De novo assembly and annotation of Asiatic lion (Panthera leo persica) genome

Abstract

We report the first draft of the whole genome assembly of a male Asiatic lion, Atul and whole transcriptomes of five Asiatic lion individuals. Evaluation of genetic diversity placed the Asiatic lion in the lowest bracket of genomic diversity index highlighting the gravity of its conservation status. Comparative analysis with other felids and mammalian genomes unraveled the evolutionary history of Asiatic lion and its position among other felids. The genome is estimated to be 2.3 Gb (Gigabase) long with 62X sequence coverage and is found to have 20,543 protein-coding genes. About 2.66% of the genome is covered by simple sequence repeats (SSRs) and 0.4% is estimated to have segmental duplications. Comparison with seven well annotated genomes indicates the presence of 6,295 single copy orthologs, 4 co-orthologs, 21 paralogs uniquely present in Asiatic lion and 8,024 other orthologs. Assessment of male and female transcriptomes gave a list of genes specifically expressed in the male. Our genomic analyses provide candidates for phenotypes characteristic to felids and lion, inviting further confirmation of their contribution through population genetic studies. An Asiatic lion-specific expansion is detected in the Cysteine Dioxygenase-I (CDO-I) family that is responsible for taurine biosynthesis in cats. Wilms tumor-associated protein (WT1) family, a non-Y chromosome genetic factor underlying male-sex determination and differentiation is found to have undergone expansion, interestingly like that of the human genome. Another protein family, translation machinery-associated protein 7 (TMA7) that has undergone expansion in humans, also expanded in Asiatic lion and can be further investigated as a candidate responsible for mane in lions because of its role in hair follicle morphogenesis.