赤箭又名天麻(Gastrodia sp.)為蘭科赤箭屬的多年生草本腐生蘭，全世界現發現約有50-60種，為蘭科之中最大的真菌異營屬，天麻無法執行光合作用，一生從種子萌芽到成長熟成都需要和蘭花菌根菌形成共生關係吸取養分。天麻主要分布集中於亞洲，為高經濟藥材植物，台灣至少有19赤箭屬的分類群，其中12種目前只發現分佈於台灣，除了G. elata能人工大量栽培外，其他赤箭原生品種尚未能人工栽培開發利用，主要是因為對赤箭和菌根菌共生生理尚未了解，加上無法仿造和自然完全相同的獨特菌相及生長環境，種子發芽率低、植株無法正常發育因而無法大量生產。
本研究計畫目的為研究赤箭及共生菌相互作用機制。在這個研究中，我們已經從棲息地收集了八個赤箭品種。在這些收集的品種間，我們選擇相對族群數較多的進行下一步分析。目前我們已經成功的建立根莖繁殖在冬赤箭及日本赤箭。我們也用微生物培養方式從冬赤箭、春赤箭及三個來自中國不同來源的高赤箭塊莖，收集了33種內生真菌。幾乎我們所收集的菌種都為病原菌，尤其是在成熟的高赤箭塊莖。也無法分離出應該是在高赤箭培養中最主要的蜜環菌。並建立了蜜環菌及赤箭共培養方式及條件並且發現蜜環菌對於高赤箭是非常專一性的共生關係，其他種類赤箭無法使用蜜環菌進行相同方式來培養。從以上這些發現我們提出了假說，1)每一品種之赤箭都有獨特的微生物群來幫助其生長及發育，2)蜜環菌對於高赤箭是在生長初期階段才需要的，3)在不同品種赤箭本生基因調控和內生微生物族群會交互作用並影響其本身生物活性酚類化合物-天麻素的產生。為了測試這些假說，首先我們檢測了來自不同人工培養及野外採集的赤箭和六個不同品系的蜜環菌並利用HPLC進行天麻素的測定。從結果明顯顯示在不同的赤箭品種、新鮮高赤箭以及經過後熟處理高赤箭的天麻素含量都不同。我們也利用多源基因體學來解釋真菌菌相結構深度及廣度，檢測了四個赤箭品種(高赤箭、冬赤箭、爪哇赤箭和春赤箭)。我們設計分子標記在六個條碼區域並利用Illumina MiSeq high-throughput paired-end定序。藉由比較多源基因體學結果，可讓我們了解不同赤箭塊莖真菌菌相如何影響植物本身生長及發育；也能從中得知真菌菌相如何影響塊莖之天麻素的產生。

Gastrodia sp. is myco-heterotrophic (MH) orchid belong to Orchidaceae. The orchid is achlorophyllous laking ability for photosynthesis. Whole life completely depends on symbiosis with different mycorrhizal conterparts for nutrients from seed germination to reproduction. There are 50-60species mainly found in Asia. Taiwan alone has 19 species and 12 of them are endemic. Other than G. alata, most of these species have not been evaluated for utilization. We know very little the physiology of Gastrodia sp. and microbial symbiosis. Gastrodia sp. is unique plant receive little attention regardless its importance in medicine, ecology and conservation. For this research, we have collected 8 Gastrodia species from their natural habitats. Among these, we selected species that are relative abundant for our work. We have successful established rhizome-like propagules for G. pubilabiata, and G. niponica in vitro. We have also isolated 33 endophytic fungi by microbial culture using rhizomes of G. pubilabiata, G. fontinalis, and 3 different sources of G. elata from China. Nearly all the fungi we isolated are pathogenic from all the species we examined especially the G. elata mature rhizomes. We also could not isolate Armillaria mellea which supposed to be the dominant fungi in cultivated G. elata. We have also established co-culture method for Armellaria and Gastrodia sp. under in vitro condition and found A. mellea only can co-culture with G. elata but no other species. These findings lead us to hypothesize 1) each Gastrodia specie has its unique microbiome required for plant growth and development, 2) A. melllea is only required for initial growth of young G. elata rhizome, and 3) interaction of genotype and microbiome determine the levels of bioactive phenolic compound-gastrodin production in different Gastrodia species. To test these, we first measured gastrodin levels in different cultivated and wild Gastrodia species and 6 stains of A. melllea collected by HPLC. Our data shows significant differences in gastrodin levels in the rhizomes of cultivated G. elata obtained from different sources in China using fresh and dried samples, and in different Gastrodia species. We have used metagenomic approach to decipher fungal community structure in breadth and depth for 4 Gastrodia species (G. elata, G. pubilabiata, G. javanica and G. fontinalis). We used Illumina MiSeq high-throughput paired-end sequencing by designing molecular markers for six barcoding regions. Comparative metagenomics can lead to our understanding how fungal microbiome in different Gastrodia species affect plant growth and development; and perhaps also give use some clue how fungal microbiome affect gastrodin production in the rhizomes.

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