| 不同温度下TMV侵染枯斑三生烟的LncRNA差异表达 |
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| 引用本文： | 贾海燕,宋丽云,徐翔,解屹,张超群,刘天波,赵存孝,申莉莉,王杰,李莹,王凤龙,杨金广. 不同温度下TMV侵染枯斑三生烟的LncRNA差异表达[J]. 中国农业科学, 2020, 53(7): 1381-1396. DOI: 10.3864/j.issn.0578-1752.2020.07.008 |
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| 作者姓名： | 贾海燕 宋丽云 徐翔 解屹 张超群 刘天波 赵存孝 申莉莉 王杰 李莹 王凤龙 杨金广 |
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| 作者单位： | 1. 中国农业科学院烟草研究所/烟草行业病虫害监测与综合治理重点开放实验室,山东青岛2661012. 江西省烟叶科学研究所,南昌3300293. 中国烟草总公司中南农业试验站,长沙4101284. 甘肃省烟草公司庆阳市公司,甘肃庆阳745099 |
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| 基金项目： | 烟草绿色防控重大专项(110101601024LS-04);烟草绿色防控重大专项(110101601024LS-04);甘肃省烟草公司科技项目(201862100020016);甘肃省烟草公司科技项目(201862100020017);湖南省烟草公司科技项目(201743010020088);江西省烟草公司科技项目(201701002) |
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| 摘 要： | 【目的】筛选不同温度下烟草花叶病毒(Tobacco mosaic virus,TMV)侵染后枯斑三生烟(Nicotiana tabacum var. Samsun NN)差异表达的长链非编码RNA(long non-coding RNA,lncRNA),研究lncRNA在枯斑三生烟抗性反应中的作用。【方法】N基因的温度敏感性使枯斑三生烟在25℃时具备对TMV的抗性、在31℃抗性丧失,在这两个温度条件下对枯斑三生烟接种TMV和磷酸盐缓冲盐水(phosphate buffered saline,PBS),48 h后提取系统叶总RNA,构建链特异性文库后进行深度测序。对测序结果进行过滤后利用HTSeq将有效数据与近缘品种TN90(N. tabacum var. TN90)基因组比对,筛选得到lncRNA后利用FPKM法估计lncRNA的表达水平。通过edgeR筛选差异表达lncRNA(differentially expressed lncRNA,DElncRNA),并利用qRT-PCR技术对这一结果进行验证。通过共定位及共表达分析预测DElncRNA的靶基因,通过参考基因组注释、GO和KE...
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| 关 键 词： | 烟草花叶病毒 N基因 枯斑三生烟 长链非编码RNA 系统获得性抗性 深度测序 基因富集分析 |
| 收稿时间： | 2019-09-16 |
Differential Expression of LncRNAs in Nicotiana tabacum var. Samsun NN Infected by TMV at Different Temperatures |
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| HaiYan JIA,LiYun SONG,Xiang XU,Yi XIE,ChaoQun ZHANG,TianBo LIU,CunXiao ZHAO,LiLi SHEN,Jie WANG,Ying LI,FengLong WANG,JinGuang YANG. Differential Expression of LncRNAs in Nicotiana tabacum var. Samsun NN Infected by TMV at Different Temperatures[J]. Scientia Agricultura Sinica, 2020, 53(7): 1381-1396. DOI: 10.3864/j.issn.0578-1752.2020.07.008 |
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| Authors: | HaiYan JIA LiYun SONG Xiang XU Yi XIE ChaoQun ZHANG TianBo LIU CunXiao ZHAO LiLi SHEN Jie WANG Ying LI FengLong WANG JinGuang YANG |
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| Affiliation: | 1．Tobacco Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Tobacco Disease and Pest Monitoring, Controlling & Integrated Management, Qingdao 266101, Shandong;2. Tobacco Science Institute of Jiangxi Province, Nanchang 3300293. Central South Agricultural Experimental Station of China National Tobacco Corporation, Changsha 4101284. Qingyang Tobacco Company of Gansu Provincial Company, Qingyang 745099, Gansu |
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| Abstract: | 【Objective】 The objective of this study is to screen out the differentially expressed lncRNAs in Nicotiana tabacum var. Samsun NN after Tobacco mosaic virus (TMV) infection at different temperatures, and to investigate the role of identified lncRNAs in Samsun NN’s resistance response.【Method】 The temperature sensitivity of N gene makes Samsun NN have the resistance to TMV at 25℃, but lose it at 31℃. TMV and phosphate buffered saline (PBS) were mechanically inoculated into Samsun NN at 25℃ and 31℃. Total RNAs were extracted from systemic leaves at 48 hpi (hours post infection). Deep sequencing was performed after strand-specific database construction, and the sequencing results were filtered to get clean reads. Using N. tabacum var. TN90 as a reference, HTseq was employed to compare obtained reads. LncRNAs were screened out, and their expression levels were estimated by FPKM method. Differentially expressed lncRNAs (DElncRNAs) were then identified by edgeR and verified by qRT-PCR. The target genes of DElncRNAs were predicted by co-localization and co-expression analyses. Gene annotations, GO and KEGG pathways were analyzed for functional prediction of target genes. 【Result】 Altogether, 80 million clean reads were detected for each of 12 samples from 4 treatments by lncRNA-seq. A total of 4 737 annotated lncRNAs and 40 169 novel lncRNAs were obtained. Among them, 64 lncRNAs were differentially expressed after TMV infection at different temperatures. qRT-PCR results showed that the sequencing accuracy of these DElncRNAs was about 80%, which indicated the sequencing data obtained in this study had high reliability. Importantly, some target genes were simultaneously targeted by DElncRNAs that were down-regulated at 25℃ and up-regulated at 31℃. Gene annotations showed that DElncRNAs’ target genes involved in many functions, such as plant resistance, hormone and metabolic pathways. Particularly, some lncRNAs that may be associated with hormone pathways showed a down-regulation trend after TMV infection at 25℃, while up-regulated at 31℃. Furthermore, GO enrichment analysis showed that target genes were mainly involved in the composition of membranes, vesicles, and acted as calcium and potassium ion channel inhibitor activity, so that consequently the corresponding ions could be transported to their sites of action to trigger subsequent reactions. Moreover, these genes were also involved in pathogenesis, antigen processing and presentation, cytokinin metabolism and other physiological processes. The plant hormone signaling pathway was significantly enriched by target genes during KEGG pathway analysis. DElncRNAs related genes down-regulated at 25℃ and up-regulated at 31℃ were simultaneously enriched in pathways such as hormone signaling, ABC transporters, and phenylpropanoid biosynthesis.【Conclusion】 LncRNAs were differentially expressed in Samsun NN after TMV infection at different temperatures (25℃ and 31℃). DElncRNAs participated in host plant systemic acquired resistance by acting on hormone signaling transduction, substance transport and other processes. Taken together, this study lays a foundation for further research on lncRNA’s regulatory function in plant systemic acquired resistance and the development of new strategies to overcome virus invasion into host plant. |
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| Keywords: | Tobacco mosaic virus (TMV) N gene Nicotiana tabacum var. Samsun NN long non-coding RNA (lncRNA) systemic acquired resistance deep sequencing affinity enrichment analysis |
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