Genomic signatures of sensory adaptation and evolution in pangolins

Abstract

Background Pangolin is one of the most endangered mammals with many peculiar characteristics, yet the understanding of its sensory systems is still superficial. Studying the genomic basis of adaptation and evolution of pangolin’s sensory system is expected to provide further potential assistance for their conservation in the future. Results In this study, we performed a comprehensive comparative genomic analysis to explore the signature of sensory adaptation and evolution in pangolins. By comparing with the aardvark, Cape golden mole, and short-beaked echidna, 124 and 152 expanded gene families were detected in the genome of the Chinese and Malayan pangolins, respectively. The enrichment analyses showed olfactory-related genomic convergence among five concerned mammals. We found 769 and 733 intact OR genes, and 704 and 475 OR pseudogenes in the Chinese and Malayan pangolin species, respectively. Compared to other mammals, far more intact members of OR6 and OR14 were identified in pangolins, particularly for four genes with large copy numbers ( OR6C2 , OR14A2 , OR14C36 , and OR14L1 ). On the genome-wide scale, 1,523, 1,887, 1,110, and 2,732 genes were detected under positive selection (PSGs), intensified selection (ISGs), rapid evolution (REGs), and relaxed selection (RSGs) in pangolins. GO terms associated with visual perception were enriched in PSGs, ISGs, and REGs. Those related to rhythm and sound perception were enriched in both ISGs and REGs, ear development and morphogenesis were enriched in ISGs, and mechanical stimulus and temperature adaptation were enriched in RSGs. The convergence of two vision-related PSGs ( OPN4 and ATXN 7), with more than one parallel substituted site, was detected among five concerned mammals. Additionally, the absence of intact genes of PKD1L3 , PKD2L1 , and TAS1R2 and just six single-copy TAS2Rs ( TAS2R1 , TAS2R4 , TAS2R7 , TAS2R38 , TAS2R40 , and TAS2R46 ) were found in pangolins. Interestingly, we found two large insertions in TAS1R3 , distributed in the N-terminal ectodomain, just in pangolins. Conclusions We found new features related to the adaptation and evolution of pangolin-specific sensory characteristics across the genome. These are expected to provide valuable and useful genome-wide genetic information for the future breeding and conservation of pangolins. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-024-11063-x.