Comparative genomic investigation of high-elevation adaptation in ectothermic snakes

Abstract

Several previous genomic studies have focused on adaptation to high elevations, but these investigations have been largely limited to endotherms. Snakes of the genus are endemic to the Tibetan plateau and therefore present an opportunity to study high-elevation adaptations in ectotherms. Here, we report the de novo assembly of the genome of a Tibetan hot-spring snake () and then compare its genome to the genomes of the other two species of , as well as to the genomes of two related species of snakes that occur at lower elevations. We identify 308 putative genes that appear to be under positive selection in We also identified genes with shared amino acid replacements in the high-elevation hot-spring snakes compared with snakes and lizards that live at low elevations, including the genes for proteins involved in DNA damage repair () and response to hypoxia (). Functional assays of the alleles reveal that the allele is more stable under UV radiation than is the ancestral allele found in low-elevation lizards and snakes. Functional assays of alleles suggest that the protein has lower transactivation activity than the low-elevation forms. Our analysis identifies some convergent genetic mechanisms in high-elevation adaptation between endotherms (based on studies of mammals) and ectotherms (based on our studies of ).

Whole-genome sequencing of wild Siberian musk deer (Moschus moschiferus) provides insights into its genetic features

“…It might be attributed possibly to musk deer adaptation to the cold and highaltitude environment (1000-4200 m) where food sources and odorants are limited and diffused slowly, and the interactions between odorants and receptors weakened [79,80]. Similar results have been obtained in some high plateau animal genome studies, such as avian [81], wild boars [82], hot-spring snake [83] and Tibetan chicken [84]. Moreover, we observed 12 PSGs and 2 PSGs were involved in DNA damage and retinoid X receptor binding categories, respectively.…”

Genetic Variation Related to High Elevation Adaptation Revealed by Common Garden Experiments in Pinus yunnanensis

“…Both cold stress and strong UV radiation result in the oxidative stress due to generation of reactive oxygen species (ROS), such as hydrogen peroxide, superoxide anion, and hydroxyl radical (Halliwell, 2007;Wang et al, 2010;Lidon and Ramalho, 2011). Previous studies revealed that the DNA repair and radiation responses pathways may contribute to highland adaptation of the Crucihimalaya himalaica (Qiao et al, 2016;Zhang et al, 2019), Tibetan highland barley (Zeng et al, 2015), Tibetan antelope (Ge et al, 2013), Tibetan chicken (Zhang et al, 2016), and Tibetan hot-spring snake (Li et al, 2018). In the present study, we found that many outlier genes are involved in response to UV, DNA repair, response to ROS, and membrane lipid metabolic process.…”

Genomic signature of ongoing alkaline adaptation in a Schizothoracine fish (Cyprinidae) inhabiting soda lake on the Tibetan Plateau

“…Large numbers of endemic Tibetan species had developed unique morphological, physiological or genetic features to tolerate harsh living conditions (Wen 2014). Recent studies employing genome-wide approaches mainly focused on the hypoxia and metabolic adaptation of Tibetan terrestrial animals, such as wild yak (Qiu et al 2012), ground tit (Qu et al 2013), and Tibetan snake (Li et al 2018). Nevertheless, the draft genomes of very few Tibetan aquatic wildlife are sequenced (Liu et al 2019;Yang et al 2019), the genomic basis of aquatic animals adaptation to harsh water environments on the Tibetan Plateau still remain largely unknown.…”