构建多组学数据分析流程用于挖掘黄草乌生物碱合成相关基因

	构建多组学数据分析流程用于挖掘黄草乌生物碱合成相关基因
	任焕幸
导师	寸玉鹏
关键词	二萜生物碱 Diterpenoid alkaloids 比较基因组学 Comparative genomics 权重基因共表达网络 Weighted gene co-expression network 最小生成树 Minimum spanning tree 代谢网络 Metabolic network
摘要	乌头属植物产生具有显著生物活性和剧烈毒性的二萜生物碱类化合物。对乌头属植物中二萜生物碱代谢合成方面的研究已经取得了一些进展，但是缺乏完整的基因组的信息使得对该属植物资源的深度开发与利用遇到阻碍。生物分子网络在探索复杂生命活动过程中发挥着重要的作用，构建和分析分子网络已成为一种预测分子间相互作用和未知功能的有效方法。本文将乌头属植物黄草乌（Aconitum vilmorinianum）作为研究对象，利用基因组、转录组以及代谢组数据，构建了一个完整的生物信息学分析流程来系统地挖掘了二萜生物碱生物合成的候选基因，这些基因与已报道的二萜生物碱生物合成有很大的相似性。这个分析流程和数据整合方式也展示了用多组学的手段来挖掘植物活性成分生物合成途径中关键基因的新思路。本文主要研究结果如下：（1）对已经组装好的黄草乌基因组和其它11个物种的比较基因组分析明确了黄草乌的系统发育中的进化关系，黄草乌与其近缘物种耧斗菜（Aquilegia coerulea）的分化时间大约在62.689百万年前。黄草乌经历了两次全基因倍增复制事件，大约在113.11百万年前与耧斗菜共享了一次全基因倍增复制事件后，黄草乌在大约59.92百万年前还发生了另外一次全基因倍增复制事件。（2）通过黄草乌中特有的和扩张基因群的功能富集分析，发现了二萜生物碱合成相关的基因，例如焦磷酸古巴合酶（ent-copalyl diphosphatedes）、贝壳杉烯合酶（ent-kaurene synthases）、贝壳杉烯氧化酶（ent-kaurene oxidases）、氧甲基转移酶（O-methyltransferases）。同时，这些基因家族也发生了明显的扩张。这些结果辅助鉴定了可能参与二萜生物代谢过程的基因群。（3）利用转录组数据进行了权重基因共表达网络分析，并使用了最小生成树算法来发现该权重基因共表达网络中的核心（hub）基因。我们发现了86个黄草乌二萜生物碱生物合成的候选基因。此外，我们还构建了基因-代谢物相关性网络，发现199个基因与二萜生物碱代谢产物高度相关。（4）在黄草乌基因组中预测了与37类转录因子相关的1949个基因，筛选了169个转录因子可能参与调控32个通路基因，其中有20个通路基因与AP2/ERF转录因子高度相关。（5）对黄草乌多组学的数据整合分析，筛选到参与二萜生物碱合成的71个候选基因，包括2个geranylgeranyl pyrophosphate synthases、3个ent-copalyl diphosphatedes、3个ent-kaurene synthases、4个ent-kaurene oxidases、11个aminotransferases、21个P450 monooxygenases、14个O-methyltransferases、2个BAHD acyltransferases以及2个C4-sterol methyl oxidases，这些基因不仅是权重基因共表达网络的关键节点，还存在于与侧根高度相关的模块中。此外，有些基因还和AP2/ERF转录因子高度相关。; Aconitum produce secondary metabolites of the diterpenoid alkaloids class that are potent and highly toxic. At present, some progress has been made in the research on the metabolism and biosynthesis of diterpenoid alkaloids in Aconitum, but the lack of complete genome information has hindered the in-depth research and utilization of Aconitum resources. Biological networks play important role in exploring complex life activities, which made network analysis has become an effective method and tool to predict intermolecular interactions and unknown functions. In this study, taking Aconitum vilmorinianum as the research subject, employed the sequencing data of genome, transcriptome and metabolome, we constructed a full complete bioinformatics analysis pipeline to systematically discovery candidate genes related to the biosynthesis of diterpenoid alkaloids. These findings were consistent with former researches in diterpenoid alkaloids biosynthesis. At the same time, the analysis pipeline also opened a new window for employing multi-omic integration and mining methods to find key genes in the biosynthetic pathways of active ingredients in plants. These findings of this study were summarized as follows: (1) Using the assembled A. vilmorinianum genome, and compared to 11 other species’s genome to clarified relationship in phylogenetic evolution analysis. The divergence time of A. vilmorinianum and Aquilegia coerulea was around 62.689 million years ago. Two whole gene duplication events were identified by the synteny analysis in the genome of A. vilmorinianum and other species. After a common whole genome duplication (sharing a WGD) with A. coerulea in around 113.11 million years ago, A. vilmorinianum also had a WGD event about 59.92 million years ago. (2)Through the functional analysis of specific and expanded genes in A. vilmorinianum, it was found that genes related to the biosynthesis of diterpene alkaloids such as ent-copalyl diphosphatedes systhases, ent-kaurene synthases, ent-kaurene oxidases and O-methyltransferases. At the same time, these gene families have also undergone significant expansion, and these results assisted in the identification of gene groups that may be involved in the biological metabolism of diterpenes. (3) Network analysis in transcriptome data. Gene co-expression network on the gene expression profile of A. vilmorinianum was constructed, and minimum spanning tree (MST) algorithm was applied to discover hub genes of the gene co-expression network, which found 71 candidate genes in the biosynthesis of diterpene alkaloids were found. Using the metabolite data of diterpene alkaloids in A. vilmorinianum, a gene-metabolite network was constructed, and 199 genes were found to be highly correlated with diterpene alkaloid metabolites. (4) Among 1949 genes, thirty-seven types of transcription factors were predicted in the A. vilmorinianum genome. By constructing the co-expression network of transcription factors and pathway genes, 16
语种	中文
	2022-05
学位授予单位	中国科学院大学
文献类型	学位论文
条目标识符	http://ir.kib.ac.cn/handle/151853/75144
专题	昆明植物所硕博研究生毕业学位论文
推荐引用方式 GB/T 7714	任焕幸. 构建多组学数据分析流程用于挖掘黄草乌生物碱合成相关基因[D]. 中国科学院大学,2022.

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