How to Make an Elephant

Elephants are large and charismatic land mammals that have recently garnered attention for their potential cancer suppressive phenotype. Genomic resources from this group are essential for understanding the mechanisms underlying elephant-specific traits as well as supporting efforts in their conservation. We report here the first Asian elephant (Elephas maximus) genome assembly, an improved African bush elephant (Loxodonta africana) assembly, as well as the whole genome sequence (WGS) of an additional bush elephant. This data was combined with publicly available WGS data of 15 individuals from five species of living and extinct elephant and the whole genomes of 10 other mammals. We analyzed the evolution of TP53 in Asian and African elephants and found that the expansion of TP53 retrogenes occurred in a common ancestor of both species. Across living and extinct species, we find a lack of correlation between TP53 copy number and body size, and that both demographic and selective forces may have controlled the fate of many TP53 retrogenes. Results from genome-wide selection scans suggested positive selection in genetic regions controlling many traits popularly associated with elephants, including tusk development, memory, as well as somatic maintenance, providing further evidence that elephants are good potential models for cancer research.