Basis Of High-altitude Adaptation Research Articles

Selection of species specific panel of reference genes in peripheral blood mononuclear cells of native livestock species adapted to trans-Himalayan region of Leh-Ladakh

The identification of appropriate references genes is an integral component of any gene expression-based study for getting accuracy and reliability in data interpretation. In this study, we evaluated the expression stability of 10 candidate reference genes (GAPDH, RPL4, EEF1A1, RPS9, HPRT1, UXT, RPS23, B2M, RPS15, ACTB) in peripheral blood mononuclear cells of livestock species that are adapted to high altitude hypoxia conditions of Leh-Ladakh. A total of 37 PBMCs samples from six native livestock species of Leh-Ladakh region such as Ladakhi cattle, Ladakhi yak, Ladakhi donkey, Chanthangi goat, Double hump cattle and Zanskar ponies were included in this study. The commonly used statistical algorithms such as geNorm, Normfinder, BestKeeper and RefFinder were employed to assess the stability of these RGs in all the livestock species. Our study has identified different panel of reference genes in each species; for example, EEF1A1, RPL4 in Ladakhi cattle; GAPDH, RPS9, ACTB in Ladakhi yak; HPRT1, B2M, ACTB in Ladakhi donkey; HPRT1, B2M, ACTB in Double hump camel, RPS9, HPRT1 in Changthangi goat, HPRT1 and ACTB in Zanskar ponies. To the best of our knowledge, this is the first systematic attempt to identify panel of RGs across different livestock species types adapted to high altitude hypoxia conditions. In future, the findings of the present study would be quite helpful in conducting any transcriptional studies to understand the molecular basis of high altitude adaptation of native livestock population of Leh-Ladakh.

High altitude adaptation of the schizothoracine fishes (Cyprinidae) revealed by the mitochondrial genome analyses

The schizothoracine fishes, also known as “mountain carps” are widely distributed in the Qinghai-Tibetan Plateau and its peripheral regions. Although they provide a prime example of high altitude adaptation, the phylogenetic relationships and the divergence times among these carp lineages are still controversial. Moreover, the genetic basis for high altitude adaptation is also poorly understood. In this study, we determined the mitochondrial genomes from two species of the schizothoracine fishes, representing a “morphologically primitive” clade and “morphologically specialized” clade, respectively. The phylogenetic tree and the divergence times were estimated within the evolutionary framework of the entire order Cypriniformes. Our results indicate a polyphylyetic relationship of the schizothoracine fishes and suggest two independent migration events into the Qinghai-Tibetan Plateau: one by the “morphologically primitive” clade in the Late Miocene and another by the “morphologically specialized” clade in the Eocene. Rapid speciation events of each clade from the Late Miocene to the Pliocene correspond to the timing of the geologic acceleration of the Qinghai-Tibetan Plateau. Interestingly, we found evidence for positive selection acting on the protein coding genes in the mitochondrial genomes of the “morphologically specialized” clade, implying a possible genetic basis for high altitude adaptation in this derived lineage of cypriniform fishes.

Mitogenomic analysis of Chinese snub-nosed monkeys: Evidence of positive selection in NADH dehydrogenase genes in high-altitude adaptation

Chinese snub-nosed monkeys belong to the genus Rhinopithecus and are limited in distribution to six isolated mountainous areas in the temperate regions of Central and Southwest China. Compared to the other members of the subfamily Colobinae (or leaf-eating monkeys), these endangered primates are unique in being adapted to a high altitude environment and display a remarkable ability to tolerate low temperatures and hypoxia. They thus offer an interesting organismal model of adaptation to extreme environmental stress. Mitochondria generate energy by oxidative phosphorylation (OXPHOS) and play important roles in oxygen usage and energy metabolism. We analyzed the mitochondrial genomes of two Chinese snub-nosed monkey species and eight other colobines in the first attempt to understand the genetic basis of high altitude adaptation in non-human primates. We found significant evidence of positive selection in one Chinese snub-nosed monkey, Rhinopithecus roxellana, which is suggestive of adaptive change related to high altitude and cold weather stress. In addition, our study identified two potentially important adaptive amino acid residues (533 and 3307) in the NADH2 and NADH6 genes, respectively. Surprisingly, no evidence for positive selection was found in Rhinopithecus bieti (the other Chinese snub-nosed monkey analyzed). This finding is intriguing, especially considering that R. bieti inhabits a higher altitudinal distribution than R. roxellana. We hypothesize that a different adaptive genetic basis to high altitude survival exists in R. bieti from those seen in other mammals, and that positive selection and functionally associated mutations in this species may be detected in nuclear genes related to energy and oxygen metabolism. More information on the structure, function, and evolution of mitochondrial and nuclear genomes in Chinese snub-nosed monkeys is required to reveal the molecular mechanisms that underlie adaptations to high altitude survival in non-human primates.