菠萝在常温贮藏过程中易发生黑心病,为了探索黑心病的发生机制,选取菠萝黑心病初期果实的发病部位和健康部位,每个部位选取3个样本分别进行测转录组RNA-Seq分析,对差异基因进行GO、KEGG、各代谢通路基因表达聚类分析和RT-qPCR验证,对比...菠萝在常温贮藏过程中易发生黑心病,为了探索黑心病的发生机制,选取菠萝黑心病初期果实的发病部位和健康部位,每个部位选取3个样本分别进行测转录组RNA-Seq分析,对差异基因进行GO、KEGG、各代谢通路基因表达聚类分析和RT-qPCR验证,对比病部(IB)和健部(WT)的差异基因表达量。通过分析发现,IB vs WT共有1037个差异基因,其中上调886个,下调130个。GO和KEGG分析发现氨基酸生物合成差异基因最显著,而且差异基因数量占比大;通过聚类分析和RT-qPCR验证,糖代谢路径发现果实发病后糖酵解、三羧酸循环(TCA)和氧化磷酸化过程中相关酶基因表达量显著上调;植物应对外界环境信号通路发现抗性酶基因表达量显著下调,致病蛋白基因表达量显著上调,抗病蛋白基因表达量显著下调;抗氧化物质通路发现谷胱甘肽合成基因表达量显著下调,类黄酮生物合成相关基因表达量显著上调,L-抗坏血酸过氧化物酶(APX)基因表达量显著下调,而L-抗坏血酸氧化酶(AOX)同系物基因表达量显著上调。RNA-Seq和RT-qPCR分析结果表明,菠萝组织通过显著上调糖代谢关键基因加速果实病部糖代谢、显著上调表达信号传导关键通路MAPK途径中的关键基因以及显著下调抗氧化物质等代谢通路变化而导致黑心病的发生。通过这些结果可以丰富菠萝黑心病发生的基因网络,为后续菠萝黑心病相关基因筛选提供信息参考。展开更多
The bacterial brown spot disease（BBS）, caused primarily by Pseudomonas syringae pv. syringae van Hall（Pss）, reduces plant vigor, yield and quality in maize. To reveal the nature of the defense mechanisms and ident...The bacterial brown spot disease（BBS）, caused primarily by Pseudomonas syringae pv. syringae van Hall（Pss）, reduces plant vigor, yield and quality in maize. To reveal the nature of the defense mechanisms and identify genes involved in the effective host resistance, the dynamic changes of defense transcriptome triggered by the infection of Pss were investigated and compared between two maize near-isogenic lines（NILs）. We found that Pss infection resulted in a sophisticated transcriptional reprogramming of several biological processes and the resistant NIL employed much faster defense responses than the susceptible NIL. Numerous genes encoding essential components of plant basal resistance would be able to be activated in the susceptible NIL, such as PEN1, PEN2, PEN3, and EDR1, however, in a basic manner, such resistance might not be sufficient for suppressing Pss pathogenesis. In addition, the expressions of a large number of PTI-, ETI-, PR-, and WRKY-related genes were pronouncedly activated in the resistant NIL, suggesting that maize employ a multitude of defense pathways to defend Pss infection. Six R-gene homologs were identified to have significantly higher expression levels in the resistant NIL at early time point, indicating that a robust surveillance system（gene-to-gene model） might operate in maize during Pss attacks, and these homolog genes are likely to be potential candidate resistance genes involved in BBS disease resistance. Furthermore, a holistic group of novel pathogen-responsive genes were defined, providing the repertoire of candidate genes for further functional characterization and identification of their regulation patterns during pathogen infection.展开更多
The analysis of messenger Ribonucleic acid obtained through sequencing techniques (RNA-se- quencing) data is very challenging. Once technical difficulties have been sorted, an important choice has to be made during pr...The analysis of messenger Ribonucleic acid obtained through sequencing techniques (RNA-se- quencing) data is very challenging. Once technical difficulties have been sorted, an important choice has to be made during pre-processing: Two different paths can be chosen: Transform RNA- sequencing count data to a continuous variable or continue to work with count data. For each data type, analysis tools have been developed and seem appropriate at first sight, but a deeper analysis of data distribution and structure, are a discussion worth. In this review, open questions regarding RNA-sequencing data nature are discussed and highlighted, indicating important future research topics in statistics that should be addressed for a better analysis of already available and new appearing gene expression data. Moreover, a comparative analysis of RNAseq count and transformed data is presented. This comparison indicates that transforming RNA-seq count data seems appropriate, at least for differential expression detection.展开更多
RNA-sequencing(RNA-seq),based on next-generation sequencing technologies,has rapidly become a standard and popular technology for transcriptome analysis.However,serious challenges still exist in analyzing and interpre...RNA-sequencing(RNA-seq),based on next-generation sequencing technologies,has rapidly become a standard and popular technology for transcriptome analysis.However,serious challenges still exist in analyzing and interpreting the RNA-seq data.With the development of high-throughput sequencing technology,the sequencing depth of RNA-seq data increases explosively.The intricate biological process of transcriptome is more complicated and diversified beyond our imagination.Moreover,most of the remaining organisms still have no available reference genome or have only incomplete genome annotations.Therefore,a large number of bioinformatics methods for various transcriptomics studies are proposed to effectively settle these challenges.This review comprehensively summarizes the various studies in RNA-seq data analysis and their corresponding analysis methods,including genome annotation,quality control and pre-processing of reads,read alignment,transcriptome assembly,gene and isoform expression quantification,differential expression analysis,data visualization and other analyses.展开更多
文摘目的为了初步了解广藿香酮抗金黄色葡萄球菌(Staphylococcus aureus)的分子机制。方法本研究用琼脂稀释法测定广藿香酮的药物敏感性,通过对金黄色葡萄球菌ATCC25923在1倍最低抑菌浓度(minimum inhibitory concentration,MIC)广藿香酮药物浓度作用1h时进行转录组的高通量测序然后对数据进行KEGG(kyoto encyclopedia of genes and genomes)和GO(gene ontology)差异基因表达以及热图聚类分析。结果药敏实验发现广藿香酮对金黄色葡萄球菌有抑制活性,经广藿香酮处理后,筛选出225个差异表达的基因,发现广藿香酮使金黄色葡萄球菌膜蛋白的表达、蛋白质的合成发生变化,并且使葡萄糖以及多糖的转运和合成受到控制。结论广藿香酮可能与金黄色葡萄球菌的细胞膜蛋白相互作用从而抑制细菌生长,为进一步的实验提供数据支持。
文摘菠萝在常温贮藏过程中易发生黑心病,为了探索黑心病的发生机制,选取菠萝黑心病初期果实的发病部位和健康部位,每个部位选取3个样本分别进行测转录组RNA-Seq分析,对差异基因进行GO、KEGG、各代谢通路基因表达聚类分析和RT-qPCR验证,对比病部(IB)和健部(WT)的差异基因表达量。通过分析发现,IB vs WT共有1037个差异基因,其中上调886个,下调130个。GO和KEGG分析发现氨基酸生物合成差异基因最显著,而且差异基因数量占比大;通过聚类分析和RT-qPCR验证,糖代谢路径发现果实发病后糖酵解、三羧酸循环(TCA)和氧化磷酸化过程中相关酶基因表达量显著上调;植物应对外界环境信号通路发现抗性酶基因表达量显著下调,致病蛋白基因表达量显著上调,抗病蛋白基因表达量显著下调;抗氧化物质通路发现谷胱甘肽合成基因表达量显著下调,类黄酮生物合成相关基因表达量显著上调,L-抗坏血酸过氧化物酶(APX)基因表达量显著下调,而L-抗坏血酸氧化酶(AOX)同系物基因表达量显著上调。RNA-Seq和RT-qPCR分析结果表明,菠萝组织通过显著上调糖代谢关键基因加速果实病部糖代谢、显著上调表达信号传导关键通路MAPK途径中的关键基因以及显著下调抗氧化物质等代谢通路变化而导致黑心病的发生。通过这些结果可以丰富菠萝黑心病发生的基因网络,为后续菠萝黑心病相关基因筛选提供信息参考。
基金supported by the National High-Tech R&D Program of China (2012AA10A305 and 2011AA10A103)
文摘The bacterial brown spot disease（BBS）, caused primarily by Pseudomonas syringae pv. syringae van Hall（Pss）, reduces plant vigor, yield and quality in maize. To reveal the nature of the defense mechanisms and identify genes involved in the effective host resistance, the dynamic changes of defense transcriptome triggered by the infection of Pss were investigated and compared between two maize near-isogenic lines（NILs）. We found that Pss infection resulted in a sophisticated transcriptional reprogramming of several biological processes and the resistant NIL employed much faster defense responses than the susceptible NIL. Numerous genes encoding essential components of plant basal resistance would be able to be activated in the susceptible NIL, such as PEN1, PEN2, PEN3, and EDR1, however, in a basic manner, such resistance might not be sufficient for suppressing Pss pathogenesis. In addition, the expressions of a large number of PTI-, ETI-, PR-, and WRKY-related genes were pronouncedly activated in the resistant NIL, suggesting that maize employ a multitude of defense pathways to defend Pss infection. Six R-gene homologs were identified to have significantly higher expression levels in the resistant NIL at early time point, indicating that a robust surveillance system（gene-to-gene model） might operate in maize during Pss attacks, and these homolog genes are likely to be potential candidate resistance genes involved in BBS disease resistance. Furthermore, a holistic group of novel pathogen-responsive genes were defined, providing the repertoire of candidate genes for further functional characterization and identification of their regulation patterns during pathogen infection.
文摘The analysis of messenger Ribonucleic acid obtained through sequencing techniques (RNA-se- quencing) data is very challenging. Once technical difficulties have been sorted, an important choice has to be made during pre-processing: Two different paths can be chosen: Transform RNA- sequencing count data to a continuous variable or continue to work with count data. For each data type, analysis tools have been developed and seem appropriate at first sight, but a deeper analysis of data distribution and structure, are a discussion worth. In this review, open questions regarding RNA-sequencing data nature are discussed and highlighted, indicating important future research topics in statistics that should be addressed for a better analysis of already available and new appearing gene expression data. Moreover, a comparative analysis of RNAseq count and transformed data is presented. This comparison indicates that transforming RNA-seq count data seems appropriate, at least for differential expression detection.
文摘RNA-sequencing(RNA-seq),based on next-generation sequencing technologies,has rapidly become a standard and popular technology for transcriptome analysis.However,serious challenges still exist in analyzing and interpreting the RNA-seq data.With the development of high-throughput sequencing technology,the sequencing depth of RNA-seq data increases explosively.The intricate biological process of transcriptome is more complicated and diversified beyond our imagination.Moreover,most of the remaining organisms still have no available reference genome or have only incomplete genome annotations.Therefore,a large number of bioinformatics methods for various transcriptomics studies are proposed to effectively settle these challenges.This review comprehensively summarizes the various studies in RNA-seq data analysis and their corresponding analysis methods,including genome annotation,quality control and pre-processing of reads,read alignment,transcriptome assembly,gene and isoform expression quantification,differential expression analysis,data visualization and other analyses.
