臺灣博碩士論文加值系統

蘭花是開花植物中最大、最具多樣性的科，約有超過800個屬和25,000個種。況且蘭花是台灣重要的高經濟價值花卉，目前產量最高的花卉為蝴蝶蘭。由於蝴蝶蘭深受全球人民喜愛，在栽種技術以及育種上有相當的基礎，目前在功能性基因體學上有許多研究。
而本篇論文是以RNA定序技術產生的片段序列來重組蘭花基因轉錄體，並且將這些資料經過組合、註解以及表現量分析，從這之中可以得到更多有價值的資料。接著使用相關演算法、程式來分析此物種，透過資料庫所提供的資訊有效地節省生物實驗者的時間與經費。最後我們得到樣本BUDB-0.2有68,245,430 paired-end reads資料,而樣本BUD+0.2 則有68,241,474 paired-end reads。另一方面也讓生物實驗者能有更多的參考依據，或者是作為實驗結果的一個初步驗證工具。而實驗中則以蝴蝶蘭的野生型與突變型兩種資料，來進行轉錄因子的分析，並且使用Java、JSP和MySQL環境建構成一個整合性網站資料庫，提供相關註解查詢分析以及Blast等結果。

Orchids belong to one of the largest, most diverse flowering plant families. There are over 800 genera of Orchids in the world and more than 25,000 species as well. Orchids are the high value crops in Taiwan. Nowadays the best production is the Phalaenopsis. Phalaenopsis is a beautiful flower in the world, and many people love it. Until now it has a lot of studies for planting technology and plant breeding. The orchid research includes functional genomics, Expressed sequence tag (ESTs), Complementary DNA (cDNA) researches with the databases that helps molecular breeding about gene identification and screening.
In this thesis, we used RNA-seq data of the Phalaenopsis wild type (BUD+0.2) and mutant type (BUD-0.2) to study the transcriptome and expression of Phalaenopsis. The BUD-0.2 Orchid sample has 68,245,430 paired-end reads, and the BUD+0.2 Orchid sample has 68,241,474 paired-end reads. Additionally, the OrchidWeb may serve as a basis for the study of experimental results of a preliminary validation tool. The webserver should enable experimental biologist to get more information and biological implication. The OrchidWeb is written in Java, JSP and MySQL. We established a comprehensive web server database, and provided Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation, Blast page. The OrchidWeb database is freely available at http://syslab.nchu.edu.tw/orchid/.

摘要 i
Abstract ii
Table of Contents iii
List of Tables v
List of Figures vi
1. Introduction 1
1.1 Research Background 1
1.2 Research Purpose and Value 4
1.3 Overview of the Thesis 4
2. Related Research 6
2.1 Plant Functional Genomics 6
2.2 Transcription Factor 6
2.3 EST (Expressed sequence tag) 7
2.4 Genetically Modified Crops 8
2.4.1 Genetic Screening 9
2.4.2 Gene Cloning 10
2.5 Blast2GO 12
2.6 KEGG Automatic Annotation Server (KAAS) 13
3. Method 16
3.1 Materials and Data analysis 16
3.1.1 Data Source 16
3.1.2 Data Analysis 20
3.2 To Avoid Alternative Splicing by Using Usearch 25
3.2 Transcriptome Annotation 26
3.3 Differential Expression Analysis using Cuffdiff 27
3.4 Enrichment Analysis 27
3.5 BLAST (Basic Local Alignment Search Tool) 29
4. Results and Discussion 30
4.1 De novo Orchid transcriptome 30
4.2 GO and KEGG pathway Enrichment Analysis 30
4.3 OrchidWeb 33
4.3.1 Programming 38
4.3 The Flower Factor 41
5. Discussion and Conclusions 42
5.1 Conclusions 42
5.2 Suggestions for Future Research 42
Reference 43
Appendix I 46
Appendix II 50

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