Cao Weilin, Gan Liming, Wang Chenchen, Zhao Xuechen, Zhang Mingyu, Du Jinwen, Zhou Shumei, Zhu Changxiang
State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China.
Front Plant Sci. 2021 Feb 10;12:619062. doi: 10.3389/fpls.2021.619062. eCollection 2021.
Long non-coding RNA (lncRNA) is a crucial regulatory mechanism in the plant response to biotic and abiotic stress. However, their roles in potato ( L.) resistance to () largely remain unknown. In this study, we identify 2857 lncRNAs and 33,150 mRNAs of the potato from large-scale published RNA sequencing data. Characteristic analysis indicates a similar distribution pattern of lncRNAs and mRNAs on the potato chromosomes, and the mRNAs were longer and had more exons than lncRNAs. Identification of alternative splicing (AS) shows that there were a total of 2491 lncRNAs generated from AS and the highest frequency (46.49%) of alternative acceptors (AA). We performed R package TCseq to cluster 133 specific differentially expressed lncRNAs from resistance lines and found that the lncRNAs of cluster 2 were upregulated. The lncRNA targets were subject to KEGG pathway enrichment analysis, and the interactive network between lncRNAs and mRNAs was constructed by using GENIE3, a random forest machine learning algorithm. Transient overexpression of in significantly suppresses growth compared with a control, and the expression of extensin (), the ortholog of the target gene, was significantly upregulated in the overexpression line. Together, these results suggest that lncRNAs play potential functional roles in the potato response to infection.
长链非编码RNA（lncRNA）是植物应对生物和非生物胁迫的关键调控机制。然而，它们在马铃薯（Solanum tuberosum L.）对晚疫病菌（Phytophthora infestans）抗性中的作用 largely 仍不清楚。在本研究中，我们从大规模已发表的RNA测序数据中鉴定出2857个马铃薯lncRNA和33150个mRNA。特征分析表明lncRNA和mRNA在马铃薯染色体上具有相似的分布模式，且mRNA比lncRNA更长、外显子更多。可变剪接（AS）鉴定显示共有2491个lncRNA由AS产生，其中可变受体（AA）的频率最高（46.49%）。我们使用R包TCseq对来自抗性品系的133个特异性差异表达lncRNA进行聚类，发现聚类2的lncRNA上调。对lncRNA靶标进行KEGG通路富集分析，并使用随机森林机器学习算法GENIE3构建lncRNA与mRNA之间的相互作用网络。与对照相比，在本氏烟草（Nicotiana benthamiana）中瞬时过表达显著抑制了致病疫霉（Phytophthora infestans）的生长，且过表达株系中致病疫霉靶基因的直系同源基因伸展蛋白（EXTENSIN）的表达显著上调。总之，这些结果表明lncRNA在马铃薯对致病疫霉感染的应答中发挥潜在功能作用。
