genomes within the Platanista genus and provides an essential resource for advancing our understanding of freshwater cetacean evolution and forms a critical foundation for population genomic studies to inform conservation and management strategies.