基于全基因组的灵芝药用模式真菌创建研究
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摘要
灵芝(Ganoderma lucidum)又称仙草,是担子菌纲(Basidiomycetes)多孔菌目(Polyporales)多孔菌科(Polyporaceae)灵芝属(Ganodermae)真菌,是传统珍贵药材,最早记载于《神农本草经》中,被列为上品。灵芝作为药用真菌已被《中国药典》(2010版)和《美国草药药典》中收录。灵芝具有扶正固本等功效,现代药理和临床研究表明,灵芝在抗肿瘤,抗病毒,调节血糖,增强免疫力等方面均具有显著的作用。灵芝被誉为“生物活性化合物的细胞工厂”,已经从灵芝中分离得到400多种活性成分,其中三萜和多糖是灵芝的主要活性成分。灵芝次生代谢产物的种类和含量与其发育密切相关,同时,灵芝的遗传转化体系成熟、栽培技术完善,便于室内培养和研究,因此灵芝也被看作研究次生代谢产物合成与发育调控的潜在药用模式生物。
对灵芝的遗传背景研究不足,这阻碍了其作为模式生物被广泛研究。本研究首先评估了灵芝作为模式生物的可行性,并应用二代测序技术及光学图谱绘制整染色体级的灵芝基因组精细图。结果显示,灵芝基因组大小约为43.3Mb,包含13条染色体,82个scaffolds。应用ab initio方法和比较方法预测灵芝可能的编码基因并进行注释,整合工作由MAKER程序包完成,对部分预测基因应用Apollo软件进行人工校正。转录本序列和基因表达分析分别应用454和RNA-seq检测。预测结果显示,灵芝基因组编码16,113个基因,基因的表达水平在不同的发育阶段差异显著,以羊毛甾醇合酶为代表的次生合成及调控的相关酶与灵芝发育有关联。分析结果还显示,灵芝富含细胞色素P450、转运蛋白和转录调控蛋白,这些蛋白家族在生物次生代谢产物合成中发挥重要作用。灵芝也是在已测序的担子菌中编码木质素降解酶基因最丰富的物种之一,在生物能源的应用中有很大潜力。P450基因被认为是三萜下游修饰的关键基因。灵芝中78个CYP基因与羊毛甾醇合成酶共表达,其中16个与动物中具有特异睾酮羟化功能的CYP基因高度相似,这些基因更可能是三萜生下游的修饰基因。此外,灵芝基因组中存在24个CYP基因簇。基因组研究进一步巩固了灵芝在药用生物中的模式地位。
灵芝中的代谢物多样性早就为人们所关注。本文以灵芝免疫球蛋白家族,灵芝倍半萜类物质及灵芝三萜类物质为例,分析探讨灵芝活性物质多样性的成因。结果显示,灵芝中不同种类代谢物多样产生原因各有不同。以灵芝免疫球蛋白家族为代表的蛋白多肽类活性物质,其多态性来自于基因复制后的序列变异。倍半萜类物质的多态性与植物类似,来源于合成酶的多态性和不专一性,部分倍半萜合酶位于基因簇内,因此,灵芝倍半萜类物质的多样性也部分源多种修饰酶的修饰。灵芝中有超过150种三萜类物质,它们都来源于共同的前体——羊毛甾醇。分析结果显示,灵芝中只存在一个三萜环化酶即羊毛甾醇合酶但存在着大量的单加氧酶等修饰酶。多种修饰酶的存在、表达和调控是导致灵芝三萜类多态性的重要因素。多种多样性机制共存使灵芝也成为研究药源生物代谢产物多样性的良好模式。
基于本研究的研究成果我们还开发了一些研究辅助平台,以期在灵芝栽培、育种、发酵和生产中有应用的价值。如1、灵芝交配型座位的确定及单倍型的快速鉴定。通过基因组分析,灵芝交配型座位A位于Scaffoldl,跨度90kb,编码31个基因,包括两个同源异型结构编码基因HD1和HD2。交配型座位B位于scaffoldl4,跨度为100kb,包含6个费洛蒙编码基因和7个STE3-like费洛蒙受体基因。RNA-seq结果显示不同费洛蒙和费洛蒙受体编码基因在不同的发育阶段表达水平不同,推测不同类型的费洛蒙及其受体在灵芝不同时期执行不同的功能。MIP是真菌交配型座位中的保守蛋白,基于14种真菌的进化分析表明,灵芝属MIP中具有一段保守的特征序列。PCR结果表明,这段共有序列可作为灵芝属物种单倍体型快速鉴定的通用序列。2、qRT-PCR的内参基因筛选。荧光定量PCR (qRT-PCR)是一种快速、灵敏的基因表达检测技术。qRT-PCR的准确度及可靠性取决于内参基因的稳定性。因此系统性的评估内参基因是必需的。本研究从灵芝基因组数据中选择了10个qRT-PCR内参候选基因。所选的基因序列通过手动校正并根据严格的条件设计引物。通过统计分析评估候选基因的稳定性。实验结果显示,发酵条件下,protein phosphatase2A (PP2A)为最适的内参基因；在灵芝发育研究中,Ribosomal protein L4(RPL4)是最适的内参基因。在所有的检测条件下,RPL4, PP2A和P-Tubulin (BTU)是最适的内参基因并建议选用。
本研究通过全基因组测序填补了当前灵芝研究中在遗传信息方面的空白,使灵芝研究进入分子生物学前沿,巩固了灵芝在真菌次生代谢产物与发育研究中的模式地位,为下一步灵芝次生代谢产物生源合成研究及发育研究奠定了基础。研究同时发现,灵芝存在多种次生代谢产物多样性形成机制,是研究药源生物代谢产物多样性的良好模式。灵芝也是目前中药源物种中第一个完成染色体级基因组精细图的物种,一定程度上可以作为应用大数据进行药用生物研究的范例。
Ganoderma lucidum, a white rot basidiomycete belonging to the order Polyporales, is one of the most well-known medicinal mushrooms in the world. G. lucidum has been used as a remedy for thousands years in East Asia. This species is documented as LingZhi in Chinese Pharmacopoeia and is included in the American Herbal Pharmacopoeia and Therapeutic Compendium. G. lucidum is known as a "cellular factory for biologically useful compounds," and more than400bioactive compounds have been identified in G. lucidum, including polysaccharides, triterpenoids, fatty acids and alkaloids. Modern studies have reported that G. lucidum possesses multiple pharmacological activities, including antitumor. anti-hypertensive, anti-inflammatory and immunomodulatory activities. This species is amenable to genetic transformation and artificial cultivation, making it an ideal system for traditional medicine research.
Here, we sequenced and assembled its genome using next-generation sequencing and optical mapping approaches. The43.3-Mb genome of G. lucidum contained13chromosomes and was assembled into82scaffolds. The gene prediction and annotation was using MAKER pipeline, combining the ab initio method and comparative ways, constructed gene models were further manual curated using Apollo programm. Gene expression profile was detected using454transcriptome technology and RNA-seq technology. Results show that G.lucidum's genome encoded16,113predicted genes, some genes'expression level changed dramatically during different development stages. More importantly, the analysis revealed an impressive array of genes encoding cytochrome P450s (CYPs), transporters, and regulatory proteins which cooperate in secondary metabolism. The genome also encodes one of the richest sets of wood degradation enzymes among all sequenced basidiomycetes. Twenty-four physical CYP gene clusters were identified. Moreover,78CYP genes were co-expressed with lanosterol synthase, and16of these show high similarity to fungal CYPs that specifically hydroxylate testosterone, suggesting their possible roles in triterpenoid biosynthesis. The elucidation of the relationship between G.lucidum secondary metabolites and development based on omic scale analysis enables this organism to be a potential model system for the study of secondary metabolic pathways and their regulation in fungi.
The G. lucidum genome and transcriptome have wild applications in this specie's breeding, cultivation, production and research. In this paper, we introduced two examples. First, mating-type loci were identified based on genomic data. A90kb region in scaffold1was deemed as mating type A(matA) locus, two genes (GL30604and GL30607) in this region were inferred to encoding the HDl and HD2proteins. There are also29other genes in this region. Thirteen sequences were identified as mating type B (matB) locus genes. Six pheromone encoding genes were clustered with seven STE3-like pheromone receptor genes in a region of approximately100kb on scaffold14. The results suggested that mating-type locus in G. lucidum were conserved with other fungi which have been sequenced. The RNA-seq analysis showed that the expression level of different pheromone coding genes and pheromone receptor coding genes were not the same. This result indicated that different pheromones and their receptors may play diverse roles in variety conditions. The phylogenetic analysis of MIP coding genes from14fungi indicated a conserved region in Ganodermae. Based on the consensus sequences of mip in Ganodermae, a pair of primer was designed for the identification of the ploidy and the mating type of fungi strains from Ganodermae. Second, reference genes for qRT-PCR were selected from predicted gene models. Quantitative real-time reverse transcription PCR (qRT-PCR) is a rapid, sensitive and reliable technique for gene expression studies. The accuracy and reliability of qRT-PCR results depend on the stability of the reference genes used for gene normalization. Therefore, a systematic process of reference gene evaluation is needed. Ganoderma lucidum is a famous medicinal mushroom in East Asia. In the current study,10potential reference genes were selected from the G. lucidum genomic data. The sequences of these genes were manually curated, and primers were designed following strict criteria. The experiment was conducted using qRT-PCR, and the stability of each candidate gene was assessed using4commonly used statistical programs-geNorm, NormFinder, BestKeeper and RefFinder. According to our results, PP2A was expressed at the most stable levels under different fermentation conditions, and RPL4was the most stably expressed gene in different tissues. RPL4, PP2A and β-tubulin are the most commonly recommended reference genes for normalizing gene expression in the entire sample set.
对灵芝的遗传背景研究不足,这阻碍了其作为模式生物被广泛研究。本研究首先评估了灵芝作为模式生物的可行性,并应用二代测序技术及光学图谱绘制整染色体级的灵芝基因组精细图。结果显示,灵芝基因组大小约为43.3Mb,包含13条染色体,82个scaffolds。应用ab initio方法和比较方法预测灵芝可能的编码基因并进行注释,整合工作由MAKER程序包完成,对部分预测基因应用Apollo软件进行人工校正。转录本序列和基因表达分析分别应用454和RNA-seq检测。预测结果显示,灵芝基因组编码16,113个基因,基因的表达水平在不同的发育阶段差异显著,以羊毛甾醇合酶为代表的次生合成及调控的相关酶与灵芝发育有关联。分析结果还显示,灵芝富含细胞色素P450、转运蛋白和转录调控蛋白,这些蛋白家族在生物次生代谢产物合成中发挥重要作用。灵芝也是在已测序的担子菌中编码木质素降解酶基因最丰富的物种之一,在生物能源的应用中有很大潜力。P450基因被认为是三萜下游修饰的关键基因。灵芝中78个CYP基因与羊毛甾醇合成酶共表达,其中16个与动物中具有特异睾酮羟化功能的CYP基因高度相似,这些基因更可能是三萜生下游的修饰基因。此外,灵芝基因组中存在24个CYP基因簇。基因组研究进一步巩固了灵芝在药用生物中的模式地位。
灵芝中的代谢物多样性早就为人们所关注。本文以灵芝免疫球蛋白家族,灵芝倍半萜类物质及灵芝三萜类物质为例,分析探讨灵芝活性物质多样性的成因。结果显示,灵芝中不同种类代谢物多样产生原因各有不同。以灵芝免疫球蛋白家族为代表的蛋白多肽类活性物质,其多态性来自于基因复制后的序列变异。倍半萜类物质的多态性与植物类似,来源于合成酶的多态性和不专一性,部分倍半萜合酶位于基因簇内,因此,灵芝倍半萜类物质的多样性也部分源多种修饰酶的修饰。灵芝中有超过150种三萜类物质,它们都来源于共同的前体——羊毛甾醇。分析结果显示,灵芝中只存在一个三萜环化酶即羊毛甾醇合酶但存在着大量的单加氧酶等修饰酶。多种修饰酶的存在、表达和调控是导致灵芝三萜类多态性的重要因素。多种多样性机制共存使灵芝也成为研究药源生物代谢产物多样性的良好模式。
基于本研究的研究成果我们还开发了一些研究辅助平台,以期在灵芝栽培、育种、发酵和生产中有应用的价值。如1、灵芝交配型座位的确定及单倍型的快速鉴定。通过基因组分析,灵芝交配型座位A位于Scaffoldl,跨度90kb,编码31个基因,包括两个同源异型结构编码基因HD1和HD2。交配型座位B位于scaffoldl4,跨度为100kb,包含6个费洛蒙编码基因和7个STE3-like费洛蒙受体基因。RNA-seq结果显示不同费洛蒙和费洛蒙受体编码基因在不同的发育阶段表达水平不同,推测不同类型的费洛蒙及其受体在灵芝不同时期执行不同的功能。MIP是真菌交配型座位中的保守蛋白,基于14种真菌的进化分析表明,灵芝属MIP中具有一段保守的特征序列。PCR结果表明,这段共有序列可作为灵芝属物种单倍体型快速鉴定的通用序列。2、qRT-PCR的内参基因筛选。荧光定量PCR (qRT-PCR)是一种快速、灵敏的基因表达检测技术。qRT-PCR的准确度及可靠性取决于内参基因的稳定性。因此系统性的评估内参基因是必需的。本研究从灵芝基因组数据中选择了10个qRT-PCR内参候选基因。所选的基因序列通过手动校正并根据严格的条件设计引物。通过统计分析评估候选基因的稳定性。实验结果显示,发酵条件下,protein phosphatase2A (PP2A)为最适的内参基因；在灵芝发育研究中,Ribosomal protein L4(RPL4)是最适的内参基因。在所有的检测条件下,RPL4, PP2A和P-Tubulin (BTU)是最适的内参基因并建议选用。
本研究通过全基因组测序填补了当前灵芝研究中在遗传信息方面的空白,使灵芝研究进入分子生物学前沿,巩固了灵芝在真菌次生代谢产物与发育研究中的模式地位,为下一步灵芝次生代谢产物生源合成研究及发育研究奠定了基础。研究同时发现,灵芝存在多种次生代谢产物多样性形成机制,是研究药源生物代谢产物多样性的良好模式。灵芝也是目前中药源物种中第一个完成染色体级基因组精细图的物种,一定程度上可以作为应用大数据进行药用生物研究的范例。
Ganoderma lucidum, a white rot basidiomycete belonging to the order Polyporales, is one of the most well-known medicinal mushrooms in the world. G. lucidum has been used as a remedy for thousands years in East Asia. This species is documented as LingZhi in Chinese Pharmacopoeia and is included in the American Herbal Pharmacopoeia and Therapeutic Compendium. G. lucidum is known as a "cellular factory for biologically useful compounds," and more than400bioactive compounds have been identified in G. lucidum, including polysaccharides, triterpenoids, fatty acids and alkaloids. Modern studies have reported that G. lucidum possesses multiple pharmacological activities, including antitumor. anti-hypertensive, anti-inflammatory and immunomodulatory activities. This species is amenable to genetic transformation and artificial cultivation, making it an ideal system for traditional medicine research.
Here, we sequenced and assembled its genome using next-generation sequencing and optical mapping approaches. The43.3-Mb genome of G. lucidum contained13chromosomes and was assembled into82scaffolds. The gene prediction and annotation was using MAKER pipeline, combining the ab initio method and comparative ways, constructed gene models were further manual curated using Apollo programm. Gene expression profile was detected using454transcriptome technology and RNA-seq technology. Results show that G.lucidum's genome encoded16,113predicted genes, some genes'expression level changed dramatically during different development stages. More importantly, the analysis revealed an impressive array of genes encoding cytochrome P450s (CYPs), transporters, and regulatory proteins which cooperate in secondary metabolism. The genome also encodes one of the richest sets of wood degradation enzymes among all sequenced basidiomycetes. Twenty-four physical CYP gene clusters were identified. Moreover,78CYP genes were co-expressed with lanosterol synthase, and16of these show high similarity to fungal CYPs that specifically hydroxylate testosterone, suggesting their possible roles in triterpenoid biosynthesis. The elucidation of the relationship between G.lucidum secondary metabolites and development based on omic scale analysis enables this organism to be a potential model system for the study of secondary metabolic pathways and their regulation in fungi.
The G. lucidum genome and transcriptome have wild applications in this specie's breeding, cultivation, production and research. In this paper, we introduced two examples. First, mating-type loci were identified based on genomic data. A90kb region in scaffold1was deemed as mating type A(matA) locus, two genes (GL30604and GL30607) in this region were inferred to encoding the HDl and HD2proteins. There are also29other genes in this region. Thirteen sequences were identified as mating type B (matB) locus genes. Six pheromone encoding genes were clustered with seven STE3-like pheromone receptor genes in a region of approximately100kb on scaffold14. The results suggested that mating-type locus in G. lucidum were conserved with other fungi which have been sequenced. The RNA-seq analysis showed that the expression level of different pheromone coding genes and pheromone receptor coding genes were not the same. This result indicated that different pheromones and their receptors may play diverse roles in variety conditions. The phylogenetic analysis of MIP coding genes from14fungi indicated a conserved region in Ganodermae. Based on the consensus sequences of mip in Ganodermae, a pair of primer was designed for the identification of the ploidy and the mating type of fungi strains from Ganodermae. Second, reference genes for qRT-PCR were selected from predicted gene models. Quantitative real-time reverse transcription PCR (qRT-PCR) is a rapid, sensitive and reliable technique for gene expression studies. The accuracy and reliability of qRT-PCR results depend on the stability of the reference genes used for gene normalization. Therefore, a systematic process of reference gene evaluation is needed. Ganoderma lucidum is a famous medicinal mushroom in East Asia. In the current study,10potential reference genes were selected from the G. lucidum genomic data. The sequences of these genes were manually curated, and primers were designed following strict criteria. The experiment was conducted using qRT-PCR, and the stability of each candidate gene was assessed using4commonly used statistical programs-geNorm, NormFinder, BestKeeper and RefFinder. According to our results, PP2A was expressed at the most stable levels under different fermentation conditions, and RPL4was the most stably expressed gene in different tissues. RPL4, PP2A and β-tubulin are the most commonly recommended reference genes for normalizing gene expression in the entire sample set.
引文
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