软紫草框架基因组与朱草类植物转录组的测序、组装与初步分析

发布时间：2018-04-22 16:56

本文选题：朱草 + 软紫草　；参考：《南京大学》2016年博士论文

【摘要】：“朱草”类植物是一类根部由于富含红色萘醌类化合物(即紫草素及其衍生物)而呈红色的植物。紫草素类化合物不仅是一种著名的天然色素,还是一种重要的药用天然产物。然而,由于缺乏相关基因组和转录组数据,目前国内外研究者对紫草素生物合成的基因与分子生物学层面的研究依然不够深入。因此,本研究对软紫草(Arnebia euchroma)的框架基因组进行了测序、组装与初步分析;同时,还分别对三种"朱草"植物,即软紫草、紫草(Lithospermum ervthrorhizon)与车前叶蓝蓟(Echium plantagineum)的转录组进行了测序、组装与初步分析。通过K-mer分析本研究估算软紫草基因组大小约为2.7Gb,基因组杂合度约1.5-1.7%,基因组重复率在50%以上。这说明软紫草基因组较大,而且是高杂合、高重复的复杂基因组。因此,本研究仅对其进行了框架基因组的组装;组装所得基因组大小约 1.2Gb(Contig N50 为 1.9 Kb,Scaffold N50 为 2.3 Kb);并且注释获得28157个蛋白编码基因。此外,通过比较基因组与分子进化分析,本研究推测紫草目可能与茄目更近缘,其可能约在7530万年前(约为白垩纪晚期与第二纪早期的交界点)与茄目进化分离。利用组装获得的软紫草叶绿体基因组的分子进化分析也支持紫草目植物与茄目更近缘。通过对三种“朱草”植物的转录组测序分析,本研究发现在三种"朱草"植物的绿茎叶(GL)和红根(RR)样品中存在一些极显著差异表达的基因(HDEGs)。从中本研究进一步筛选得到了与紫草素生物合成相关的一些候选基因,如G10H(属于紫草素代谢途径)、12OPR(属于茉莉酸甲酯代谢途径)、SAMDC(属于多胺/乙烯代谢途径)等。另外,本研究通过比较转录组与分子进化分析进一步构建了唇形支植物的初步系统进化模型。所得结果与基于软紫草基因组所构建的系统进化模型几乎完全一致。这更进一步证明了紫草目可能与茄目更近缘,而与唇形目较远。此外,本研究进一步鉴定得到了在以上三种"朱草"植物红根中特异表达并且处于正选择地位的4CL基因拷贝(属于紫草素代谢途径)。综上所述,本研究对"朱草"类植物的起源以及紫草素生物合成与调控领域的研究奠定了一定的基础,对紫草素代谢工程的发展具有一定的参考价值。
[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.
【学位授予单位】：南京大学
【学位级别】：博士
【学位授予年份】：2016
【分类号】：Q943.2

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