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

doi:10.1016/j.gene.2018.12.082

	Alternative splicing coupled to nonsense-mediated mRNA decay contributes to the high-altitude adaptation of maca (Lepidium meyenii)
	Shi, Yong 1; Su, Zechun 2; Yang, Hong 1,3; Wang, Wenzhi1,4 ; Jin, Guihua 1,3; He, Guiqing 2; Siddique, Abu Nasar 1,5; Zhang, Liangsheng 6; Zhu, Andan 1; Xue, Runguang 2; Zhang, Chengjun1
通讯作者	Xue, Runguang(13988877562@139.com) ; Zhang, Chengjun(zhangchengjun@mail.kib.ac.cn)
	2019-04-30
发表期刊	GENE
ISSN	0378-1119
卷号	694 页码:7-18
摘要	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 mace (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 in Nov and Dec comparing to Oct. In addition, 17 positively selected genes were identified, which could be involved in mitochondrion. 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.
关键词	Alpine plants Post-transcriptome Intron retention Alternative 3 ' splice site Long non-coding RNA Positive selection
DOI	10.1016/j.gene.2018.12.082
收录类别	SCI
语种	英语
WOS记录号	WOS:000462108500002
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/67635
专题	中国西南野生生物种质资源库
通讯作者	Xue, Runguang; Zhang, Chengjun
作者单位	1.Chinese Acad Sci, Germplasm Bank Wild Species Southwest China, Kunming Inst Bot, 132 Lanhei Rd, Kunming 650201, Yunnan, Peoples R China 2.Yunnan Acad Agr Sci, Alpine Econ Plant Res Inst, Lijiang 674100, Yunnan, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 4.Southwest Forestry Univ, Sch Life Sci, Kunming 650224, Yunnan, Peoples R China 5.Bacha Khan Univ, Dept Biotechnol, Charsadda 24420, Pakistan 6.Fujian Agr & Forestry Univ, State Key Lab Ecol Pest Control Fujian & Taiwan C, Fuzhou 350002, Fujian, Peoples R China
推荐引用方式 GB/T 7714	Shi, Yong,Su, Zechun,Yang, Hong,et al. Alternative splicing coupled to nonsense-mediated mRNA decay contributes to the high-altitude adaptation of maca (Lepidium meyenii)[J]. GENE,2019,694:7-18.
APA	Shi, Yong.,Su, Zechun.,Yang, Hong.,Wang, Wenzhi.,Jin, Guihua.,...&Zhang, Chengjun.(2019).Alternative splicing coupled to nonsense-mediated mRNA decay contributes to the high-altitude adaptation of maca (Lepidium meyenii).GENE,694,7-18.
MLA	Shi, Yong,et al."Alternative splicing coupled to nonsense-mediated mRNA decay contributes to the high-altitude adaptation of maca (Lepidium meyenii)".GENE 694(2019):7-18.

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