摘要
[目的]本研究旨在全基因组范围内识别木霉(Trichoderma guizhouense)NJAU4742(NJAU4742)的长链非编码RNA(long noncoding RNA,lncRNA),探究lncRNA在重寄生过程中可能参与的调控作用。[方法]用链特异性RNA-seq技术,对重寄生过程中与病原菌互作接触前、后以及独立培养的木霉菌进行转录组测序;构建生物信息学流程,识别lncRNA并用RSEM和DESeq2软件分析lncRNA在重寄生过程中的表达情况;对lncRNA的靶标预测和表达情况进行分析,探索lncRNA在重寄生过程中可能参与的调控作用。[结果]在木霉NJAU4742中识别了1676个lncRNA,其中包含1049个基因间型lncRNA,590个反义型lncRNA,32个正义型lncRNA以及5个内含子型lncRNA。与编码基因相比,lncRNA的外显子数量偏少,序列长度偏短,表达量偏低,在基因组上的跨度偏短。靶标预测结果显示:1496个lncRNA能够靶向2269个蛋白编码基因,其中1492个lncRNA以顺式作用形式靶向2262个编码基因,4个lncRNA以反式作用形式靶向7个编码基因。GO功能分类结果显示:代谢过程(metabolic process)、催化活性(catalytic activity)和细胞过程(cellular process)是lncRNA靶标分布数量较多的3个类别。KEGG通路分析结果显示:信号转导(signal transduction)、转运与分解代谢(transport and catabolism)和碳水化合物代谢(carbohydrate metabolism)是lncRNA靶标分布数量较多的3类通路。进一步分析发现:147个lncRNA靶向编码碳水化合物活性酶和蛋白酶的基因以及次生代谢物合成相关的基因,其中30个lncRNA在重寄生过程中表达水平发生显著变化,有10个lncRNA的表达和靶标基因显著相关。[结论]木霉在NJAU4742中存在长链非编码RNA,部分成员参与对病原菌重寄生过程的调控。
[Objectives] This study was to identify the long noncoding RNA(lncRNA)of Trichoderma guizhouense NJAU 4742(NJAU 4742)in genome-wide and to explore the regulatory mechanism of lncRNA in mycoparasitism.[Methods] The transcriptome of the hypha from independently cultivated NJAU 4742,the hypha from NJAU 4742 before directly contacting with pathogenic fungi and the hypha from the zone of interaction of NJAU 4742 after contacting with pathogenic fungi were sequenced using strand-specific RNA-seq technology.Then a computational pipeline was designed to identify the lncRNA.RSEM and DESeq2 were used to analyze the expression levels of lncRNA during mycoparasitism.The regulation role of lncRNA during mycoparasitism was analyzed based on the function of targets and the expression profiles of lncRNA.[Results] A total of 1 676 lncRNA were identified in NJAU 4742,including 1 049 intergenic,590 antisense,32 sense and 5 intronic lncRNA.Compared to protein-coding genes,lncRNA had less exons,lower expression levels,shorter sequence length and shorter span distance in genome.The 1 496 lncRNA were predicted to target 2 269 protein-coding genes,including 1 492 lncRNA targeting 2 262 protein-coding genes by cis -form and 4 lncRNA targeting 7 protein-coding genes by trans -form.Metabolic process,catalytic activity and cellular process were the three most assigned GO subcategories.Signal transduction,transport and catabolism,and carbohydrate metabolism were the three most assigned pathway categories.Furthermore,147 lncRNA were predicted to target genes coding carbohydrate-active enzymes(CAZys),proteases and genes involved in the formation of secondary metabolites,which possibly associated with mycoparasitism.In the 147 lncRNA,there were 30 significantly differently expressed lncRNA during mycoparasitism.The significant correlations in the expression profiles were observed between 10 lncRNA and corresponding targets.[Conclusions]:Long-chain non-coding RNA exists in Trichoderma sp.NJAU 4742,and some members participate in the regulation of pathogenic bacterial parasitism.
作者
刘金定
王权
黄水清
沈其荣
LIU Jinding;WANG Quan;HUANG Shuiqing;SHEN Qirong(Jiangsu Provincial Key Lab of Solid Organic Waste Utilization/Jiangsu Collaborative Innovation Center of Solid Organic Wastes/Educational Ministry Engineering Center of Resource-saving Fertilizers,Nanjing Agricultural University,Nanjing 210095,China;College of Information Science and Technology/Research Center for Correlation of Domain Knowledge,Nanjing Agricultural University,Nanjing 210095,China)
出处
《南京农业大学学报》
CAS
CSCD
北大核心
2019年第5期877-886,共10页
Journal of Nanjing Agricultural University
基金
国家自然科学基金项目(31301691)
中央高校基本科研业务费专项资金(KYZ201667)
