Identification and characterization of pineapple leaf lncRNAs in crassulacean acid metabolism (CAM) photosynthesis pathway
Identification and characterization of pineapple leaf lncRNAs in crassulacean acid metabolism (CAM) photosynthesis pathway
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景天酸代谢（CAM）光合作用途径中菠萝叶 lncRNA 的鉴定和表征
DOI：
10.1038/s41598-019-43088-8
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发表时间：
2019-04-30
影响因子：
4.6
通讯作者：
Qin, Yuan
中科院分区：
文献类型：
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作者：
Bai, Youhuang;Dai, Xiaozhuan;Qin, Yuan
长非编码RNA(LncRNAs)在许多哺乳动物和植物中被发现，并被认为在多种生物过程中发挥着关键作用。菠萝是一种重要的热带水果，也是研究植物对干旱环境的进化适应和景天酸代谢(CAM)光合作用策略的良好模式，但参与CAM途径的lncRNAs仍未得到很好的研究。在这里，我们分析了来自13个时间点的26个菠萝叶片样本的RNA-SEQ数据集，鉴定出2888个叶片LncRNAs，其中包括2046个长的基因间非编码非编码RNA(LincRNAs)和842个长的非编码自然反义转录本(LncNAs)。菠萝叶片lncRNAs以高度组织特异性的方式表达。叶片lncRNA和mRNA的共表达分析表明，叶片lncRNAs优先与光合作用基因相关。我们进一步鉴定了可能作为两个CAM光合作用途径基因PPCK和PEPC竞争内源RNA(CeRNAs)的叶片lncRNAs，并揭示了它们在叶片中的日表达模式。此外，我们还发现48%的lncRNAs在叶片中表现出日间表达模式，这表明它们在CAM中起着重要的作用。本研究对菠萝叶片中的lncRNAs进行了全基因组分析，并确定了它们在光合作用途径的基因表达调控中的作用。
Long noncoding RNAs (lncRNAs) have been identified in many mammals and plants and are known to play crucial roles in multiple biological processes. Pineapple is an important tropical fruit and a good model for studying the plant evolutionary adaptation to the dry environment and the crassulacean acid metabolism (CAM) photosynthesis strategy; however, the lncRNAs involved in CAM pathway remain poorly characterized. Here, we analyzed the available RNA-seq data sets derived from 26 pineapple leaf samples at 13 time points and identified 2,888 leaf lncRNAs, including 2,046 long intergenic noncoding RNAs (lincRNAs) and 842 long noncoding natural antisense transcripts (lncNATs). Pineapple leaf lncRNAs are expressed in a highly tissue-specific manner. Co-expression analysis of leaf lncRNA and mRNA revealed that leaf lncRNAs are preferentially associated with photosynthesis genes. We further identified leaf lncRNAs that potentially function as competing endogenous RNAs (ceRNAs) of two CAM photosynthesis pathway genes,PPCKandPEPC, and revealed their diurnal expression pattern in leaves. Moreover, we found that 48% of lncRNAs exhibit diurnal expression patterns in leaves, suggesting their important roles in CAM. This study conducted a comprehensive genome-wide analysis of leaf lncRNAs and identified their role in gene expression regulation of the CAM photosynthesis pathway in pineapple.