Plant Cell Reports ( IF 5.3 ) Pub Date : 2023-03-27 , DOI: 10.1007/s00299-023-03005-w Xiaolei Yu 1 , Pei Wei 1 , Shuqi Zhao 1 , Zhuyifu Chen 1 , Xinzhong Li 2 , Wencai Zhang 2 , Chenlai Liu 1 , Yujiao Yang 1 , Xiaoyan Li 3 , Xing Liu 1, 2
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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.
中文翻译：
种群转录组学揭示了正选择和差异表达在青藏高原适应中的相对作用
关键信息
正选择基因与代谢有关，而差异表达基因与光合作用有关，表明遗传适应和表达调控可能在不同基因类别中发挥独立作用。
抽象的
高海拔适应分子机制的全基因组研究是进化生物学中一个有趣的话题。环境多变的青藏高原是研究高原适应的理想场所。在这里，我们使用从青藏高原不同海拔高度收集的 20 个种群的 100 个个体的转录组数据来研究水生植物 Batrachium bungei的适应机制在遗传和转录水平上。为了探索可能有助于 QTP 适应的基因和生物途径，我们采用了两步法，其中我们使用景观基因组和差异表达方法鉴定了阳性选择基因和差异表达基因。正选择分析表明，参与代谢调控的基因在文革白菜适应青藏高原极端环境，尤其是强烈的紫外线辐射中起着至关重要的作用。基于海拔的差异表达分析表明B. bungei可以通过下调光合作用相关基因的表达来提高能量耗散率或降低光能吸收效率，以适应强紫外线辐射。加权基因共表达网络分析将核糖体基因鉴定为B. bungei的海拔适应中心。B. bungei中只有一小部分基因（约10%）在阳性选择基因和差异表达基因之间重叠，表明遗传适应和基因表达调控可能在不同类别的功能基因中发挥相对独立的作用。综上所述，本研究丰富了我们对青藏高原白蚁高原适应机制的认识。
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