蝴蝶蘭以其持久、獨特而美麗的花朵外形及多樣化的顏色而成為世界主要的暢銷花卉作物，新的商業品種的育種更讓台灣成為世界上主要的蝴蝶蘭出口國家。蝴蝶蘭的分子基因研究更可以加速蘭花品質的改善。本論文的研究內容主要分成兩大部分：第一部份是探討蝴蝶蘭的基因體組成結構與long terminal repeat 反轉位子 (LTR-retrotransposons) 對蝴蝶蘭基因體大小的影響；第二部分是探討蝴蝶蘭花形和花色的調控機制。在第一部分，以蝴蝶蘭的細菌人工染色體末端序列 (bacterial artificial chromosome end sequences, BESs) 分析其中的基因、重複序列及微衛星序列組成。這些研究將可以幫助我們瞭解蝴蝶蘭與其他植物基因體組成的相似和差異。進一步，利用BESs和部分解序的蝴蝶蘭基因體序列 (partial Phalaenopsis genome sequences)，分析其中LTR-反轉位子在蝴蝶蘭基因體的數量，並分析LTR-反轉位子對於蘭花基因體大小的影響。在第二部分，選殖五個B群的MADS基因 (PeMADS2~6) 的啟動子，以探討調控這五個基因的機制。PeMADS2~6在不同的花器表現並調控蝴蝶蘭的花朵形態發育。此外，分析啟動子上的DNA甲基化與染色質修飾(chromatin modification) 狀態。確認B群基因以啟動子序列及組蛋白乙醯基化修飾 (histone acetylation)作用，調控B群基因在不同花器中有不同的表現模式。在蝴蝶蘭花色色素圖案 (pigmentation patterning) 部分，以全基因體方式鑑定出MYB轉錄因子，發現其中三個MYB轉錄因子 (PeMYB2, PeMYB11, and PeMYB12) 不但在不同時間與空間參與花青素生合成，且會調控花朵不同的花色色素圖案。其中PeMYB2調控花萼和花瓣上全面粉紅色(full-red)，PeMYB11調控花萼、花瓣與唇辦上的紅色班點(red-spot)，PeMYB12調控花萼和花瓣上沿著維管束分佈的紅色線條(venation pattern)與唇辦上的紅色。這些結果顯示蝴蝶蘭具有複雜的MYB轉錄因子進行花青素生合成與花色色素圖案的調控。此外，不同的蝴蝶蘭商業品種含不同比例的PeMYB2、PeMYB11及 PeMYB12的基因表現，造成蝴蝶蘭具有非常多樣的花色色素圖案。綜合以上，本論文內容促使我們更瞭解蝴蝶蘭的基因體組成，並能以研究基因體的觀點探討蝴蝶蘭在花形與花色上獨特而複雜的調控機制。這些研究增進我們對於蘭花特殊花形與多樣花色的認識，進而提升蘭花在花卉產業上與眾不同的價值性。

Phalaenopsis orchids have become very popular for their long-lasting flowers with elegant floral morphology and various flower colors. Development of new cultivars is economically important for floricultural industry worldwide. This thesis contains two parts: (1) analysis of the genome structure and composition, and (2) study of the regulatory mechanism for the promoters of B-class floral organ identity genes and the transcription factors regulating flower color in Phalaenopsis. For the first part, pair-end sequences from 2,920 bacterial artificial chromosome (BAC) clones of P. equestris were analyzed for the compositions of protein-coding regions, repeat sequences, and microsatellites in the P. equestris genome. The LTR-retrotransposons were identified from the BAC end sequences (BESs) and partial genome sequences, and examined for their retrotransposition/recombination events and effects on Phalaenopsis genome sizes. Their copy numbers were assessed in the genome sequences of four Phalaenopsis species with either small or large chromosomes. For the second part of studying the regulation of orchid morphogenesis, the promoter sequences of five B-class MADS-box genes (PeMADS2~6) were identified and analyzed. These included four APETALA3 (AP3)-like PeMADS2~5 and one PISTILLATA (PI)-like PeMADS6, displaying distinct expression profiles in various floral organs and specifying the spectacular flower morphology in orchids. Further studies on DNA methylation and histone modification status of PeMADS2~6 were performed. The regulation via the upstream sequences as well as increased histone acetylation levels may involve in the distinct expression profiles of the AP3-like genes for Phalaenopsis floral morphogenesis. To investigate the floral pigmentation patterning, genome-wide identification of regulatory genes involved in the flower color and anthocyanin biosynthesis pathway in Phalaenopsis, such as MYBs was performed. Three R2R3-MYB transcription factors, PeMYB2, PeMYB11, and PeMYB12, were characterized for their roles in regulating three distinct floral pigmentation patterns, full-red, red-spot, and venation patterns, respectively, in one single flower of Phalaenopsis. In addition, various ratios of these three PeMYBs were concomitant with distinct floral pigmentation patterns in six commercial cultivars. These results unravel the complicated regulation of anthocyanin pigmentation patterning in Phalaenopsis which leads to the highly abundant color patterns in orchid flowers. All these results together improve our knowledge on the genome composition and the regulation of floral morphogenesis and pigmentation patterning in Phalaenopsis orchids through genomics approach.

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