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国家重点基础研究发展计划(2007CB108800)

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Functional Identification of Genes Related to Anthocyanin Biosynthesis in Sweet Potato (Ipomoea batatas Lam.)
Many sweet potato cultivars could accumulate high amount of anthocyanins in their storage roots[1], showing a ...
HongxiaWang, Peng Zhang* SIBS-ETH Shanghai Center for Cassava Biotechnology, National Laboratory of Plant Molecular Genetics, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
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Overview of available methods for diverse RNA-Seq data analyses被引量:16
2011年
RNA-Seq technology is becoming widely used in various transcriptomics studies;however,analyzing and interpreting the RNA-Seq data face serious challenges.With the development of high-throughput sequencing technologies,the sequencing cost is dropping dramatically with the sequencing output increasing sharply.However,the sequencing reads are still short in length and contain various sequencing errors.Moreover,the intricate transcriptome is always more complicated than we expect.These challenges proffer the urgent need of efficient bioinformatics algorithms to effectively handle the large amount of transcriptome sequencing data and carry out diverse related studies.This review summarizes a number of frequently-used applications of transcriptome sequencing and their related analyzing strategies,including short read mapping,exon-exon splice junction detection,gene or isoform expression quantification,differential expression analysis and transcriptome reconstruction.
CHEN GengWANG CharlesSHI TieLiu
关键词:TRANSCRIPTOMETRANSCRIPTOMICS
De novo transcriptome assembly of RNA-Seq reads with different strategies被引量:4
2011年
De novo transcriptome assembly is an important approach in RNA-Seq data analysis and it can help us to reconstruct the transcriptome and investigate gene expression profiles without reference genome sequences.We carried out transcriptome assemblies with two RNA-Seq datasets generated from human brain and cell line,respectively.We then determined an efficient way to yield an optimal overall assembly using three different strategies.We first assembled brain and cell line transcriptome using a single k-mer length.Next we tested a range of values of k-mer length and coverage cutoff in assembling.Lastly,we combined the assembled contigs from a range of k values to generate a final assembly.By comparing these assembly results,we found that using only one k-mer value for assembly is not enough to generate good assembly results,but combining the contigs from different k-mer values could yield longer contigs and greatly improve the overall assembly.
CHEN GengYIN KangPingWANG CharlesSHI TieLiu
关键词:RNA-SEQ
两个不同来源的番茄GGPS基因克隆和序列分析被引量:14
2009年
据本实验室得到的GGPS基因片段与NCBI公布的GGPS基因cDNA(DQ267903)序列设计引物,以两份番茄红素含量差异显著的番茄材料:普通番茄(编号E6203)和源于多毛番茄的渐渗系(编号TA517)为试材,分别克隆其DNA和cDNA序列。序列分析显示:GGPS基因不含有内含子。所推导氨基酸序列比对表明:2个不同来源的GGPS基因存在13个差异位点,其中9个位点的氨基酸性质发生了变化。氨基酸变异导致了2个GGPS基因的二级结构与磷酸化位点的不同,初步推测番茄红素含量的差异可能与氨基酸变异有关;采用双链接头介导的染色体步移技术,克隆了GGPS基因5′侧翼序列,进一步分析结果显示:两份材料GGPS上游区序列差异明显,但所包含的顺式元件的分布相对保守,且存在明显的转录调控序列;利用RT-PCR方法对不同器官的GGPS基因表达进行初步研究,结果表明:GGPS基因主要在果实和花器官中表达。
钟秋月国艳梅梁燕王孝宣杜永臣朱德蔚高建昌戴善书
关键词:番茄基因克隆
利用色差仪估测番茄果实番茄红素含量的研究被引量:47
2008年
利用色差仪评价了果实番茄红素含量差异明显的TA517、TA1527及E6203等番茄材料的果实颜色,采用HPLC技术测定了番茄红素含量,建立了果实颜色系数对番茄红素含量的回归方程,然后对28份番茄材料进行了番茄红素含量预测,进一步证实了3个果实颜色系数的回归方程得到的番茄红素含量的预测值与实际测定值符合程度高。结果表明,色差仪法具有简便、快速、成本低等特点,可以用来预测番茄红素含量。
国艳梅杜永臣王孝宣高建昌
关键词:番茄番茄红素色差仪
Are small RNAs a big help to plants?被引量:7
2009年
The discovery of RNA interference(RNAi) has augmented our knowledge of gene regulation and presents a fascinating technology that has a great potential for application in genetic analysis,disease therapy,plant protection,and many other areas.In this review,we will focus on the biological functions of RNAi and its application in agriculture with a brief introduction to the history of its discovery and molecular mechanism.
MAO YingBo,XUE XueYi & CHEN XiaoYa National Key Laboratory of Plant Molecular Genetics,Institute of Plant Physiology and Ecology,Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences,Shanghai 200032,China
关键词:INTERFERENCEGENEREGULATION
Defective Etioplasts Observed in Variegation Mutants May Reveal the Light-Independent Regulation of White/Yellow Sectors of Arabidopsis Leaves被引量:6
2011年
Leaf variegation resulting from nuclear gene mutations has been used as a model system to elucidate the molecular mechanisms of chloroplast development. Since most variegation genes also function in photosynthesis, it remains unknown whether their roles in photosynthesis and chloroplast development are distinct. Here, using the variegation mutant thylakoid formation1 (thfl) we show that variegation formation is light independent. It was found that slow and uneven chloroplast development in thfl can be attributed to defects in etioplast development in darkness. Ultrastructural analysis showed the coexistence of plastids with or without prolamellar bodies (PLB) in cells of thfl, but not of WT. Although THF1 mutation leads to significant decreases in the levels of Pchlide and Pchliide oxidoreductase (POR) expression, genetic and 5-aminolevulinic acid (ALA)-feeding analysis did not reveal Pchlide or POR to be critical factors for etioplast formation in thfl. Northern blot analysis showed that plastid gene expression is dramatically reduced in thfl compared with that in WT, particularly in the dark. Our results also indicate that chlorophyll biosynthesis and expression of plastidic genes are coordinately suppressed in thfl. Based on these results, we propose a model to explain leaf variegation formation from the plastid development perspective.
Wenjuan WuNabil ElsheeryQing WeiLingang ZhangJirong Huang
关键词:ARABIDOPSISCHLOROPLASTETIOPLASTVARIEGATION
Elucidation and Engineering of Gossypol Biosynthesis
Cotton plants accumulate sesquiterpene aldehydes,including gossypol,in pigmented glands of aerial tissues and ...
Xiao-Ya ChenChang-Qing YangYing-Bo Mao
植物小RNA与RNA干扰:生物学功能与应用前景被引量:13
2009年
RNA干扰(RNAi)的发现使人们对基因调控有了新的认识,同时它也逐渐发展为遗传分析、疾病治疗以及植物保护等方面一种非常有用的新技术.本文重点介绍RNAi的生物学功能及其在农业上的应用前景.为更好地了解RNAi,本文还简要回顾了RNAi的发现历史并简单阐述小RNA生成途径和RNAi的分子机制.
毛颖波薛学义陈晓亚
关键词:RNA干扰基因调控植物保护
Transcriptional Regulation of Plant Secondary Metabolism被引量:33
2012年
Plant secondary metabolites play critical roles in plant-environment interactions. They are synthesized in different organs or tissues at particular developmental stages, and in response to various environmental stimuli, both biotic and abiotic. Accordingly, corresponding genes are regulated at the transcriptional level by multiple transcription factors. Several families of transcription factors have been identified to participate in controlling the biosynthesis and accumulation of secondary metabolites. These regulators integrate internal (often developmental) and external signals, bind to corresponding cis-elements -- which are often in the promoter regions -- to activate or repress the expression of enzyme-coding genes, and some of them interact with other transcription factors to form a complex. In this review, we summarize recent research in these areas, with an emphasis on newly-identified transcription factors and their functions in metabolism regulation.
Chang-Qing YangXin FangXiu-Ming WuYing-Bo MaoLing-Jian WangXiao-Ya Chen
关键词:ALKALOIDPHENYLPROPANOIDTERPENOID
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