不同温度下TMV侵染枯斑三生烟的LncRNA差异表达

doi:10.3864/j.issn.0578-1752.2020.07.008

Abstract

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.

Key words: Tobacco mosaic virus (TMV), N gene, Nicotiana tabacum var. Samsun NN, long non-coding RNA (lncRNA), systemic acquired resistance, deep sequencing, affinity enrichment analysis

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.

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https://www.chinaagrisci.com/EN/Y2020/V53/I7/1381

Figures/Tables 10

Fig. 1

Table 1

Primer sequences of differentially expressed lncRNAs at 25℃"

转录本ID Transcript ID	基因ID Gene ID	正向引物序列 Forward primer sequence (5′ to 3′)	反向引物序列 Reverse primer sequence (5′ to 3′)
LNC_000098	XLOC_000472	CCCTCCACGCAGTTCTTCTGA	TGCCGGGAGTTTCGGGTTTA
LNC_000799	XLOC_003050	GCCTTCTGCCGAATTGTTGG	GCTCAAAGGAGGCCAAGTCC
LNC_001093	XLOC_004138	ATGCGTCAGTTTGCATGGGA	GAAATCTCAAGGGTAGCTGTACCA
LNC_006130	XLOC_023441	GCCTTCGACTTGTCGTTTGCT	ATCCGCAAATCAGCCCTTCC
LNC_012986	XLOC_049416	CCTCTGCCTCAGGCTGTCTCG	TTCTGCCGCTTCCGTTATTGCTG
LNC_019285	XLOC_073034	GGATTGAATCTAAGATGAATGCTTGGT	ACAGTCACAAGGGTCTAGAAGG
LNC_028742	XLOC_108482	ACGCTGGCGAACGATAATAGAACC	ACGGTCGAGATTCTCCTGGTCAG
LNC_037710	XLOC_141968	TCTCTTTCTACCGGGAATTTAAAAAGT	CCATTACGTATTGATTGGTGAGCT
XR_001643474.1	107765638	CCACTTGCATGGGCAGTGAT	GCCACCACACCAACTTCCTC
XR_001643621.1	107766213	CGGAGAGGTGGAATGGCAAGTG	TCCGAGATGTGCCTCCAAGACC
XR_001644424.1	107769516	AACATTCACGGCCAGCAGAACC	CTGAAGGCGCGACTGAGATTAGC
XR_001645141.1	107772701	TCATTCTCAGGTCCTCCGTTGT	TCTCTCTGTGCTTTCCGCCT
XR_001650509.1	107796801	CGCCCATGTACCCGATTCTG	CTTGTTCCAGATGCGCCAGT
XR_001654053.1	107812073	CACTGCCTACACAACCTACACGTC	AACAACATGCTGCGAAGAGACTCC
XR_001657220.1	107826167	AATGGCTTTGTCTGCCTCGG	AGGCGCGTTGATGAAAGAGG
LNC_001159	XLOC_004417	GACACAGGTACTTGGTTCGCTC	AAGAACCGGCACAATACGCC
LNC_003116	XLOC_011996	GGTTTGCAGCGATAACTCGG	TGGCTTCAACTATTCCCGCA
LNC_004594	XLOC_017602	AGTGAATGTAACGGAGGCAGCAAC	ACACAGAAGAGGATCGAGGTCGTC
LNC_015076	XLOC_057288	CTCTTGCAGGAAGGTTGGCT	CCTCATACGGCTCCTCCCTT
LNC_015077	XLOC_057288	CTCTTGCAGGAAGGTTGGCT	CCTCATACGGCTCCTCCCTT
LNC_028743	XLOC_108482	ACGCTGGCGAACGATAATAGAACC	ACGGTCGAGATTCTCCTGGTCAG
LNC_030105	XLOC_113591	TCCCAACGTGTTACATAAGGCA	GCACGGTGTTCTTCGACTCA
LNC_036321	XLOC_136711	CTCTGTCATTCTTCGGTGCCGATG	TGAGCTGCCATGCCATGATACAAG
LNC_038081	XLOC_143307	GCTTAGTGTGTGACTCGTTGGT	TGCGAAGTGATGGGTTGGTT
XR_001643840.1	107767123	GTTAGTTCGAGGCTGCGGTCAAG	CATCGGCGGCGGACAATTACC
XR_001646643.1	107779549	GGTTGGATCAGCAGCAGCAGTAG	AGCAGCAGTCTCATTAGCAGCAAC
XR_001648910.1	107789767	ATCCGAACGACCACTCCCAG	TTGCAAGTCATCACCGTCCG
XR_001649452.1	107792124	TGTTGGAGAAGGCTGGGACT	CGGCATCTGCTGCTTCTAGT
XR_001651797.1	107802252	GGCATCAATCACACATGCCGT	AGCAGCCACTGACTTGGAAAC
XR_001654265.1	107813134	GCACTCGAACCAGAAGGCAA	CAGCAGAAGCTCGACCACAA
XR_001654587.1	107814577	GTTCATCGCCTTCTTCTGCCTCTC	AAGCACCGAGAGCAACCAACATAG
XR_001655076.1	107816953	AATGGCTTTGTCTGCCTCGG	AGGCGCGTTGATGAAAGAGG
XR_001657217.1	107826167	GTGGATGGCGAATGCGATCT	CTGAGGTCCAGCTGCCAATG
XR_001657841.1	107829108	GTGGTGGTGCATGGCCGTTC	TAGCAGGCTGAGGTCTCGTTCG
XR_001658459.1	107831913	GTGGTGGTGCATGGCCGTTC	TAGCAGGCTGAGGTCTCGTTCG

Table 1

Table 2

Primer sequences of differentially expressed lncRNAs at 31℃"

转录本ID Transcript ID	基因ID Gene ID	正向引物序列 Forward primer sequence (5′ to 3′)	反向引物序列 Reverse primer sequence (5′ to 3′)
LNC_008396	XLOC_031876	GCGATCTGCCGAAGCTGTGG	TGCGTTACTCAAGCCGACATTCTC
LNC_008562	XLOC_032544	TCCTGTTGCTTCATTGCTGCT	ACAGATGAACACAGCGCAGG
LNC_008815	XLOC_033553	GACTGTGAAACTGCGAATGGC	GCATCCCTTCCAGAAGTCGG
LNC_010207	XLOC_038635	AGACGAACAACTGCGAAAGCA	CTGGTCGGCATCGTTTATGGT
LNC_013541	XLOC_051547	AGCACCATCCTCACTTCCACCAG	CGCAGGCTGCCTCACAACTTG
LNC_016042	XLOC_060869	GATTAAGACAGCAGGACGGTGGTC	GGCTAGTTGATTCGGCAGGTGAG
LNC_018096	XLOC_068634	AGCCAAGCGTTCATAGCGAC	AACCCAGCTCACGTTCCCTA
LNC_024626	XLOC_093025	ACCACCTGTGGCTCCAGTTACC	TAGGCGGACCTCGCAGAATCTTAG
LNC_033085	XLOC_124537	AGCGAGCAGTCTGGACTCCTATG	ACGAGTAACCAGCGCAATTGGAG
LNC_033563	XLOC_126355	GTGGTGGTGCATGGCCGTTC	TAGCAGGCTGAGGTCTCGTTCG
LNC_036321	XLOC_136711	CTCTGTCATTCTTCGGTGCCGATG	TGAGCTGCCATGCCATGATACAAG
LNC_037998	XLOC_143050	GATTAAGACAGCAGGACGGTGGTC	GGCTAGTTGATTCGGCAGGTGAG
LNC_038712	XLOC_145744	CAACCGCTCAGCCATCTCTC	GGGGTATCCACCCCTATGGC
XR_001648128.1	107786374	GGAGGGAAGCTGGGTCGTAT	GGCAATTCTCCATCGGCTCC
XR_001655221.1	107817578	GAGAGTCGGGCTGCAACTTC	GGGAAGCATGGCACCAACAA
XR_001655293.1	107817783	GTCTGAGGTTGCGGTGAAGGC	ATTGGCGGCAGAGAATTGACAGAG
XR_001656793.1	107824145	TCTCATGTGGGATGGCACGA	CATTCCACTGCGCACCTCTC
XR_001657266.1	107826393	TTGAGGCCACTGTTCAAGACTTGG	CGCGAGCAAGGTCATCAGAGC
LNC_018541	XLOC_070302	ACTTCACAAGCAGCAGCTAGTTCC	GTAATGCGCCAGGTGCCGTAG
LNC_034892	XLOC_131403	GTGGGTTCCAGACCACAACC	AGATGGAAGGGGCAGGTGTT
XR_001644489.1	107769825	CCGTGGACGTGACAACATTGGAG	CGGTGACTGTCGCTGAGATACTTG
XR_001646112.1	107776988	TCGCTGCTGATTGTTGCTGTCTC	GACTCGTCGGCAACCTCAACTG
XR_001647877.1	107785495	ATCAATGTGGGAGCTTGCCT	GCTTGTGCGTGTCTCGACTA
XR_001647999.1	107785872	GCGGATGAGGTATGGTTCACAGC	AGCTGCTTCCATAGTCTGTTGCTG
XR_001648126.1	107786374	ATGAGAGTGGAGTGGGGCAG	TGCGCCCAATAGGTTATGCG
XR_001649356.1	107791865	ACGTTGCTTTACACTTTACCCTG	TGGAGGAAGAAACCAAGCGT
XR_001654070.1	107812109	TCCGTTCAAGTCCACCTGAAGTTC	GCAGCTCACCGTGGAAGTCTC
XR_001656841.1	107824342	CAAGCCATCATGCCTCACAGT	CCGGAGTCTACCACCCATTCT
XR_001656939.1	107824792	CTGCTGGTCCAGAAGCCGTTAAG	AATGTCGTCACGAGTTCGGTCATG
XR_001658441.1	107831745	CAGACGAGGGGTGGAGATGT	GCAAATGCCAACAAACAGGGA

Table 2

Table 3

Fig. 2

Fig. 3

Fig. 4

Fig. 5

Table 4

Number of DElncRNA target genes enriched in GO terms"

条目类型 Term type	GO条目 GO term	比较组合 Comparison group	基因数 Number of genes
生物过程 Biological process (BP)	单组织进程Single-organism process	TMV_25_vs_PBS_25	133
	单组织细胞进程Single-organism cellular process	TMV_25_vs_PBS_25	113
	氮化合物代谢过程Nitrogen compound metabolic process	TMV_25_vs_PBS_25	108
	有机环状化合物代谢过程Organic cyclic compound metabolic process	TMV_25_vs_PBS_25	105
	细胞氮化合物代谢过程Cellular nitrogen compound metabolic process	TMV_25_vs_PBS_25	104
	单组织进程Single-organism process	TMV_31_vs_PBS_31	21
	囊泡介导的运输Vesicle-mediated transport	TMV_31_vs_PBS_31	20
	细胞对刺激的反应Cellular response to stimulus	TMV_31_vs_PBS_31	9
	自RNA聚合酶II启动子转录Transcription from RNA polymerase II promoter	TMV_31_vs_PBS_31	8
	端粒维持Telomere maintenance	TMV_31_vs_PBS_31	7
细胞组分 Cellular component (CC)	细胞Cell	TMV_25_vs_PBS_25	188
	细胞组分Cell part	TMV_25_vs_PBS_25	188
	细胞内组分Intracellular part	TMV_25_vs_PBS_25	166
	细胞内膜结合细胞器Intracellular membrane-bounded organelle	TMV_25_vs_PBS_25	114
	膜结合细胞器Membrane-bounded organelle	TMV_25_vs_PBS_25	114
	质膜组分Plasma membrane part	TMV_31_vs_PBS_31	8
	微管组织中心Microtubule organizing center	TMV_31_vs_PBS_31	4
	反式高尔基体转运囊泡膜Trans-Golgi network transport vesicle membrane	TMV_31_vs_PBS_31	2
	网格蛋白囊膜Clathrin vesicle coat	TMV_31_vs_PBS_31	2
	网格蛋白外壳Clathrin coat	TMV_31_vs_PBS_31	3
分子功能 Molecular function (MF)	阳离子结合Cation binding	TMV_25_vs_PBS_25	69
	锌离子结合Zinc ion binding	TMV_25_vs_PBS_25	41
	糖基转移酶活性Transferase activity, transferring glycosyl groups	TMV_25_vs_PBS_25	31
	己糖基转移酶活性Transferase activity, transferring hexosyl groups	TMV_25_vs_PBS_25	23
	DNA解旋酶活性DNA helicase activity	TMV_25_vs_PBS_25	13
	UDP-糖基转移酶活性UDP-glycosyltransferase activity	TMV_31_vs_PBS_31	8
	抗氧化活性Antioxidant activity	TMV_31_vs_PBS_31	8
	过氧化物酶活性Peroxidase activity	TMV_31_vs_PBS_31	7
	作为受体作用于过氧化物的氧化还原酶活性 Oxidoreductase activity, acting on peroxide as acceptor	TMV_31_vs_PBS_31	7
	翻译监管活动Translation regulator activity	TMV_31_vs_PBS_31	5

Table 4

Table 5

References 50

[1]	WHITHAM S, DINESH-KUMAR S P, CHOI D, HEHL R, CORR C, BAKER B. The product of the Tobacco mosaic virus resistance gene N: Similarity to toll and the interleukin-1 receptor. Cell, 1994,78(6):1101-1115.
[2]	WANG H V, CHEKANOVA J A . Long noncoding RNAs in plants//RAO M R S. Long Non Coding RNA Biology. Singapore: Springer, 2017: 133-154.
[3]	QUAN M, CHEN J, ZHANG D . Exploring the secrets of long noncoding RNAs. International Journal of Molecular Sciences, 2015,16(3):5467-5496.
[4]	RYALS J A, NEUENSCHWANDER U H, WILLITS M G, MOLINA A, STEINER H Y, HUNT M D . Systemic acquired resistance. The Plant Cell, 1996,8(10):1809-1819.
[5]	ERICKSON F L, HOLZBERG S, CALDERON‐URREA A, HANDLEY V, AXTELL M, CORR C, BAKER B. The helicase domain of the TMV replicase proteins induces the N‐mediated defence response in tobacco. The Plant Journal, 1999,18(1):67-75.
[6]	GAFFNEY T, FRIEDRICH L, VERNOOIJ B, NEGROTTO D, NYE G, UKNES S, WARD E, KESSMANN H, RYALS J . Requirement of salicylic acid for the induction of systemic acquired resistance. Science, 1993,261(5122):754-756.
[7]	MUR L A, KENTON P, LLOYD A J, OUGHAM H, PRATS E . The hypersensitive response; the centenary is upon us but how much do we know? Journal of Experimental Botany, 2008,59(3):501-520.
[8]	YANG Y X, AHAMMED G J, WU C, FAN S Y, ZHOU Y H . Crosstalk among jasmonate, salicylate and ethylene signaling pathways in plant disease and immune responses. Current Protein and Peptide Science, 2015,16(5):450-461.
[9]	BAKER B, ZAMBRYSKI P, STASKAWICZ B, DINESH-KUMAR S P. Signaling in plant-microbe interactions. Science, 1997,276(5313):726-733.
[10]	SMITH H B . Signal transduction in systemic acquired resistance. The Plant Cell, 2000,12(2):179-181.
[11]	CUTT J R, KLESSIG D F . Pathogenesis-Related Proteins: Genes Involved in Plant Defense. Vienna: Springer, 1992: 209-243.
[12]	肖万福 . 烟草感染花叶病过程中差异表达基因与蛋白质的筛选及应用[D]. 郑州: 河南农业大学, 2017.
	XIAO W F . Screening and application of differential expressed genes and proteins in tobacco mosaic disease[D]. Zhengzhou: Henan Agricultural University, 2017. (in Chinese)
[13]	WANG J, YANG Y, JIN L, LING X, LIU T, CHEN T, JI Y, YU W, ZHANG B . Re-analysis of long non-coding RNAs and prediction of circRNAs reveal their novel roles in susceptible tomato following TYLCV infection. BMC Plant Biology, 2018,18:104.
[14]	YANG Y, LIU T, SHEN D, WANG J, LING X, HU Z, CHEN T, HU J, HUANG J, YU W, DOU D, WANG M B, ZHANG B . Tomato yellow leaf curl virus intergenic siRNAs target a host long noncoding RNA to modulate disease symptoms. PLoS Pathogens, 2019,15(1):e1007534.
[15]	SEO J S, SUN H X, PARK B S, HUANG C H, YEH S D, JUNG C, CHUA N H . ELF18-induced long-noncoding RNA associates with mediator to enhance expression of innate immune response genes in Arabidopsis. The Plant Cell, 2017,29(5):1024-1038.
[16]	SEO J S, DILOKNAWARIT P, PARK B S, CHUA N H . ELF18- induced long noncoding RNA 1 evicts fibrillarin from mediator subunit to enhance pathogenesis-related gene 1 (PR1) expression. New Phytologist, 2019,221(4):2067-2079.
[17]	ANDERS S . HTSeq: Analysing high-throughput sequencing data with Python[EB/OL]. .
[18]	PERTEA M, PERTEA G M, ANTONESCU C M, CHANG T C, MENDELL J T, SALZBERG S L . StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology, 2015,33(3):290-295.
[19]	TRAPNELL C, WILLIAMS B A, PERTEA G, MORTAZAVI A, KWAN G, VAN BAREN M J, SALZBERG S L, WOLD B J, PACHTER L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology, 2010,28(5):511-515.
[20]	SUN L, LUO H, BU D, ZHAO G, YU K, ZHANG C, LIU Y, CHEN R, ZHAO Y . Utilizing sequence intrinsic composition to classify protein- coding and long non-coding transcripts. Nucleic Acids Research, 2013,41(17):e166.
[21]	KANG Y J, YANG D C, KONG L, HOU M, MENG Y Q, WEI L, GAO G . CPC2: A fast and accurate coding potential calculator based on sequence intrinsic features. Nucleic Acids Research, 2017,45(Web Server issue):W12-W16.
[22]	MISTRY J, BATEMAN A, FINN R D . Predicting active site residue annotations in the Pfam database. BMC Bioinformatics, 2007,8:298.
[23]	CABILI M N, TRAPNELL C, GOFF L, KOZIOL M, TAZON-VEGA B, REGEV A, RINN J L . Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes and Development, 2011,25(18):1915-1927.
[24]	ROBINSON M D, MCCARTHY D J, SMYTH G K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 2010,26(1):139-140.
[25]	LIVAK K J, SCHMITTGEN T D . Analysis of relative gene expression data using real-time quantitative PCR and the 2 ^-ΔΔCT method . Methods, 2001,25(4):402-408.
[26]	LI T, ZHANG G, WU P, DUAN L, LI G, LIU Q, WANG J . Dissection of myogenic differentiation signatures in chickens by RNA-Seq analysis. Genes, 2018,9(1):34.
[27]	WANG K C, CHANG H Y . Molecular mechanisms of long noncoding RNAs. Molecular Cell, 2011,43(6):904-914.
[28]	YOUNG M D, WAKEFIELD M J, SMYTH G K, OSHLACK A . Gene ontology analysis for RNA-seq: Accounting for selection bias. Genome Biology, 2010,11(2):R14.
[29]	KANEHISA M, ARAKI M, GOTO S, HATTORI M, HIRAKAWA M, ITOH M, KATAYAMA T, KAWASHIMA S, OKUDA S, TOKIMATSU T, YAMANISHI Y . KEGG for linking genomes to life and the environment. Nucleic Acids Research, 2007,36(Database issue):D480-D484.
[30]	MAO X, CAI T, OLYARCHUK J G, WEI L . Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics, 2005,21(19):3787-3793.
[31]	OSATO N, SUZUKI Y, IKEO K, GOJOBORI T . Transcriptional interferences in cis natural antisense transcripts of humans and mice. Genetics, 2007,176(2):1299-1306.
[32]	FAGHIHI M A, WAHLESTEDT C . Regulatory roles of natural antisense transcripts. Nature Reviews. Molecular Cell Biology, 2009,10(9):637-643.
[33]	BENJAMINS R, SCHERES B . Auxin: The looping star in plant development. Annual Review of Plant Biology, 2008,59:443-465.
[34]	WILSON M S, LIVERMORE T M, SAIARDI A . Inositol pyrophosphates: Between signalling and metabolism. Biochemical Journal, 2013,452(3):369-379.
[35]	SAHA M, SARKAR S, SARKAR B, SHARMA B K, BHATTACHARJEE S, TRIBEDI P . Microbial siderophores and their potential applications: A review. Environmental Science and Pollution Research, 2016,23(5):3984-3999.
[36]	ZHENG Y, DING B, FEI Z, WANG Y . Comprehensive transcriptome analyses reveal tomato plant responses to tobacco rattle virus-based gene silencing vectors. Scientific Reports, 2017,7:9771.
[37]	KWENDA S, BIRCH P R, MOLELEKI L N . Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection. BMC Genomics, 2016,17(1):614.
[38]	CUI J, LUAN Y, JIANG N, BAO H, MENG J . Comparative transcriptome analysis between resistant and susceptible tomato allows the identification of lncRNA16397 conferring resistance to Phytophthora infestans by co-expressing glutaredoxin. The Plant Journal, 2017,89(3):577-589.
[39]	LI X, XING X, XU S, ZHANG M, WANG Y, WU H, SUN Z, HUO Z, CHEN F, YANG T . Genome-wide identification and functional prediction of tobacco lncRNAs responsive to root-knot nematode stress. PLoS ONE, 2018,13(11):e0204506.
[40]	赵长江 . 纹枯病菌侵染后水稻防御反应相关基因的表达分析[D]. 福州: 福建农林大学, 2005.
	ZHAO C J . Expression analysis of rice defence-related genes after infected by Rhizoctonia solani[D]. Fuzhou: Fujian Agriculture and Forestry University, 2005. (in Chinese)
[41]	MALAMY J, CARR J P, KLESSIG D F, RASKIN I . Salicylic acid: A likely endogenous signal in the resistance response of tobacco to viral infection. Science, 1990,250(4983):1002-1004.
[42]	许志刚 . 普通植物病理学. 4版. 北京: 高等教育出版社, 2009: 296-315.
	XU Z G . General Plant Pathology. 4th ed. Beijing: Higher Education Press, 2009: 296-315. (in Chinese)
[43]	ZHU F, XI D H, YUAN S, XU F, ZHANG D W, LIN H H . Salicylic acid and jasmonic acid are essential for systemic resistance against Tobacco mosaic virus in Nicotiana benthamiana. Molecular Plant- Microbe Interactions, 2014,27(6):567-577.
[44]	VERBERNE M C, HOEKSTRA J, BOL J F, LINTHORST H J . Signaling of systemic acquired resistance in tobacco depends on ethylene perception. The Plant Journal, 2003,35(1):27-32.
[45]	BEIS K . Structural basis for the mechanism of ABC transporters. Biochemical Society Transactions, 2015,43(5):889-893.
[46]	HUANG T, JANDER G . Abscisic acid-regulated protein degradation causes osmotic stress-induced accumulation of branched-chain amino acids in Arabidopsis thaliana. Planta, 2017,246(4):737-747.
[47]	SHADLE G L, WESLEY S V, KORTH K L, CHEN F, LAMB C, DIXON R A . Phenylpropanoid compounds and disease resistance in transgenic tobacco with altered expression of L-phenylalanine ammonia-lyase. Phytochemistry, 2003,64(1):153-161.
[48]	MERCER T R, DINGER M E, MATTICK J S . Long non-coding RNAs: Insights into functions. Nature Reviews. Genetics, 2009,10(3):155-159.
[49]	BERTERAME N M, BERTAGNOLI S, CODAZZI V, PORRO D, BRANDUARDI P. Temperature-induced lipocalin(TIL): A shield against stress-inducing environmental shocks in Saccharomyces cerevisiae. FEMS Yeast Research, 2017, 17(6): fox056.
[50]	SADE D, EYBISHTZ A, GOROVITS R, SOBOL I, CZOSNEK H . A developmentally regulated lipocalin-like gene is overexpressed in Tomato yellow leaf curl virus-resistant tomato plants upon virus inoculation, and its silencing abolishes resistance. Plant Molecular Biology, 2012,80(3):273-287.

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样本名称 Sample name	原始读段 Raw reads	有效读段 Clean reads	测序错误率 Error rate (%)	可定位序列总数及占比 Total mapped	多定位序列计数及占比 Multiple mapped	单定位序列计数及占比 Uniquely mapped
PBS_25_1	81285872	80011202	0.02	76771937 (95.95%)	36818251 (46.02%)	39953686 (49.94%)
PBS_25_2	79744462	78438974	0.02	75316854 (96.02%)	36751852 (46.85%)	38565002 (49.17%)
PBS_25_3	82086686	81323058	0.02	78074493 (96.01%)	38211722 (46.99%)	39862771 (49.02%)
PBS_31_1	112775324	110071878	0.01	106555280 (96.81%)	51925797 (47.17%)	54629483 (49.63%)
PBS_31_2	110922928	108381110	0.01	105100267 (96.97%)	51096062 (47.14%)	54004205 (49.83%)
PBS_31_3	111456946	109144098	0.01	105971578 (97.09%)	51922061 (47.57%)	54049517 (49.52%)
TMV_25_1	82779880	81084374	0.02	77865206 (96.03%)	38330300 (47.27%)	39534906 (48.76%)
TMV_25_2	81397982	79800752	0.02	76525369 (95.90%)	36994028 (46.36%)	39531341 (49.54%)
TMV_25_3	84779126	83206166	0.02	79834756 (95.95%)	40768694 (49.00%)	39066062 (46.95%)
TMV_31_1	86454182	85145676	0.02	81734255 (95.99%)	39993324 (46.97%)	41740931 (49.02%)
TMV_31_2	82671238	81754880	0.01	78713311 (96.28%)	35893618 (43.90%)	42819693 (52.38%)
TMV_31_3	96258450	93993096	0.02	90712104 (96.51%)	44629779 (47.48%)	46082325 (49.03%)

通路 Pathway	TMV_25_vs_PBS_25	TMV_31_vs_PBS_31
植物激素信号转导Plant hormone signal transduction	22	15
苯丙烷类生物合成Phenylpropanoid biosynthesis	12	9
mRNA监测途径mRNA surveillance pathway	11	6
嘧啶代谢Pyrimidine metabolism	10	6
ABC运输蛋白ABC transporters	3	3
非同源末端连接Non-homologous end-joining	3	1
RNA转运RNA transport	6	_
碱基切除修复Base excision repair	5	_
错配修复Mismatch repair	4	_
氨酰基-tRNA生物合成Aminoacyl-tRNA biosynthesis	4	_
缬氨酸、亮氨酸和异亮氨酸的生物合成Valine, leucine and isoleucine biosynthesis	3	_
缬氨酸、亮氨酸和异亮氨酸降解Valine, leucine and isoleucine degradation	3	_
同源重组Homologous recombination	3	_
一个叶酸碳库One carbon pool by folate	3	_
二萜生物合成Diterpenoid biosynthesis	1	_
苯丙氨酸代谢Phenylalanine metabolism	_	7
水泡运输中的SNARE相互作用SNARE interactions in vesicular transport	_	1
磷脂酰肌醇信号系统Phosphatidylinositol signaling system	_	1
肌醇磷酸代谢Inositol phosphate metabolism	_	1
酮体的合成和降解Synthesis and degradation of ketone bodies	_	1
丁酸代谢Butanoate metabolism	_	1
鞘脂代谢Sphingolipid metabolism	_	1

Differential Expression of LncRNAs in Nicotiana tabacum var. Samsun NN Infected by TMV at Different Temperatures

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