Abstract
Key message
Positive selection genes are related to metabolism, while differentially expressed genes are related to photosynthesis, suggesting that genetic adaptation and expression regulation may play independent roles in different gene classes.
Abstract
Genome-wide investigation of the molecular mechanisms for high-altitude adaptation is an intriguing topic in evolutionary biology. The Qinghai-Tibet Plateau (QTP) with its extremely variable environments is an ideal site for studying high-altitude adaptation. Here, we used transcriptome data of 100 individuals from 20 populations collected from various altitudes on the QTP to investigate the adaptive mechanisms of the aquatic plant Batrachium bungei at both the genetic and transcriptional level. To explore genes and biological pathways that may contribute to QTP adaptation, we employed a two-step approach, in which we identified positively selected genes and differentially expressed genes using the landscape genomic and differential expression approaches. The positive selection analysis showed that genes involved in metabolic regulation played a crucial role in B. bungei adaptation to the extreme environments of the QTP, especially intense ultraviolet radiation. Altitude-based differential expression analysis suggested that B. bungei could increase the rate of energy dissipation or reduce the efficiency of light energy absorption by down regulating the expression of photosynthesis-related genes to adapt to the strong ultraviolet radiation. Weighted gene co-expression network analysis identified ribosomal genes as hubs of altitude adaptation in B. bungei. Only a small part of genes (about 10%) overlapped between positively selected genes and differentially expressed genes in B. bungei, suggesting that genetic adaptation and gene expression regulation might play relatively independent roles in different categories of functional genes. Taken together, this study enriches our understanding of the high-altitude adaptation mechanism of B. bungei on the QTP.
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Data availability
The raw sequencing data has been deposited in the National Centre for Biotechnology Information (NCBI) under Accession Number SRR18512371-SRR18512470 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA820952).
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Acknowledgements
This work was supported in part by the National Natural Science Foundation of China (31860046), Local Development Funds of Science and Technology Department of Tibet (XZ202001YD0028C), and Plateau Ecology Youth Innovative Fund of Wuhan University (413100105). We sincerely thank Feifei Chen, Liya Ji, Guoqi Xu, Xuanfeng Wu, Xinzhong Li and Pincuo Zhaxi from Tibet University for their critical assistance on sample collection.
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Xiaoyan Li and Xing Liu conceived the study. XY completed the data analysis with the help of ZC, PW, SZ, CL and YY helped with the data visualization. Xinzhong Li and WZ collected the samples, and XY wrote the manuscript with the help of Xing Liu.
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Yu, X., Wei, P., Zhao, S. et al. Population transcriptomics uncover the relative roles of positive selection and differential expression in Batrachium bungei adaptation to the Qinghai–Tibetan plateau. Plant Cell Rep 42, 879–893 (2023). https://doi.org/10.1007/s00299-023-03005-w
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DOI: https://doi.org/10.1007/s00299-023-03005-w