Scientia Agricultura Sinica ›› 2018, Vol. 51 ›› Issue (11): 2094-2105.doi: 10.3864/j.issn.0578-1752.2018.11.007

• PLANT PROTECTION • Previous Articles     Next Articles

Mining and Characterization of MicroRNAs Associated with Pathogenicity by Different Sweet Potato Viruses

LI HuaWei, LIU ZhongHua, ZHANG Hong, XU YongQing, LI GuoLiang, LIN ZhaoMiao, QIU YongXiang, LUO WenBin, JI RongChang, TANG Hao, QIU SiXin   

  1. Crop Research Institute, Fujian Academy of Agricultural Sciences/Scientific Observing and Experimental Station of Tuber and Root Crops in South China, Ministry of Agriculture, Fuzhou 350013
  • Received:2017-12-20 Online:2018-06-01 Published:2018-06-01

Abstract: 【Objective】Various viruses had been identified from sweet potato. Infections with different sweet potato viruses may result in different pathological symptoms of plants. The objective of this study is to investigate the microRNAs (miRNAs) in response to different pathogens from sweet potato viruses in sweet potato.MethodIllumina RNA sequencing was performed to mine and identify the differentially expressed miRNAs among samples with different infection pathological symptoms (yellowing and deformity, herpes, chlorotic and dwarf, and curl; sample was named Fj01, Fj02, Fj03 and 1H, respectively) of ‘Longshu 9’ from Quanzhou, Fujian, China. Total and differentially expressed miRNAs among samples were identified. Real-time PCR analysis of several miRNAs and viruses was performed to validate the quality of sequencing data. Target predication and functional enrichment for these miRNAs were analyzed. Association between miRNAs and virus infections would be discussed.ResultAfter the alignment to the virus database of sweet potato, 3 samples (without 1H) were simultaneously infected with common sweet potato viruses, including Sweet potato chlorotic stunt virus (SPCSV), Sweet potato virus 2 (SPV2), Sweet potato feathery mottle virus (SPFMV), Sweet potato virus G (SPVG), and Sweet potato virus C (SPVC), although they showed different pathological symptoms. In addition, uncommon viruses were identified in different samples. Using PCR analysis of SPFMV and SPVC viruses, the consistence with sequencing data were validated. Using sequencing analysis, 679 known miRNAs and 1 004 novel miRNAs were found in these 4 samples. With comparative analysis, it was identified that 288 known miRNAs and 433 novel miRNAs were differentially expressed among these 4 samples. These miRNAs showed different expression profiles among samples, such as the members of miR-156, miR-157, and miR-166 families. qRT-PCR analysis showed these expression profiles of several miRNAs (including miR-156, novel-miR-40 and miR-319m) were in consistence with their profiles by sequencing. In comparison with that in virus-free seedling, the expression of 3 miRNAs (miR-160a, miR-2096 and miR-5387b) was differentially upregulated in these 4 sequencing samples. These results suggested that these miRNAs might be related to virus infections. Further target predication found that most of these miRNA targets were transcription factors, including genes encoding ZFP, WD, Myb, and SPL domain-containing proteins. Enrichment analysis for those targets showed that they were associated with plant growth and development, morphogenesis, and stress resistance via regulating genes, signaling pathways, and antigen recognition. These represented the multipotent functions of these miRNAs’ targets.ConclusionDifferent sweet potato viruses induced differences in miRNA profiling, and these miRNAs were mainly associated with plant growth, resistance and plant defense.

Key words: sweet potato, microRNA, Illumina sequencing, sweet potato virus

[1]    王冰, 宋娜, 孙燕飞, 冯浩, 王晓杰, 康振生. MircoRNA156家族在小麦非生物胁迫中的表达分析. 植物病理学报, 2013, 43(2): 201-204.
WANG B, SONG N, SUN Y F, FENG H, WANG X J, KANG Z S. Expression analysis of wheat mircoRNA156 family in response to abiotic stress. Acta Phytopathologica Sinica, 2013, 43(2): 201-204. (in Chinese)
[2]    冯静弦, 汪启明, 胡琪, 饶力群. 拟南芥中热胁迫相关microRNA的差异表达. 湖南农业科学, 2012(3): 10-13.
FENG J X, WANG Q M, HU Q, RAO L Q. Differential expression of heat stress related microRNA in Arabidopsis thaliana. Hunan Agricultural Science, 2012(3): 10-13. (in Chinese)
[3]    俞正, 庄然. 病毒感染miRNA的免疫调控机制研究进展. 细胞与分子免疫学杂志, 2016, 32(2): 261-264.
YU Z, ZHUANG R. Advances in immunoregulation mechanism of virus infection associated miRNA. Chinese Journal of Cellular and Molecular Immunology, 2016, 32(2): 261-264. (in Chinese)
[4]    王维, 张玉娟, 陈洁, 刘聚波, 夏民旋, 沈法富. 植物逆境胁迫相关miRNA研究进展. 生物技术通报, 2015, 31(1): 1-10.
WANG W, ZHANG Y J, CHEN J, LIU J B, XIA M X, SHEN F F. Research progress of microRNAs in plant stresses responses. Biotechnology Bulletin, 2015, 31(1): 1-10. (in Chinese)
[5]    冉莉萍, 孔月琴, 方婷婷, 王幼平. 逆境胁迫下植物表观遗传机制的研究进展. 生物技术通报, 2014(8): 8-15.
RAN L P, KONG Y Q, FANG T T, WANG Y P. Research progress of stress-induced epigenetic regulation mechanism in plant. Biotechnology Bulletin, 2014(8): 8-15. (in Chinese)
[6]    ZHOU Q L, ZHANG Y J, HUANG Y D, LI Y M, HE S L, YANG H K, LIU L S, WANG M. Effects of SPVD on sweet potato yield formation. Agricultural Science & Technology, 2014, 15(9): 1446-1449.
[7]    包改丽, 左瑞娟, 饶维力, LI Ru-Hui, 李凡. 云南甘薯病毒的检测及主要病毒的多样性分析. 微生物学通报, 2013, 40(2): 236-248.
[8]    刘辛. 番茄microRNA及其靶基因对几种病毒侵染的反应[D]. 杭州: 浙江理工大学, 2008.
LIU X. Response of tomato microRNA and their target mRNAs to virus infection[D]. Hangzhou: Zhejiang Sci-Tech University, 2008. (in Chinese)
[9]    陈莎. 深度测序鉴定玉米病毒及感病玉米组织中小RNA分析[D]. 杭州: 浙江大学, 2015.
CHEN S. Identification of plant viruses from maize by deep sequencing and analysis of small RNA in virus infected maize[D]. Hangzhou: Zhejiang University, 2015. (in Chinese)
[10]   王园龙, 曹林, 邓敏捷, 马一平, 赵振利, 牛苏燕, 王晓丹, 范国强. 利用高通量测序分析白花泡桐盐胁迫相关microRNAs. 河南农业大学学报, 2015, 49(4): 461-467.
WANG Y L, CAO L, DENG M J, MA Y P, ZHAO Z L, NIU S Y, WANG X D, FAN G Q. Analysis of salt stress-responsive microRNA in Paulownia fortunei by high-throughout sequencing. Journal of Henan Agricultural University, 2015, 49(4): 461-467. (in Chinese)
[11]   陈洁. 重金属铅胁迫下玉米苗期根系miRNA的鉴定及相关miRNA的表达分析[D]. 雅安: 四川农业大学, 2010.
CHEN J. Identification and expression analysis of miRNAs in immature maize root under the stress of heavy metal Pb[D]. Yaan: Sichuan Agricultural University, 2010. (in Chinese)
[12]   马骢毓. 马铃薯抗旱相关microRNA的鉴定及分析[D]. 兰州: 甘肃农业大学, 2012.
MA C Y. Identification and analysis of microRNA related to drought resistance of potato[D]. Lanzhou: Gansu Agricultural University, 2012. (in Chinese)
[13]   詹琳琳. 烟草抗马铃薯Y病毒miRNA的筛选及相关miRNA的功能分析[D]. 杭州: 浙江农林大学, 2015.
ZHAN L L. Screening for miRNA of tobacco resistance to potato virus Y and function analysis of relevant miRNA[D]. Hangzhou: Zhejiang A & F University, 2015. (in Chinese)
[14]   乔奇, 张振臣, 张德胜, 秦艳红, 田雨婷, 王永江. 中国甘薯病毒种类的血清学和分子检测. 植物病理学报, 2012, 42(1): 10-16.
QIAO Q, ZHANG Z C, ZHANG D S, QIN Y H, TIAN Y T, WANG Y J. Serological and molecular detection of viruses infecting sweet potato in China. Acta Phytopathologica Sinica, 2012, 42(1): 10-16. (in Chinese)
[15]   Meyers B C, Axtell M J, Bartel B, Bartel D P, Baulcombe D, Bowman J L, Cao X, Carrington J C, Chen X, Green P J,  Griffiths-Jones S. Criteria for annotation of plant MicroRNAs. The Plant Cell, 2008, 20(12): 3186-3190.,Jacobsen SE,Mallory A C,Martienssen R A,Poethig R S,Qi Y,Vaucheret H,Voinnet O,Watanabe Y,Weigel D,Zhu J K
[16]   Lavorgna G, Guffanti A, Borsani G, Ballabio A, Boncinelli E. TargetFinder: searching annotated sequence databases for target genes of transcription factors. Bioinformatics, 1999, 15(2): 172-173.
[17]   黄利利, Binhdan P, 何芳练, 刘奕君, 刘义明, 陈保善, 廖咏梅. 广西甘薯病毒病的病原病毒种类检测. 基因组学与应用生物学, 2016, 35(5): 1213-1218.
HUANG L L, Binhdan P, HE F L, LIU Y J, LIU Y M, CHEN B S, LIAO Y M. The pathogenic virus species detection of sweet potato viral diseases in Guangxi. Genomics and Applied Biology, 2016, 35(5): 1213-1218. (in Chinese)
[18]   姜珊珊, 谢礼, 吴斌, 辛相启, 陈剑平, 赵玖华. 山东甘薯主要病毒的鉴定及多样性分析. 植物保护学报, 2017, 44(1): 93-102.
JIANG S S, XIE L, WU B, XIN X Q, CHEn J P, ZHAO J H. Identification and genetic diversity analysis on sweet potato viruses in Shandong Province. Journal of Plant Protection, 2017, 44(1): 93-102. (in Chinese)
[19]   彭小琴, 王浩然, 张俊, 张玮华, 郭灵芳, 方守国, 章松柏. 湖北甘薯病毒病的检测与鉴定. 中国植保导刊, 2017, 37(8): 20-23.
PENG X Q, WANG H R, ZHANG J, ZHANG W H, GUO L F, FANG S G, ZHANG S B. Detection and identification of sweet potato virus diseases in Hubei. China Plant Protection, 2017, 37(8): 20-23. (in Chinese)
[20]   张爱红, 苗洪芹, 朱宝成, 路银贵, 陈丹, 邸垫平. 水稻黑条矮缩病毒在不同抗性玉米自交系叶片内的积累研究. 河北农业大学学报, 2007, 30(2): 79-82.
ZHANG A H, MIAO H Q, ZHU B C, LU Y G, CHEN D, DI D P. Studies on the concentration of RBSDV in corn inbred lines with different resistance to the disease. Journal of Agricultural University of Hebei, 2007, 30(2): 79-82. (in Chinese)
[21]   刘起丽. 共生丛植菌根减轻番茄黄化卷叶撒丁岛病毒症状和降低病毒浓度. 农业生物技术学报, 2014, 22(2): 149.
LIU Q L. The arbuscular mycorrhizal symbiosis attenuates symptom severity and reduces virus concentration in TYLCSV. Journal of agricultural biotechnology, 2014, 22(2): 149. (in Chinese)
[22]   季志强, 杨青林, 桑利民, 盖颜欣. 脱毒马铃薯的增产机理和增产原因分析. 种子世界, 2014(5): 23.
JI Z Q, YANG Q L, SANG L M, GAI Y X. Analysis of the mechanism and cause of increased production of detoxification potato plant. Seed World, 2014(5): 23. (in Chinese)
[23]   牟慧芳, 齐雯雯, 刘艳玲, 李毅, 吴莹. microRNA参与调控植物抵御病原微生物的研究进展. 现代农业科技, 2016(23): 144-147.
MU H F, QI W W, LIU Y L, LI Y, WU Y. Research advances of microRNAs in plant resistance to pathogens. Modern Agricultural Sciences and Technology, 2016(23): 144-147. (in Chinese)
[24]   王晟. 水稻小RNA的基因组分布和分子进化研究[D]. 杭州: 浙江大学, 2008.
WANG S. Genome-wide profiling and evolution of small RNAs in rice[D].Hangzhou: Zhejiang University, 2008. (in Chinese)
[25]   Chuck G, Cigan A M, Saeteurn K, Hake S. The heterochronic maize mutant Corngrass1 results from overexpression of a tandem microRNA. Nature genetics, 2007, 39(4): 544-549.
[26]   雷凯健, 刘浩. 植物调控枢纽miR156及其靶基因SPL家族研究进展. 生命的化学, 2016, 36(1): 13-20.
LEI K J, LIU H. Research advances in plant regulatory hub miRNA156 and target SPL family. Chemistry of Life, 2016, 36(1): 13-20. (in Chinese)
[27]   Chen X, Chen Z, Zhao H L, Zhao Y, Cheng B J, Xiang Y. Genome-wide analysis of soybean HD-Zip gene family and expression profiling under salinity and drought treatments. PLoS ONE, 2014, 9(2): e87156.
[28]   González-Grandío E, Pajoro A, Franco-Zorrilla J M, Tarancón C, Immink R G, Cubas P. Abscisic acid signaling is controlled by a BRANCHED1/HD-ZIP I cascade in Arabidopsis axillary buds. Proceedings of the National Academy of Sciences of the United States of America, 2017, 114(2): E245-E254.
[29]   王宏, 李刚波, 张大勇, 蔺经, 盛宝龙, 韩金龙, 常有宏. 植物HD-Zip转录因子的生物学功能. 遗传, 2013, 35(10): 1179-1188.
WANG H, LI G B, ZHANG D Y, LIN J, SHENG B L, HAN J L, CHANG Y H. Biological functions of HD-Zip transcription factors. Hereditas, 2013, 35(10): 1179-1188. (in Chinese)
[30]   董云, 王毅, 靳丰蔚, 孙万仓, 刘自刚, 方彦, 徐妙云, 王磊. 油菜Bna-miR169d基因的分离与过表达初步分析. 西北农业学报, 2016, 25(12): 1809-1815.
DONG Y, WANG Y, JING F W, SUN W C, LIU Z G, FANG Y, XU M Y, WANG L. Isolation and preliminary overexpression of Bna-miR169d gene in oilseed rapes Sinica, 2016, 25(12): 1809-1815. (in Chinese). Acta Agriculturae Boreali-occidentali
[31]   Hu T, Ye J, Tao P, Li H, Zhang J, Zhang Y, Ye Z. The tomato HD-Zip I transcription factor SlHZ24 modulates ascorbate accumulation through positive regulation of the d-mannose/l- galactose pathway. The Plant Journal, 2016, 85(1): 16-29.
[32]   许振华, 谢传晓. 植物microRNA与逆境响应研究进展. 遗传, 2010, 32(10): 1018-1030.
XU Z H, XIE C X. Advances in plant microRNA and stresses response. Hereditas, 2010, 32(10): 1018-1030. (in Chinese)
[33]   王炳南. 小麦SPL基因的比较分析和功能研究[D]. 北京: 中国农业科学院, 2015.
WANG B N. Comparative analysis and functional study of SQUAMOSA promoter binding protein-like (SPL) genes in wheat[D]. Beijing: Chinese Academy of Agricultural Sciences, 2015. (in Chinese)
[34]   伍翀, 杨兆春, 秦双双, 袁媛, 黄璐琦, 陈平. 植物MYB转录因子研究进展//中华中医药学会中药鉴定学术会议暨中药材鉴定方法和技术研讨会, 2010.
WU C, YANG Z C, QIN S S, YUAN Y, HUANG L Q, CHEN P. Advances in plant MYB transcription factors//China Chinese medicine institute academic conference on Chinese medicine identification, the seminar of Chinese medicine identification method and technic, 2010. (in Chinese)
[35]   Ren L, Sun J, Chen S, Gao J, Dong B, Liu Y, Xia X, Wang Y, Liao Y, Teng N, Fang W, Guan Z, Chen F, Jiang J. A transcriptomic analysis of Chrysanthemum nankingense provides insights into the basis of low temperature tolerance. BMC genomics, 2014, 15(1): 844.
[36]   郭彤. 低温胁迫下菊花叶片转录组比较分析[D]. 郑州: 河南农业大学, 2016.
GUO T. Comparative transcriptome analysis of the regulation of responding to low temperature in Dendranthema morifolium by RNA-seq[D]. Zhengzhou: Henan Agricultural University, 2016. (in Chinese)
[37]   刘维. 番茄钙调蛋白和类钙调蛋白的抗病调控功能分析[D]. 杭州: 浙江大学, 2015.
LIU W. Functional analyses of tomato calmodulin and calmodulin-like genes in disease resistance[D]. Hangzhou: Zhejiang University, 2015. (in Chinese)
[38]   Radwan O, Gandhi S, Heesacker A, Whitaker B, Taylor C, Plocik A, Kesseli R, Kozik A, Michelmore R W, Knapp S J. Genetic diversity and genomic distribution of homologs encoding NBS-LRR disease resistance proteins in sunflower. Molecular genetics and genomics, 2008, 280(2): 111-125.
[1] LI Ning,LIU Kun,LIU TongTong,SHI YuGang,WANG ShuGuang,YANG JinWen,SUN DaiZhen. Identification of Wheat Circular RNAs Responsive to Drought Stress [J]. Scientia Agricultura Sinica, 2022, 55(23): 4583-4599.
[2] FENG RuiRong,FU ZhongMin,DU Yu,ZHANG WenDe,FAN XiaoXue,WANG HaiPeng,WAN JieQi,ZHOU ZiYu,KANG YuXin,CHEN DaFu,GUO Rui,SHI PeiYing. Identification and Analysis of MicroRNAs in the Larval Gut of Apis cerana cerana [J]. Scientia Agricultura Sinica, 2022, 55(1): 208-218.
[3] DU Yu,FAN XiaoXue,JIANG HaiBin,WANG Jie,FENG RuiRong,ZHANG WenDe,YU KeJun,LONG Qi,CAI ZongBing,XIONG CuiLing,ZHENG YanZhen,CHEN DaFu,FU ZhongMin,XU GuoJun,GUO Rui. MicroRNA-Mediated Cross-Kingdom Regulation of Apis mellifera ligustica Worker to Nosema ceranae [J]. Scientia Agricultura Sinica, 2021, 54(8): 1805-1820.
[4] LÜ ShiKai, MA XiaoLong, ZHANG Min, DENG PingChuan, CHEN ChunHuan, ZHANG Hong, LIU XinLun, JI WanQuan. Post-transcriptional Regulation of TaNAC Genes by Alternative Splicing and MicroRNA in Common Wheat (Triticum aestivum L.) [J]. Scientia Agricultura Sinica, 2021, 54(22): 4709-4727.
[5] ZHAO Shan,ZHONG LingLi,QIN Lin,HUANG ShiQun,LI Xi,ZHENG XingGuo,LEI XinYu,LEI ShaoRong,GUO LingAn,FENG JunYan. Effects of Different Drying Methods on Functional Components and Antioxidant Activity in Sweet Potato Leaves [J]. Scientia Agricultura Sinica, 2021, 54(21): 4650-4663.
[6] ZHAO FuMei,WANG Shuang,TIAN YuTing,QIAO Qi,WANG YongJiang,ZHANG DeSheng,ZHANG ZhenChen. An Investigation into Key Factors Influencing the Occurrence of Virus Disease in Sweet Potato [J]. Scientia Agricultura Sinica, 2021, 54(15): 3232-3240.
[7] WANG JinQiang,LI SiPing,LIU Qing,LI Huan. Mechanism of Spraying Growth Regulators to Alleviate Drought Stress of Sweet Potato [J]. Scientia Agricultura Sinica, 2020, 53(3): 500-512.
[8] GENG SiHai,SHI CaiYun,FAN XiaoXue,WANG Jie,ZHU ZhiWei,JIANG HaiBin,FAN YuanChan,CHEN HuaZhi,DU Yu,WANG XinRui,XIONG CuiLing,ZHENG YanZhen,FU ZhongMin,CHEN DaFu,GUO Rui. The Mechanism Underlying MicroRNAs-Mediated Nosema ceranae Infection to Apis mellifera ligustica Worker [J]. Scientia Agricultura Sinica, 2020, 53(15): 3187-3204.
[9] DU Yu,FAN XiaoXue,JIANG HaiBin,WANG Jie,FAN YuanChan,ZHU ZhiWei,ZHOU DingDing,WAN JieQi,LU JiaXuan,XIONG CuiLing,ZHENG YanZhen,CHEN DaFu,GUO Rui. The Potential Role of MicroRNAs and MicroRNA-Mediated Competing Endogenous Networks During the Developmental Process of Apis mellifera ligustica Worker’s Midgut [J]. Scientia Agricultura Sinica, 2020, 53(12): 2512-2526.
[10] QIN YanHong,WANG YongJiang,WANG Shuang,QIAO Qi,TIAN YuTing,ZHANG DeSheng,ZHANG ZhenChen. Complete Nucleotide Sequence Analysis and Genetic Characterization of the Sweet potato feathery mottle virus O and RC Strains Isolated from China [J]. Scientia Agricultura Sinica, 2020, 53(11): 2207-2218.
[11] XU Shu,LI Ling,ZHANG SiMeng,CAO RuXia,CHEN LingLing,CUI Peng,Lü ZunFu,WU LieHong,LU GuoQuan. Evaluation of Genotype Differences of Cold Tolerance of Sweet Potato Seedlings by Subordinate Function Value Analysis [J]. Scientia Agricultura Sinica, 2019, 52(17): 2929-2938.
[12] GUO Rui,DU Yu,TONG XinYu,XIONG CuiLing,ZHENG YanZhen,XU GuoJun,WANG HaiPeng,GENG SiHai,ZHOU DingDing,GUO YiLong,WU SuZhen,CHEN DaFu. Differentially Expressed MicroRNAs and Their Regulation Networks in Apis mellifera ligustica Larval Gut During the Early Stage of Ascosphaera apis Infection [J]. Scientia Agricultura Sinica, 2019, 52(1): 166-180.
[13] JIANG ShanShan, FENG Jia, ZHANG Mei, WANG ShengJi, XIN ZhiMei, WU Bin, XIN XiangQi. Development of RT-LAMP Assay for Rapid Detection of Sweet potato feathery mottle virus (SPFMV) [J]. Scientia Agricultura Sinica, 2018, 51(7): 1294-1302.
[14] Rui GUO,Yu DU,CuiLing XIONG,YanZhen ZHENG,ZhongMin FU,GuoJun XU,HaiPeng WANG,HuaZhi CHEN,SiHai GENG,DingDing ZHOU,CaiYun SHI,HongXia ZHAO,DaFu CHEN. Differentially Expressed MicroRNA and Their Regulation Networks During the Developmental Process of Apis mellifera ligustica Larval Gut [J]. Scientia Agricultura Sinica, 2018, 51(21): 4197-4209.
[15] XU Xi, REN MingJian, LI LuHua, YANG XiCui, XU RuHong. Differential Expression of Grain Pigment Related Genes of Guizimai No.1 [J]. Scientia Agricultura Sinica, 2018, 51(2): 203-216.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
No Suggested Reading articles found!