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1、1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 影响因子：5.578 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 rhi
2、zome 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 rhizome girth enlargement. In this study, using RNA-seq, transcriptomic analyses were performed at thr
3、ee rhizome developmental stagesthe 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 2678
4、3 genes identified, 24069 genes were previously predicted in the reference, and 2714 genes were novel transcripts. Moreover, 8821 genes were differentially expressed between the cultivars at the three stages. Functional analysis identified that these genes were significantly enriched in pathways car
5、bohydrate 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 several differentially expressed genes
6、 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取 材建 库测 序信息分析温 带（ZO） 和 热 带（RL） 莲 花的根状茎种植后 115，154， 207 天三个阶段共 6 个样本，各取 3 ug RNA 构建 cDNA 文库Illumine HiSeq 2000 PE100 6G
7、 clean reads/ 样本1、基因表达水平分析 2、基因差异表达分析研究背景莲根状茎，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。方法流程植 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。 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,UGPas
8、e,AGPase,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
9、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, 513059.23提升 CO2的浓度可增强小球藻的碳代谢从而提 高脂质堆积
10、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 involve
11、d in lipid accumulation under conditions of elevated CO2, however, remain to be fully elucidated. To understand how elevated CO2 improves lipid production, we performed sequencing of Chlorella sorokiniana LS-2 cellular transcripts during growth and compared transcriptional dynamics of genes involved
12、 in carbon flow from CO2 to triacylglycerol. These analyses identified the majority genes of carbohydrate metabolism and lipid biosynthesis pathways in C. sorokiniana LS-2. Under high doses of CO2, despite down-regulation of most de novo fatty acid biosynthesis genes, genes involved in carbohydrate
13、metabolic pathways including carbon fixation, chloroplastic glycolysis, components of the pyruvate dehydrogenase complex (PDHC) and chloroplastic membrane transporters were upexpressed at the prolonged lipid accumulation phase. The data indicate that lipid production is largely independent of de nov
14、o fatty acid synthesis. Elevated CO2 might push cells to channel photosynthetic carbon precursors into fatty acid synthesis pathways, resulting in an increase of overall triacylglycerol generation. In support of this notion, genes involved in triacylglycerol biosynthesis were substantially up-regula
15、ted. Thus, elevated CO2 may influence regulatory dynamics and result in increased carbon flow to triacylglycerol, thereby providing a feasible approach to increase lipid production in microalgae.关键词小球藻 LS-2；碳水化合物代谢取 材建 库测 序分析10%CO2和 空 气培养的小球藻提 取 总 RNA 3 g 构建 200 bp 文库Illumina HiSeq 2000 PE100基因拼接注释
16、差异表达分析 富集分析实验验证qRT-PCR 等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。方法流程植 物研究结果1、通过 RNA-seq 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 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 CO2 improves lipid accumulation by increasing carb
