Comparative analysis of corrected tiger genome provides clues to their neuronal evolution

Abstract

15The availability of completed and draft genome assemblies of tiger, leopard, and other felids 16 provides an opportunity to gain comparative insights on their unique evolutionary adaptations. 17However, genome-wide comparative analyses are very sensitive to errors in genome sequences and 18 thus require accurate genomic assemblies for reliable evolutionary insights. In this study, while 19 analyzing the tiger genome, we found almost one million erroneous substitutions in the coding and 20 non-coding region of the genome affecting 4,472 genes, hence, biasing the current understanding of 21 tiger evolution. Moreover, these errors produced several misleading observations in previous 22 studies. Thus, to gain insights into the tiger evolution, we corrected the erroneous bases in the 23 genome assembly and gene set of tiger, which was also validated by resequencing of a Bengal tiger 24 genome and transcriptome. A comprehensive evolutionary analysis was performed using 10,920 25 orthologs from nine mammalian species including the corrected gene sets of tiger and leopard, and 26 using five different methods at three hierarchical levels i.e. felids, Panthera, and tiger. The unique 27 genetic changes in tiger revealed that the genes showing the signatures of adaptation in tiger were 28 enriched in development and neuronal functioning. Specifically, the genes belonging to Notch 29 signalling pathway, which is among the most conserved pathways involved in embryonic and 30 neuronal development, were found to be significantly diverged in tiger in comparison to the other 31 mammals. Our findings suggest the role of adaptive evolution in neuronal functions and 32 development processes, which correlates well with the presence of exceptional traits such as 33 sensory perception, strong neuro-muscular coordination, and hypercarnivorous behavior in tiger. 35correction.The advancement in genomic sequencing technologies has provided a tremendous impetus for 38 studying the molecular and genetic basis of adaptive evolution. A recent accomplishment is the 39 genome sequencing of tiger, the largest felid and a model species to identify the molecular 40 adaptations to hypercarnivory 1-3 . Tiger is a prominent member of the big cats, which are the 41 topmost predators in the food chain, and play a key role in the ecological niche 4 . It is a solitary 42 animal with extraordinary muscle strength and predatory capabilities 2,3 . The tiger genome 43 sequencing revealed several molecular signatures of selection, particularly the rapid evolution in 44 genes related to muscle strength, energy metabolism, and sensory nerves 1 . Similar studies in felids, 45including the tiger, had also shown strong positive selection in genes related to sensory perception 46 and neurotransmitters 5 . 47While genome sequences are indispensable for comparative genome-wide evolutionary studies, 48 quality of a genome is crucial for such analyses and in deriving reliable inferences [6][7][8][9] . The quality of a 49 genomic assembly is commonly assessed based on t...