伤残温带和热带莲根状茎形成过程中的转录组分析
Transcriptomic Analysis of the Regulation of Rhizome Formation in Temperate and
Tropical Lotus (Nelumbo nucifera )
研究对象：莲根状茎
期刊：Scientific Reports
川藏旅游影响因子：5.578ps怎么编辑文字
合作单位：中国科学院武汉植物园
发表时间：2015年7月
摘 要
Rhizome is the storage organ of lotus derived from modified stems. The development of rhizome is a complex process and depends on the balanced expression of the genes that is controlled by environmental and endogenous factors. However, little is known about the mechanism that regulates rh
izome girth enlargement. In this study, using RNA-q, transcriptomic analys were performed at three rhizome developmental stages—the stolon, middle swelling and later swelling stage —in the cultivars ‘ZO’ (temperate lotus with enlarged rhizome) and ‘RL’ (tropical lotus with stolon). About 348 million high-quality reads were generated, and 88.5% of the data were mapped to the reference genome. Of 26783 genes identified, 24069 genes were previously predicted in the reference, and 2714 genes were novel transcripts. Moreover, 8821 genes were differentially expresd between the cultivars at the three stages. Functional analysis identified that the genes were significantly enriched in pathways carbohydrate metabolism and plant hormone signal transduction. Twenty-two genes involved in photoperiod pathway, starch metabolism and hormone signal transduction were candidate genes inducing rhizome girth enlargement. Comparative transcriptomic analysis detected veral differentially expresd genes and potential candidate genes required for rhizome girth enlargement, which lay a foundation for future studies on molecular mechanisms underlying rhizome Formation.
关键词
根状茎；变态发育； DGE 研究背景
莲根状茎，即莲藕，作为一种变态茎，是莲
的贮藏器官。根状茎的发育是一个复杂的过
程，受到与环境及内源因素调控的基因平衡
表达的影响。关于根状茎膨大的调控机制很
少为人所知。
植物
3、对差异基因进行GO 和KEGG 富集，大多数差异基因显著富集到4个GO term 中。多数差异基因被富集到次级代谢，蔗糖代谢，碳代谢等代谢通路中。鸵鸟蛋怎么吃
4、发现已报道的根状茎生长相关的光周期基因PHYB,CO,GI,FT 的同源基因在温带及热带莲根状茎中存在不同表达模式；已报道的与淀粉合成相关酶SUS,UGPa,AGPa,GBSS,SSS 等的同源基因在温带及热带莲根状茎中存在差异表达；大量的激素信号转导、激素合成、激素响应蛋白以及激素转运蛋白如GA,ABA,CTK,JA 等被鉴定出在不同的类别中存在差异表达。
研究结果
1、所有文库的reads 比对参考基因组后，发现2714个新转录本，其中1186个基因被成功注释到GO 生物学过程中的9个亚类中。
2、比较热带莲三个发育阶段的根状茎，分别发现1688，4208，4795个差异基因；比较温带莲三个发育阶段的根状茎，分别发现3206，6360，5535个差异基因。比较三个发育阶段中温带和热带两种莲，共发现10299个差异基因。对所有差异基因进行聚类，共聚为8类（图1）。
图1 差异表达基因维恩图及聚类图
图2 与淀粉合成相关基因的表达模式热图，与激素信号转导相关基因的表达模式热图
参考文献
Mei Yang, Lingping Zhu, Cheng Pan, et al. Transcriptomic Analysis of the Regulation of Rhizome
Formation in Temperate and Tropical Lotus (Nelumbo nucifera). Sci Rep, 2015, 513059.
提升CO2的浓度可增强小球藻的碳代谢从而提高脂质堆积
Elevated CO2 improves lipid accumulation by increasing carbon metabolism in Chlorella sorokiniana 研究对象：小球藻
期刊：Plant Biotechnology journal
影响因子：5.752
合作单位：江苏省农科院
发表时间：2015年5月
摘 要
Supplying microalgae with extra CO2 is a promising means for improving lipid production. The molecular mechanisms involved in lipid accumulation under conditions of elevated CO2, however, remain to be fully elucidated. To understand how elevated CO2 improves lipid production, we perfor
med quencing of Chlorella sorokiniana LS-2 cellular transcripts during growth and compared transcriptional dynamics of genes involved in carbon flow from CO2 to triacylglycerol. The analys identified the majority genes of carbohydrate metabolism and lipid biosynthesis pathways in C. sorokiniana LS-2. Under high dos of CO2, despite down-regulation of most de novo fatty acid biosynthesis genes, genes involved in carbohydrate metabolic pathways including carbon fixation, chloroplastic glycolysis, components of the pyruvate dehydrogena complex (PDHC) and chloroplastic membrane transporters were upexpresd at the prolonged lipid accumulation pha. The data indicate that lipid production is largely independent of de novo fatty acid synthesis. Elevated CO2 might push cells to channel photosynthetic carbon precursors into fatty acid synthesis pathways, resulting in an increa of overall triacylglycerol generation. In support of this notion, genes involved in triacylglycerol biosynthesis were substantially up-regulated. Thus, elevated CO2 may influence regulatory dynamics and result in incread carbon flow to triacylglycerol, thereby providing a feasible approach to increa lipid production in microalgae.
关键词
小球藻LS-2；碳水化合物代谢
研究背景
给微藻提供额外的CO2是一种提高脂质产量的有效途径。但是在CO2升高时脂质堆积的分子机制并不清楚。本文通过对小球藻LS-2进行转录组测序研究了从CO2到甘油三酯碳流过程中基因的动态变化揭示了CO2升高过程中脂质堆积的分子机制。
方法流程
一年级下册植
物研究结果
1、通过RNA-q的手段，对高剂量CO2和正常空气下培养的小球藻进行转录组测序，通过转录本拼接
共得到22,432个unigene，N50长度1,680 bp，并通过基因功能注释鉴定出了很多与糖代谢和脂质合成途
生肖龙和什么生肖最配
径相关的基因（图1）。
图1 拼接得到22432个unigene的GO功能分类
图2 KEGG分类（左）和高剂量CO2 VS 空气下小球藻差异表达基因（右）
参考文献
Sun Z, Chen Y F, Du J. Elevated CO2improves lipid accumulation by increasing carbon metabolism in Chlorella sorokiniana [J]. Plant biotechnology journal, 2015, pp.1-10.
2、在高剂量CO2下，尽管大部分脂肪酸从头合成基因下调，但是参与碳水化合物代谢途径的基因，如
冒失是什么意思
碳固定、叶绿体糖酵解、丙酮酸脱氢酶复合物的成分（PDHC）和叶绿体膜转运相关的基因，均在长期的脂质
积累阶段上调（图2）。这些数据表明，脂质生产很大程度上独立于脂肪酸的从头合成。
3、CO2浓度的升高可能会推动细胞将光合碳前体引入脂肪酸合成途径，从而整体增加甘油三酯的合成。
参与甘油三酯合成的基因大幅上调就证明了这一观点。因此CO2浓度的提高会影响动态调控，并导致更多的
碳转化成甘油三酯，从而为提升小球藻脂类产量提供了可行的办法。
转录组分析揭示了黄瓜中微管相关基因的作用和转录因子在果实长度方面的调控作用
Transcriptomic analysis reveals the roles of microtubule-related genes and transcription factors in fruit length regulation in cucumber (Cucumis sativus L.)研究对象：正常株和突变株的早期果实
期刊： Scientific Reports
影响因子：5.578
合作单位：中国农业大学
发表时间：2015年1月
摘 要
Cucumber (Cucumis sativus L.) fruit is a type of fleshy fruit that is harvested immaturely. Early
fruit development directly determines the final fruit length and diameter, and conquently the fruit yield and quality. Different cucumber varieties display huge variations of fruit length, but how fruit len
gth is determined at the molecular level remains poorly understood. To understand the genes and gene networks that regulate fruit length in cucumber, high throughout RNA-Seq data were ud to compare the transcriptomes of early fruit from two near isogenic lines with different fruit lengths. 3955 genes were found to be differentially expresd, among which 2368 genes were significantly up-regulated and 1587 down-regulated in the line with long fruit. Microtubule and cell cycle related genes were dramatically activated in the long fruit, and transcription factors were implicated in the fruit length regulation in cucumber. Thus, our results built a foundation for discting the molecular mechanism of fruit length control in cucumber, a key agricultural trait of significant economic importance.
关键词
黄瓜；果实长度；RNA-q；微管；细胞周期
研究背景
黄瓜是一种全球性的蔬菜作物，具有重要
的经济及营养价值。作为一种新鲜肉质蔬菜，
黄瓜收获于开花后的两周左右。开花后，果实
迅速生长，最后伸长到最终的长度。这一过程
风信子种子中，细胞分裂和细胞扩张起到至关重要的作用。
同时，不同品种的黄瓜在最终长度上也具有很
大的差异。因此，黄瓜果实的早期发育对于黄
瓜的产量和质量具有重大影响。果实长度作为
一个重要的农艺性状，对于黄瓜中控制果实长
度的分子机制的研究，具有重大的理论意义和
经济价值。
