Alternative splicing coupled to nonsense-mediated mRNA decay contributes to the high-altitude adaptation of maca (Lepidium meyenii)
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.
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