De novo Assembly, Annotation, and Analysis of Transcriptome Data of the Ladakh Ground Skink Provide Genetic Information on High-Altitude Adaptation

Genes

Chitra Bahadur Baniya¹  Lars Podsiadlowski²  Sylvia Hofmann³  Matthias Stöck⁴ 

[1] Central Department of Botany, Tribhuvan University, Kirtipur 44618, Nepal;Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, D-53113 Bonn, Germany;Centre of Taxonomy and Evolutionary Research, Zoological Research Museum Alexander Koenig, D-53113 Bonn, Germany;Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, D-12587 Berlin, Germany;

关键词: adaptation;    evolution;    genomic;    high elevation;    Himalayas;    Scincidae;   

DOI  :  10.3390/genes12091423

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown