西洋参Panax quinquefolium L.是人参属多年生草本植物，以根入药，具有极高的药用和经济价值。中国已成为西洋参第一大消费国和世界三大产区之一。但目前，我国不同产地西洋参品质有差异。本研究以西洋参及根际土壤为研究材料，基于微生物组、转录组和叶绿体基因组等技术，结合气候因子和土壤理化指标，系统地研究西洋参微生物组特点及其人参皂苷与微生物、气候因子和土壤理化之间的关系，揭示气候因子对西洋参品质形成的影响，预测未来气候变化下西洋参在中国适生区格局变迁及比较当前适生区西洋参叶绿体基因组特征。主要结果如下：

1. 利用高通量测序技术研究北京、吉林及山东3个主产地的西洋参根际土壤微生物和山东不同生长年限西洋参根际土壤微生物，发现西洋参根际土壤细菌主要由酸杆菌门(Acidobacteria)、放线菌门(Actinobacteria)、变形菌门(Proteobacteria)、绿弯菌门(Chloroflexi)和壁厚菌门(Firmicutes)组成，根际土壤真菌主要包括子囊菌门(Ascomycota)和担子菌门(Basidiomycota)。3个主产地西洋参根际土壤的核心微生物为芽孢杆菌属(Bacillus)、罗河杆菌属(Rhodanobacter)、鞘氨醇单胞菌属(Sphingomonas)、镰刀菌属(Fusarium)、Plectosphaerella和青霉菌属(Penicillium)。RB41、毛壳菌属(Chaetomium)、芽孢杆菌(Bacillus)、节杆菌(Arthrobacter)、伯克霍尔德菌(Burkholderia)、被孢子霉属(Mortierella)、假裸子囊菌属 (Pseudogymnoascus)和Tetracladium是3个主产地西洋参根际差异微生物。适冷微生物假裸囊菌属(Pseudogymnoascus)的相对丰度随着西洋参生长年限的增长而增加。

2. 利用高通量测序技术研究健康与根腐病的西洋参根际土壤微生物，西洋参真菌的α-多样性分析结果表明，根腐病的西洋参根际土壤真菌的Chao 1、ACE和Sob均低于健康根。此外，土壤理化性质表明，与健康西洋参相比，根腐病西洋参的土壤pH、有效磷和有效钾的含量较低。LEfSe表明根腐病西洋参土壤中6个真菌属，即Gibellulopsis、镰刀菌属(Fusarium)、Plectosphaerella、Tetracladium、赤霉菌属(Gibberella)和Ilyonectria，相对丰度比健康西洋参土壤高 (P＜0.05)，首次发现Gibellulopsis和赤霉菌属(Gibberella)与西洋参根腐病密切相关，这为西洋参的生物防控奠定基础。

3. 利用高通量测序技术研究北京、吉林和山东3个主产地西洋参及山东不同生长年限西洋参组织内生微生物，发现内生真菌主要来源于子囊菌门(Ascomycota)和担子菌门(Basidiomycota)。叶的微生物α-多样性比根高。首次发现，适冷真菌假裸囊菌属(Pseudogymnoascus)是3个主产地、不同生长年限西洋参及不同组织(根与叶)的核心微生物。镰刀菌属(Fusarium)微生物随着西洋参生长年限的增长相对丰度增加。

4. 西洋参中人参皂苷的含量与微生物、气候因子和土壤理化的RDA分析表明，昼夜温差 (BIO2)是影响西洋参中人参皂苷含量的重要生态因子，该因子可以解释所观察到的变异的86.2%。将西洋参在不同昼夜温差下培养，结果发现西洋参的总人参皂苷在昼夜温度为25℃/25℃条件下含量最高，其次为昼夜温度为25℃/15℃，在昼夜温度为25℃/5℃条件下含量最低。转录组结果表明差异基因涉及人参皂苷生物合成途径中SQE、HMGR、HMGS和SS等关键酶。

5. MaxEnt模型预测当前及未来气候变化下(2100年)西洋参在中国的适生区，结果表明西洋参在中国的适生区将扩大而且向东北方向迁移，当前部分适生区不再适合西洋参生长。对当前适生区西洋参叶绿体基因组比较，发现7个产地西洋参叶绿体基因组有24个单碱基突变和6个位置发生插入缺失突变。西洋参叶绿体基因组系统发育分析表明西洋参在中国引种栽培近50年，陕西、北京和吉林的西洋参已经与原产地(美国与加拿大)具有差异，并发现可鉴别不同产地西洋参的候选基因：rpcoC2、trnE-UUC、accD、petD、trnL-CAA、trnR-UCU、rps14和psbB。

Panax quinquefolium L. is a perennial herbaceous plant of panax genus and its roots used as medicine with high medicinal and economic value in China. At present, China has developed into the world’s largest P. quinquefolium consumer country and the third largest P. quinquefolium producing country in the world. However, the quality of P. quinquefolium in different cultivated areas in China was different. In this study, P. quinquefolium and its rhizosphere soil were used as research materials. Based on the microbiome, transcriptome and chloroplast genome technology, combined with climatic factors and soil physicochemical index, this study systematically studied microbiome of P. quinquefolium and the relationship among ginsenosides content in  P. quinquefolium with microorganism, climatic factors and soil physicochemical properties. In addition, the distribution of P. quinquefolium under future climate was predicted and its plastid genome characteristics under current distribution was compared. The main results are:

1. The high-throughput sequencing technology was used to study the rhizosphere soil microbial communities of P. quinquefolium from Beijing, Jilin and Shandong province and 2 -, 3 - and 4-year-old P. quinquefolium from Shandong province. It was found that the bacteria in the rhizosphere soil were mainly composed of Actinobacteria, Proteobacteria, Acidobacteria, Firmicutes and Chloroflexi. Rhizosphere soil fungi mainly include Ascomycota and Basidiomycota. The core microbiota in the soil of three main producing areas of P. quinquefolium were Bacillus, Rhodanobacter, Sphingomonas, Fusarium, Plectosphaerella and Penicillium. The 8 biomarker genera in the rhizosphere soil communities of three producing areas of P. quinquefolium were RB41, Chaetomium, Bacillus, Arthrobacter, Burkholderia, Mortierella, Pseudogymnoascus and Tetracladium. The relative abundance of cold-adapted Pseudogymnoascus in the rhizosphere soil increased with the growth of P. quinquefolium.

2. The high-throughput sequencing technology was used to compare the rhizosphere soil microbial communities of healthy and rot root of p. quinquefolium. The α-diversity analysis showed that the Chao 1, ACE and Sob of rhizosphere soil fungi of root rot disease were lower than those of healthy roots. The physical and chemical properties of soil was also determined. The results showed that the pH, available phosphorus and available potassium contents of root rot of P. quinquefolium soil were lower than that of healthy P. quinquefolium. LEfSe showed that the relative abundance of six fungal genera in root rot soil, namely Gibellulopsis, Fusarium, Plectosphaerella, Tetracladium, Gibberella and Ilyonectria, was higher than that in healthy soil (P<0.05). Three of these genera (Ilyonectria, Plectosphaerella and Fusarium) can cause the rot root of p. quinquefolium. Gibellulopsis and Gibberella were found closely related to root rot of p. quinquefolium for the first time.

3. The high-throughput sequencing technology was also used to study the endophytic microbiome of P. quinquefolium from Beijing, Jilin and Shandong province and 2 -, 3 - and 4-year-old P. quinquefolium from Shandong province. Moreover, the endophytic microbiome of the root and leaves of P. quinquefolium was compared. The results showed that the endophytic fungi were mainly from Ascomycota and Basidiomycota. The microbial α-diversity of leaves was higher than that of roots. It was found for the first time that Pseudogymnoascus, a cold-adapted microorganism, was the core microbiota of roots and leaves of P. quinquefolium from three main habitats with different growth years. The relative abundance of Fusarium increased with the growth years of P. quinquefolium.

4. RDA analysis of ginsenosides content in P. quinquefolium with the relative abundance of microorganism, climatic factors and soil physicochemical properties showed that diurnal temperature difference (BIO2) was an important ecological factor affecting the ginsenosides content in P. quinquefolium, which could explain 86.2% of the observed variation. Moreover, the potted seedlings of 3-year-old P. quinquefolium were cultivated in artificial climate chamber for two month. It showed that the total ginsenosides content in P. quinquefolium was the highest under the day-night temperature of 25℃/25℃, followed by the day-night temperature of 25℃/15℃, and the lowest under the day-night temperature of 25℃/5℃. Transcriptome sequencing results showed that the differential genes were related with SQE, HMGR, HMGS and SS in ginsenoside biosynthesis pathway.

5. MaxEnt model was used to predict the suitability of P. quinquefolium in China under current and future climate (2100), the suitable area of P. quinquefolium in China will expand and migrate to the northeast, and some suitable areas at present are no longer suitable for planting P. quinquefolium in the future. Comparing the chloroplast genomes of P. quinquefolium from the present suitable regions, 24 single nucleotide polymorphisms and 6 insertions and deletions was found in the chloroplast genomes of P. quinquefolium. Phylogenetic analysis of chloroplast genome showed that P. quinquefolium were different from those from their original regions (the United States and Canada). RpcoC2, trnE-UUC, accD, petD, trnL-CAA, trnR-UCU, rps14 and psbB might be effective in distinguishing P. quinquefolium from different areas.