The selection pressure of high-altitude environments drives the phenotypic and genetic adaptation of organisms. Early studies in the research group showed that different high-altitude species tended to have morphological, physiological, biochemical and other phenotypic characteristics (Zhu et al. 2018. PNAS), and the genetic adaptation mechanisms of this convergent phenotype are diverse and can be heavily influenced by the phylogenetic background. At the same time, due to the difficulty of sampling wild birds and the high quality requirements of transcriptome sequencing samples, the early research on the genetic mechanism of high-altitude adaptation was mostly concentrated at the level of gene sequences, while the study of transcriptional regulation at the level of multi-species and multi-tissue transcription was almost blank (Hao et al. 2019. Current Genomics)。
In the same phylogenetic background, the Lei Fumin Research Group of the Institute of Zoology, Chinese Academy of Sciences selected three high-altitude passeriformes birds from the Qinghai-Tibet Plateau [Lophophanes dichrous, black-crowned (Periparus rubidiventris), brown-fronted long-tailed (Aegithalos iouschistos)] and their respective relatives of low-altitude species [Poecile.] Comparative transcriptomics analyses were performed by palustris), pardaliparus venustulus, and red-headed long-tailed (A. concinnus). The study used second-generation high-throughput sequencing technology to complete the deep transcriptome sequencing of 128 samples of 5 tissues (heart, muscle, liver, lungs, kidneys) in 28 individuals of 3 pairs of high and low altitude species, and compared the differences in sequence levels and expression levels between high and low altitude species, thus revealing how birds respond to environmental stress at high altitude. Sequence comparison analysis found that three high-altitude species showed high similarity in positive selection genes (218 shared positive selection genes), while the similarity in amino acid substitution was extremely low (only 4 genes of the three high-altitude species contained the same amino acid substitution sites), suggesting that high-altitude adaptive convergence was mainly manifested at the level of positively selected genes rather than at the level of amino acid substitution. Comparative analysis of gene expression found that the expression profile of the entire gene set showed a tissue-specific expression pattern (all species samples were clustered according to tissue), while the expression profiles of differentially expressed gene sets and altitude-related gene sets showed altitude-dependent clustering patterns, suggesting that the high-altitude environment may drive similar expression changes in high-altitude species. In addition, it was also found that there was a very low sharing rate between the positive selected genes and differentially expressed genes selected by the three high-altitude species (2.3%, 5 of the 218 positively selected genes were differentially expressed), and the interaction between gene expression, gene connectivity and altitude between the two was significantly related to the evolution rate of genes. These results reveal that three species of high-altitude birds may have achieved their adaptive evolution in a way that changes in sequence and expression levels in synergistically.
Unlike other taxa high-altitude adaptation studies, this study is the first to conduct a multi-species, multi-organization, multi-scale comparative analysis of wild birds, expanding people's understanding of how species respond to high-altitude environments. The work, titled Communicative transcriptomics of 3 high-passerine birds and their low-altitude relatives, was published online May 24 in the proceeding of the National Academy of Science USA. doi:10.1073/pnas.1819657116 )。 Lei Fumin, a researcher at the Institute of Zoology, and Qu Yanhua were co-corresponding authors of the paper; Hao Yan, a doctoral student, was the first author of the paper. The research was supported by the Strategic Pilot Project of the Chinese Academy of Sciences (XDB13020300) and the National Natural Science Foundation of China (31672275, 31630069 and 31572249).
Figures: (A) whole gene set expression profile; (B) whole gene set PCA; (C) differentially expressed gene set expression profile; (D) altitude-dependent gene set expression profile
Source: Institute of Zoology, Chinese Academy of Sciences
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