中国农业科学 ›› 2020, Vol. 53 ›› Issue (7): 1381-1396.doi: 10.3864/j.issn.0578-1752.2020.07.008
贾海燕1,宋丽云1,徐翔1,解屹1,张超群2,刘天波3,赵存孝4,申莉莉1,王杰1,李莹1,王凤龙1,杨金广1
收稿日期:
2019-09-16
接受日期:
2019-11-06
出版日期:
2020-04-01
发布日期:
2020-04-14
作者简介:
贾海燕,E-mail:基金资助:
HaiYan JIA1,LiYun SONG1,Xiang XU1,Yi XIE1,ChaoQun ZHANG2,TianBo LIU3,CunXiao ZHAO4,LiLi SHEN1,Jie WANG1,Ying LI1,FengLong WANG1,JinGuang YANG1
Received:
2019-09-16
Accepted:
2019-11-06
Online:
2020-04-01
Published:
2020-04-14
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KEGG富集分析研究靶基因的功能。【结果】 4个处理共12个样本经lncRNA-seq各测得约8 000万条clean reads,共获得4 737条已知lncRNA、40 169条新lncRNA。其中64个lncRNA在不同温度条件下TMV侵染后存在差异表达,qRT-PCR测定结果显示这些lncRNA的测序正确率在80%左右,表明本研究所得测序数据具备较高的可信度。对DElncRNA进行靶基因预测,发现一些基因同时被25℃下调和31℃上调的DElncRNA靶向。靶基因注释功能丰富,主要参与植物抗病、激素和代谢等生理过程。部分可能与激素通路相关的lncRNA,在25℃下TMV侵染时呈现下调趋势,而在31℃下TMV侵染则呈现上调趋势。GO富集分析显示靶基因主要参与构成膜、囊泡等组分,具备钙、钾离子通道抑制剂活性等分子功能,使相应离子得以转运引发随后的反应,同时也参与发病、抗原加工和呈现、细胞分裂素代谢等生理过程。KEGG分析发现靶基因显著富集在植物激素信号转导通路,25℃下调和31℃上调的DElncRNA靶基因同时富集在激素信号传导、ABC运输蛋白、苯丙烷类生物合成等通路。【结论】 不同温度(25℃和31℃)条件下TMV侵染枯斑三生烟后,长链非编码RNA差异表达,DElncRNA通过作用于激素信号传导、物质转运等过程参与寄主系统获得性抗性反应。研究结果可为揭示植物系统获得性抗性中lncRNA的调控功能以及新型抗病毒技术开发提供依据。
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.
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.
图1
不同温度下TMV接种前后的枯斑三生烟 A:25℃条件下TMV接种前的枯斑三生烟Samsun NN before TMV inoculation at 25℃;B:25℃条件下TMV接种48 h后的枯斑三生烟Samsun NN after 48 hours of TMV inoculation at 25℃;C:31℃条件下TMV接种前的枯斑三生烟Samsun NN before inoculation of TMV at 31℃;D:31℃条件下TMV接种48 h后的枯斑三生烟Samsun NN after 48 hours of TMV inoculation at 31℃。标注为小写字母的图片展示相应枯斑三生烟的接种叶The pictures marked in lowercase letters show the inoculated leaves of the corresponding tobacco"
表1
25℃下差异表达lncRNA引物序列"
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 |
表2
31℃下差异表达lncRNA引物序列"
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 |
表3
测序数据概览"
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%) |
图2
LncRNA-seq结果分析 A:lncRNA和mRNA序列长度的密度分布Density distribution of sequence lengths of lncRNA and mRNA;B:lncRNA和mRNA外显子个数的密度分布Density distribution of exon number of lncRNA and mRNA;C:lncRNA和mRNA ORF长度的密度分布Density distribution of ORF length of lncRNA and mRNA;D:不同类型转录本表达水平比较Comparison of expression levels of different types of transcripts;E:不同处理转录本表达水平比较Comparison of expression levels of different treatments of transcripts;F:25℃和31℃比较组中差异表达lncRNA数目统计The numbers of differentially expressed lncRNAs in the comparison groups of 25℃ and 31℃"
图3
差异表达lncRNA分析 A:25℃差异表达lncRNA火山图,横坐标代表转录本在不同样本中表达倍数变化,纵坐标代表转录本表达量变化差异的统计学显著性,q-value即P-adjust;图中红色点表示有显著性差异表达的上调转录本,蓝色点表示有显著性差异表达的下调转录本Volcano plot of differentially expressed lncRNAs at 25℃. The abscissa represents expression fold change in different samples, the ordinate represents the statistical significance of difference in transcript expression, and the q-value is P-adjust. The red dot in the figure indicates the up-regulated transcript with significant differential expression, and the blue dot indicates the down-regulated transcript with significant differential expression;B:31℃差异表达lncRNA火山图Volcano plot of differentially expressed lncRNAs at 31℃。C:差异表达lncRNA表达量层次聚类,以 lg (FPKM+1) 值进行聚类,红色代表基因高表达,蓝色表示低表达基因,颜色从红到蓝表示lg (FPKM+1)从大到小DElncRNA expression level hierarchical clustering, clustering was performed with lg (FPKM+1) values, with red representing high expression of genes and blue indicating low expressed genes, colors from red to blue indicate lg (FPKM+1) from large to small"
图4
25℃条件下差异表达lncRNA 的qRT-PCR验证 A:25℃和TMV处理下uDElncRNA的相对表达量Relative expression of up-regulated DElncRNAs after TMV treatment at 25℃;B:25℃和TMV处理下dDElncRNA的相对表达量Relative expression of down-regulated DElncRNAs after TMV treatment at 25℃ 误差线表示3组生物学重复的正负标准差,采用t-检验分析差异显著性 Error bars indicate the ±SD of three biological replicates. Student’s t-test. *:P<0.1; **:P<0.01; ***:P<0.001。图5同 The same as Fig. 5"
表4
GO条目富集的 DElncRNA靶基因数目"
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 |
表5
KEGG 通路富集的DElncRNA靶基因数目比较"
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 |
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