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研究生：	許嘉珍 Hsu, Chia-Chen
論文名稱：	鑑定白花蝴蝶蘭獨腳金內酯生合成路徑基因及表現模式分析 Identification of strigolactones (SLs) biosynthesis genes from Phalaenopsis aphrodite subsp. formosana and characterization of their expression patterns
指導教授：	蔡文杰 Tsai, Wen-Chieh
學位類別：	碩士 Master
系所名稱：	生物科學與科技學院 - 熱帶植物與微生物科學研究所 Institute of Tropical Plant Sciences
論文出版年：	2023
畢業學年度：	111
語文別：	英文
論文頁數：	82
中文關鍵詞：	台灣白花蝴蝶蘭、獨腳金內酯、生合成路徑、殼聚醣
外文關鍵詞：	Phalaenopsis aphrodite, strigolactones, biosynthesis pathway, chitosan
相關次數：	點閱：122 下載：35
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台灣白花蝴蝶蘭(Phalaenopsis aphrodite subsp. formosana) 在育種上被視為重要的親本。蝴蝶蘭是「部分真菌異營性」的蘭科植物，其種子不具有明顯分化之胚乳構造，因此在自然界中，蝴蝶蘭種子在萌芽時期高度仰賴蘭花菌根真菌(orchid mycorrhizal fungi, OMF)作為養分來源。目前已知大部分(80%)的陸生植物會藉由根部釋放獨腳金內酯（Strigolactones, SLs）到土壤中，促進叢枝菌根真菌(Arbuscular mycorrhizal fungi, AMF)孢子萌芽，並引導菌絲進入根細胞，進行養分交換。特定專一性SLs具有不同生理活性來增加菌絲分支數量與結構，增加養分的吸收，此外，SLs也作為內源性的植物激素調節植物生理機能。儘管許多研究證實SLs是植物與共生真菌之間關鍵的溝通橋樑，SLs在蘭花與OMF之間的角色及其分子機制尚未被闡明。
先前實驗室透過LC-MS/MS檢測出蝴蝶蘭種子會分泌兩種以上的SLs (Sorgolactone 和一群尚未定義的SLs，稱為SLXs)，並描述了其訊號傳導路徑的分子機制。為瞭解蝴蝶蘭種子萌芽時期之SLs 之生合成路徑，本篇研究首先從白花蝴蝶蘭基因組中鑑定出SLs生合成路徑中的八個基因，PaD27、PaCCD7-1、PaCCD7-2、PaCCD7-3、PaCCD8、PaMAX1/PaCYP711A、PaCYP711A-O以及PaCYP722B。演化樹分析結果發現CYP711A-O之胺基酸序列相似於MAX1/CYP711A，但唯獨存在於蘭科植物中。進一步利用真菌細胞壁的重要組成—殼聚醣(chitosan, CHT)，作為激發子(elicitor)以模擬來自微生物的訊號，透過轉錄組分析發現10 mg/L濃度的CHT在蝴蝶蘭種子確實影響SLs生合成路徑基因表現。基因表現分析結果顯示PaD27、PaCCD7-1、PaCCD7-3、PaCCD8、PaCYP722B的基因表現會受CHT處理誘導，也發現PaCCD7-2、PaMAX1/PaCYP711A、PaCYP711A-O基因表現不受CHT處理誘導，且PaCCD7-1在所有測試組織中具有最高表現量。最終透過這些結果提出台灣白花蝴蝶蘭SLs生合成路徑模型。

Phalaenopsis aphrodite subsp. formosana contributed to the various commercial Phalaenopsis varieties. Phalaenopsis is classified as partially mycoheterotrophy which contain an undifferentiated embryo without a well-define endosperm. Therefore, require nutrition from orchid mycorrhizal fungi (OMF) during the early seed germination stage is essential to Phalaenopsis. Previous study suggested most (80%) of terrestrial plants release strigolactones (SLs) into soil to induce germination of AMF spores and accelerate the colonization with host plants. The SLs could guide the fungal hyphae to penetrate into the intracellularly inner cortex for nutrient exchange, especially under the condition of drought stress and/or limitation of phosphate. Moreover, SLs also act as endogenous phytohormone to regulate plant physiology. Although several researches suggested SLs play a vital role in the symbiosis between plant-fungi interaction, the role and the molecular mechanism of SLs still little known between orchids and OMF.
Previously, more than two kinds of SLs (sorgolactone and a cluster of undefined SLs which named “SLXs”) have been detected in P. aphrodite subsp. formosana by HPLC-MS/MS analysis and the signaling transduction pathway was proposed. To investigate the biosynthesis pathway of SLs during seeds germination stage in P. aphrodite, we identified eight genes involved in the SL biosynthesis pathway, including PaD27、PaCCD7-1、PaCCD7-2、PaCCD7-3、PaCCD8、PaMAX1/PaCYP711A、PaCYP711A-O and PaCYP722B from P. aphrodite genome. Phylogenetic analysis indicated CYP711A-O subclade was specific existed in Orchidaceae. The specific component of fungal cell wall—chitosan (CHT) was further utilized as the elicitor from microbes. Transcriptome analysis suggested 10 mg/L of CHT actually affect gene expression of SLs biosynthetic pathway P. aphrodite seeds. Gene expression analysis indicated expressions level of PaD27、PaCCD7-1、PaCCD7-3、PaCCD8 and PaCYP722B are influenced by CHT. However, expressions level of PaCCD7-2、PaMAX1/PaCYP711A and PaCYP711A-O would not influenced by CHT. In addition, PaCCD7-1 showed highest expression level among tissues we examined for qRT-PCR analysis. Based on these results, we proposed a working model of SLs biosynthesis pathway in P. aphrodite orchid.

中文摘要	I
Abstract	II
誌謝	IV
Contents	V
List of Tables ………………………………………………………………………………………………..……….VI
List of Figures………………………………………………………………………………………….…….……...VII
List of Appendix Tables……………………………………………………………………………….….…….VIII
List of Appendix Figures………………………………………………………………………………...……….IX
Abbreviations………………………………………………………………………………………………………….X
1. Introduction	1
1.1 Orchidaceae	1
1.1.1	Partially and fully mycoheterotrophy orchids	1
1.1.2	Communication between orchids and OMF	1
1.2 Strigolactones	2
1.2.1 Structural diversity in the strigolactones	2
1.2.2 Strigolactones biosynthesis pathway	3
1.2.3 Agrosciences of strigolactones	3
1.3 Chitosan	4
1.3.1 Property of chitosan	4
1.3.2 Elicitor application of chitosan	5
2.Purpose	6
3. Material and Methods	7
3.1 Identification of SLs biosynthesis genes in orchids	7
3.2 Sequence alignments and phylogenetic analysis	7
3.3 Plant material growth condition	8
3.4 Chitosan stock solution preparing	8
3.5 Chitosan treatment of seeds	8
3.6 Transcriptome analysis of P. aphrodite subsp. formosana seeds	8
3.7 Real-time quantitative RT-PCR	9
3.8 Plant tissue preparation for genes expression analysis	10
3.9 Statistical analysis	10
4. Results	11
4.1 Multiple sequences alignment of cytochrome P450s family	11
4.2 Identification and phylogenetic analysis of D27 from Orchidaceae	12
4.3 Identification and phylogenetic analysis of CCD7 and CCD8 from Orchidaceae	13
4.4 Identification and phylogenetic analysis of cytochrome P450s from Orchidaceae	15
4.5 Transcriptome of sequence assembly and annotation	17
4.6 Characterization of entire DEGs in chitosan-treated seeds	18
4.7 Transcriptional changes in SLs and fatty acid metabolism pathway	19
4.8 Expression pattern of genes involved in SLs biosynthesis pathway	20
5. Discussion	23
5.1 Evolution of the genes involved in SL biosynthesis pathway in Orchidaceae	23
5.2 Influence of the seeds of P. aphrodite subsp. formosana with CHT treatment	24
5.3 Differential expression of the genes involved in SLs biosynthesis pathway	25
5.4 Putative model of SLs biosynthesis pathway in P. aphrodite subsp. formosana	27
7. References	28
 
List of Tables
Table 1. Quantity of the genes involved in SLs biosynthesis pathway of Orchidaceae.	35
Table 2. The genes are involved in the SLs biosynthesis pathway of angiosperm.	36
Table 3. Accession number of D27 used in phylogenetic and alignment analysis.	37
Table 4. Accession number of CCD7 used in phylogenetic and alignment analysis.	38
Table 5. Accession number of CCD8 used in phylogenetic and alignment analysis. 	39
Table 6. Accession number of CYP711 used in phylogenetic and alignment analysis.	40
Table 7. Accession number of CYP722 used in phylogenetic and alignment analysis. 	41
Table 8. List of primers used for qRT-PCR analysis.	42
Table 9. UP-regulated unigenes in CHT-treated seeds.	43
Table 10. Down-regulation of unigenes in CHT-treated seeds.	44
Table 11. The predicted unigenes involved in SLs biosynthesis pathway.	46
Table 12. The predicted unigenes involved in SLs signaling pathway.	47
Table 13. The predicted unigenes involved in β-oxidation.	48
Table 14. The predicted unigenes involved in glyoxylate cycle.	49
Table 15. The predicted unigenes involved in tricarboxylic acid (TCA) cycle.	50
Table 16. Number of putative genes mapped in KEGG pathways.	51
Table 17. Statistical significance of gene expression performed by qRT-PCR analysis.	56

List of Figures
Figure 1. The scientific name of partially and fully mycoheterotrophy orchids.	57
Figure 2. Mulcell divisionle sequence alignment of cytochrome P450 family proteins.	60
Figure 3. Phylogenetic analysis of D27 in plant kingdom.	61
Figure 4. Phylogenetic analysis of CCD7 in plant kingdom.	62
Figure 5. Phylogenetic analysis of CCD8 in plant kingdom.	63
Figure 6. The phylogenetic analysis of cytochrome P450 family.	64
Figure 7. Plotting PCA (Principal Component Analysis) of MS-vs-CHT seeds.	65
Figure 8. Venn diagram of number of expressed unigenes in MS-vs-CHT seeds.	66
Figure 9. Differential expression genes (DEGs) in seeds treated with MS and CHT.	67
Figure 10. Gene ontology enrichment analysis of DEGs.	68
Figure 11. KEGG pathway enrichment analysis of DEGs.	69
Figure 12. Volcano plot of DEGs in MS- and CHT-treated seeds.	70
Figure 13. Relative expression of SLs biosynthesis-related genes in MS-vs-CHT treated seeds.	71
Figure 14. Tissues of Phalaenopsis aphrodite subsp. formosana used for qRT-PCR.	72
Figure 15. Relative expression of SLs biosynthesis-related genes in different primordia.	73
Figure 16. Relative expression of SLs biosynthesis-related genes in different regions of root.	74
Figure 17. Relative expression of SLs biosynthesis-related gene in stem and young leaf.	75
Figure 18. Putative model of SLs biosynthesis pathway in P. aphrodite subsp. formosana.	76

List of Appendix Figures
Appendix Figure 1. Similar polysaccharide structure—cellulose, chitin and chitosan.	77
Appendix Figure 2. Structural diversity of SLs.	78
Appendix Figure 3. Phylogenetic tree of the D27, D27L1 and D27L2.	79
Appendix Figure 4. The phylogenetic tree of the P450 enzyme.	80
Appendix Figure 5. Phylogenetic tree of the clan 85 family.	81
Appendix Figure 6. KEGG enrichment analysis of DoTc and Do.	82
                                    

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