發(fā)布時間：2018-04-22 16:56

  本文選題：朱草 + 軟紫草��； 參考：《南京大學》2016年博士論文

【摘要】：“朱草”類植物是一類根部由于富含紅色萘醌類化合物(即紫草素及其衍生物)而呈紅色的植物。紫草素類化合物不僅是一種著名的天然色素,還是一種重要的藥用天然產(chǎn)物。然而,由于缺乏相關(guān)基因組和轉(zhuǎn)錄組數(shù)據(jù),目前國內(nèi)外研究者對紫草素生物合成的基因與分子生物學層面的研究依然不夠深入。因此,本研究對軟紫草(Arnebia euchroma)的框架基因組進行了測序、組裝與初步分析;同時,還分別對三種"朱草"植物,即軟紫草、紫草(Lithospermum ervthrorhizon)與車前葉藍薊(Echium plantagineum)的轉(zhuǎn)錄組進行了測序、組裝與初步分析。通過K-mer分析本研究估算軟紫草基因組大小約為2.7Gb,基因組雜合度約1.5-1.7%,基因組重復(fù)率在50%以上。這說明軟紫草基因組較大,而且是高雜合、高重復(fù)的復(fù)雜基因組。因此,本研究僅對其進行了框架基因組的組裝;組裝所得基因組大小約 1.2Gb(Contig N50 為 1.9 Kb,Scaffold N50 為 2.3 Kb);并且注釋獲得28157個蛋白編碼基因。此外,通過比較基因組與分子進化分析,本研究推測紫草目可能與茄目更近緣,其可能約在7530萬年前(約為白堊紀晚期與第二紀早期的交界點)與茄目進化分離。利用組裝獲得的軟紫草葉綠體基因組的分子進化分析也支持紫草目植物與茄目更近緣。通過對三種“朱草”植物的轉(zhuǎn)錄組測序分析,本研究發(fā)現(xiàn)在三種"朱草"植物的綠莖葉(GL)和紅根(RR)樣品中存在一些極顯著差異表達的基因(HDEGs)。從中本研究進一步篩選得到了與紫草素生物合成相關(guān)的一些候選基因,如G10H(屬于紫草素代謝途徑)、12OPR(屬于茉莉酸甲酯代謝途徑)、SAMDC(屬于多胺/乙烯代謝途徑)等。另外,本研究通過比較轉(zhuǎn)錄組與分子進化分析進一步構(gòu)建了唇形支植物的初步系統(tǒng)進化模型。所得結(jié)果與基于軟紫草基因組所構(gòu)建的系統(tǒng)進化模型幾乎完全一致。這更進一步證明了紫草目可能與茄目更近緣,而與唇形目較遠。此外,本研究進一步鑒定得到了在以上三種"朱草"植物紅根中特異表達并且處于正選擇地位的4CL基因拷貝(屬于紫草素代謝途徑)。綜上所述,本研究對"朱草"類植物的起源以及紫草素生物合成與調(diào)控領(lǐng)域的研究奠定了一定的基礎(chǔ),對紫草素代謝工程的發(fā)展具有一定的參考價值。
[Abstract]:Herba sinensis is a kind of plants whose roots are red due to their rich in red naphthoquinone compounds (I. e., shikonin and its derivatives). Shikonin is not only a famous natural pigment, but also an important medicinal natural product. However, due to the lack of relevant genomic and transcriptional data, the research on gene and molecular biology of Shikonin biosynthesis is still insufficient at home and abroad. Therefore, the frame genome of Arnebia euchroma was sequenced, assembled and preliminarily analyzed, and the transcriptome of three species of Herba sinensis, Lithospermum ervthhizon and Echium plantagineum. were sequenced respectively. Assembly and preliminary analysis. The genome size and heterozygosity were estimated to be about 2.7Gb and 1.5-1.7Gb by K-mer analysis. The repeat rate of the genome was more than 50%. This indicates that the genome of Arnebia chinensis is large, and is a complex genome with high heterozygosity and high duplication. Therefore, only the frame genome was assembled in this study. The genome size of the assembled genome was about 1.9Kb / L Scaffold N _ (50) = 2.3Kb, and 28157 protein coding genes were obtained by annotation. In addition, by comparing genomic and molecular evolution analysis, we speculated that Arnesia might be more closely related to Solanidae, and it might be separated from Solanidae about 7530 million years ago (the junction point between the late Cretaceous and the early second period). The molecular evolution analysis of chloroplast genomes obtained by assembly also supported the closer relationship between Arnebia and Solanidae. Based on the analysis of transcriptome sequencing of three species of "chrysanthemum", it was found that there were some highly differentially expressed genes (HDEGsN) in the samples of green stem and leaf (GLL) and red root (RRR) of the three species of "chrysanthemum". Some candidate genes related to the biosynthesis of porphyrin, such as G10H (belong to Shikonin metabolic pathway) 12OPRA (belonging to methyl jasmonate metabolism pathway), SAMDC( polyamine / ethylene metabolism pathway), were further selected in this study. In addition, a preliminary phylogenetic model of labial branching plants was constructed by comparing transcriptome and molecular evolution analysis. The results were almost identical with the phylogenetic model based on the genome of Lymus chinensis. This further proves that the order Arnesia may be more closely related to the order Solanidae, but far from the order Lithoptera. In addition, a copy of 4CL gene (which belongs to Shikonin metabolic pathway) expressed specifically in red root of the above three species was identified in this study. To sum up, this study has laid a foundation for the study of the origin, biosynthesis and regulation of shikonin, and has a certain reference value for the development of Shikonin metabolism engineering.
【學位授予單位】：南京大學
【學位級別】：博士
【學位授予年份】：2016
【分類號】：Q943.2

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