Yong Shi1, §,Zechun Su2, §, Hong Yang1, 3, §, Wenzhi Wang1, 4, Guihua Jin1, 3, Guiqing He2, Abu N. Siddique1, 5, Liangsheng Zhang6, Andan Zhu1, Runguang Xue2, *, and Chengjun Zhang1, *

 Abstract:Alpine plants remain the least studied plant communities in terrestrial ecosystems. However, how they adapt to high-altitude environments is far from clear. Here, we used RNA-seq to investigate a typical alpine plant maca (Lepidium meyenii) to understand its high-altitude adaptation at transcriptional and post-transcriptional level. At transcriptional level, we found that maca root significantly up-regulated plant immunity genes in day-time comparing to night-time, and up-regulated abiotic (cold/osmotic) stress response genes from Oct to Dec. In addition, 17 positively selected genes were identified,which could be involved in mitochondrion or RNA editing. At post-transcriptional level, we found that maca had species-specific characterized alternative splicing (AS) profile which could be influenced by stress environments. For example, the alternative 3′ splice site events (A3SS, 39.62%) were predominate AS events in maca, rather than intron retention (IR, 23.17%). Interestingly, besides serine/arginine-rich (SR) proteins and long non-coding RNAs (lncRNAs), a lot of components in nonsense-mediated mRNA decay (NMD) were identified under differential alternative splicing (DAS), supporting AS coupled to NMD as essential mechanisms for maca’s stress responses and high-altitude adaptation. Taken together, we first attempted to unveil maca’s high-altitude adaptation mechanisms based on transcriptome and post-transcriptome evidence. Our data provided valuable insights to understand the high-altitude adaptation of alpine plants.