Abstract
The availability of completed and draft genome assemblies of tiger, leopard, and other felids provides an opportunity to gain comparative insights on their unique evolutionary adaptations. However, genome-wide comparative analyses are susceptible to errors in genome sequences and thus require accurate genome assemblies for reliable evolutionary insights. In this study, while analyzing the tiger genome, we found almost one million erroneous substitutions in the coding and non-coding region of the genome affecting 4,472 genes, hence, biasing the current understanding of tiger evolution. Moreover, these errors produced several misleading observations in previous studies. Thus, to gain insights into the tiger evolution, we corrected the erroneous bases in the genome assembly and gene set of tiger using ‘SeqBug’ approach developed in this study. We sequenced the first Bengal tiger genome and transcriptome from India to validate these corrections. A comprehensive evolutionary analysis was performed using 10,920 orthologs from nine mammalian species including the corrected gene sets of tiger and leopard and using five different methods at three hierarchical levels, i.e. felids, Panthera, and tiger. The unique genetic changes in tiger revealed that the genes showing signatures of adaptation in tiger were enriched in development and neuronal functioning. Specifically, the genes belonging to the Notch signalling pathway, which is among the most conserved pathways involved in embryonic and neuronal development, were found to have significantly diverged in tiger in comparison to the other mammals. Our findings suggest the role of adaptive evolution in neuronal functions and development processes, which correlates well with the presence of exceptional traits such as sensory perception, strong neuro-muscular coordination, and hypercarnivorous behaviour in tiger.
Highlights
The availability of completed and draft genome assemblies of tiger, leopard, and other felids provides an opportunity to gain comparative insights on their unique evolutionary adaptations
Our analysis revealed that eight of the nine substitutions in this gene were due to the single nucleotide errors in the publicly available genome assembly of tiger, which produced the incorrect result shown in Supplementary Fig. S2
While using the publicly available genome sequence assembly of tiger, we found that the assembly consisted of several errors, which led to several incorrect interpretations in recent other studies
Summary
The availability of completed and draft genome assemblies of tiger, leopard, and other felids provides an opportunity to gain comparative insights on their unique evolutionary adaptations. To gain insights into the tiger evolution, we corrected the erroneous bases in the genome assembly and gene set of tiger using ‘SeqBug’ approach developed in this study. The quality of a genome assembly is commonly assessed based on the N50 values of contigs and scaffolds and does not account for single nucleotide errors, which are mainly introduced by the read error correction tools or de novo assemblers[12,13,14,15,16,17] Such sequence errors in genomes can produce drastically misleading results in comparative genomics and evolutionary studies[7,8,11]. Using the corrected genome assembly and gene set of tiger, we carried out a comparative genomic analysis of tiger with several other mammalian species, which provided novel insights into the adaptive evolution of the lineage leading to tiger
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