Abstract
The Himalayan Arc is recognized as a global biodiversity hotspot. Among its numerous cryptic and undiscovered organisms, this composite high-mountain ecosystem harbors many taxa with adaptations to life in high elevations. However, evolutionary patterns and genomic features have been relatively rarely studied in Himalayan vertebrates. Here, we provide the first well-annotated transcriptome of a Greater Himalayan reptile species, the Ladakh Ground skink Asymblepharus ladacensis (Squamata: Scincidae). Based on tissues from the brain, an embryonic disc, and pooled organ material, using pair-end Illumina NextSeq 500 RNAseq, we assembled ~77,000 transcripts, which were annotated using seven functional databases. We tested ~1600 genes, known to be under positive selection in anurans and reptiles adapted to high elevations, and potentially detected positive selection for 114 of these genes in Asymblepharus. Even though the strength of these results is limited due to the single-animal approach, our transcriptome resource may be valuable data for further studies on squamate reptile evolution in the Himalayas as a hotspot of biodiversity.
Highlights
The Himalayan arc represents one of the world’s most important faunal and floral hotspots with high species diversity and endemism [1], which result from the Tertiary orogeny of this mountain chain, its complex topography as well as its great climatic heterogeneity and isolation
To allow future studies in evolutionary biology at a genomic level and to generally provide sufficient and relevant data for Himalayan reptiles, in the present study, we have generated a new genomics data set based on RNAseq for a scincid species from the Greater Himalayas
Among the 143 PSGs previously reported for the high-elevation lineage of the toadheaded agama Phrynocephalus vlangalii [15], we found ten genes to be likewise under positive selection in Asymblepharus based on all three tests that we performed
Summary
The Himalayan arc represents one of the world’s most important faunal and floral hotspots with high species diversity and endemism [1], which result from the Tertiary orogeny of this mountain chain, its complex topography as well as its great climatic heterogeneity and isolation. Recent advances in high-throughput sequencing technologies have led to a growing number of genomic studies that address the molecular basis of high-altitude adaptation, some of them focused on reptiles [13,14,15] Such data have been scarce in non-model species of the Greater Himalayas (but see [16]). To allow future studies in evolutionary biology at a genomic level and to generally provide sufficient and relevant data for Himalayan reptiles, in the present study, we have generated a new genomics data set based on RNAseq for a scincid species from the Greater Himalayas Using these data, we aimed to identify genes known to play roles in adaptation of terrestrial ectothermic vertebrates to high elevations. Since exposure to oxidative stress can affect the physiology during early development [20] and in oxygen-sensitive organs [21,22], such as the nerve system, we focused on embryonic and brain tissue samples
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