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系統識別號 U0026-2002202022454500
論文名稱(中文) 蘭花基因資料庫:蘭花全基因組共線性及微小RNA-標地基因之比較分析
論文名稱(英文) OrchidBase: comparative genomics of synteny and miRNA-target gene among orchid whole genomes
校院名稱 成功大學
系所名稱(中) 電機工程學系
系所名稱(英) Department of Electrical Engineering
學年度 108
學期 1
出版年 109
研究生(中文) 何修頤
研究生(英文) Ho Sunny Sau Yee
學號 N26071097
學位類別 碩士
語文別 中文
論文頁數 58頁
口試委員 指導教授-吳謂勝
口試委員-張天豪
口試委員-蔡文杰
口試委員-童俊維
口試委員-蕭郁芸
中文關鍵字 蘭科  標靶預測  成熟miRNA預測 
英文關鍵字 OrchidBase  miRNA  Synteny  Gene Order 
學科別分類
中文摘要 蘭科是全球物種最多的被子植物之一,具有重要的觀賞價值。考慮到蘭花對人類的重要性,獲得有用的基因組和轉錄組信息對於蘭花在基礎研究及育種應用非常重要。於過去幾年,國立成功大學熱帶植物與微生物科學研究所成功完成三種蘭花的全基因組解序,其分別為蝴蝶蘭(Phalaenopsis equestris)、鐵皮石斛(Dendrobium catenatum)以及深圳擬蘭(Apostasia shenzhenica)。為了管理並使用龐大的蘭花基因組資訊,整合解序後的資料並組成了一個網頁資料庫OrchidBase,可供蘭花學者於線上查詢有關解序後的資料。現在OrchidBase資料庫的功能大部分的功能都是單種物種的基因體資料相關分析,對於物種之間的分析並不完整。所以為了提高OrchidBase基因庫的資訊量及功能性,故進行了本次的研究,希望為研究人員更有效率使用蘭花基因資訊。
本研究主要分成三個部份,第一部份為miRNA的研究。利用miRLocator鑑定成熟miRNA的資訊及TAPIR預測miRNA的標靶基因,並產生頁面提供給使用者瀏覽及搜尋。第二部份為利用Mcscan進行配對及計算,鑑定蘭科植物基因組之間共線性(Synteny)區域,提供蘭科植物基因組結構之比較及演化過程中基因組的變化。第三部分則提供特定基因於基因組中與鄰近基因之排列順序關係(gene order)。利用演算方法對比基因資訊及視覺化基因排序,方便研究者研究特定基因在不同物種的演化過程中,在基因組中相對位置資訊之比較。
英文摘要 Orchidaceae are the largest families of flowering plants and most important ornamental plants. Considering the importance of Orchidaceae, research in Orchidaceae and breeding communities should have access to useful genomic and transcriptomic information. Recently, National Cheng Kung University have sequenced the whole genome of Phalaenopsis equestris, Dendrobium catenatum and Apostasia shenzhenica. For the convenience of further research, OrchidBase was established by collecting all the information of the sequenced data into a database.
This study is divided into three part. The first part is about miRNA target prediction. Using the machine learning method, we can predict the position of mature miRNA. Then we use TAPIR algorithm to predict the target of miRNA. To increase the reliable of research result, we use a lot of characteristic of miRNA. The second part is synteny viewer. We defined the synteny blocks by the definition in previous paper and visualize the data by web tools. User can simulate the experiment by using our tools to reduce the cost of the actual experiment. Final part is gene order viewer. Using the algorithm to compare different sequences and the features of gene duplicate, visualize the gene sequences and convent the researchers to study the evolution of different genes.
論文目次 摘要 Ⅰ
目錄 V
表目錄 VII
圖目錄 VIII
第一章 研究背景及動機 1
1-1 蘭科植物 1
1-2 蘭花基因庫 OrchidBase 2
1-3 研究動機 6
第二章 miRNA標靶預測 7
2-1 小分子核糖核酸(miRNA) 7
2-2 軟體介紹 9
2-2-1 miRLocator 9
2-2-2 TAPIR 11
2-3 處理流程 12
2-4 資料表 14
2-5 結果與討論 15
2-5-1 數據分析 15
2-5-2 頁面介紹 18
2-5-3 實例探討 23
第三章 Synteny Viewer 25
3-1 Synteny Ortholog 25
3-2 JCVI (McScan) 26
3-3 處理流程 29
3-4 資料表 31
3-5 結果與討論 32
3-5-1 McScan數據分析 32
3-5-2 頁面介紹 35
3-5-3 實例探討 37
第四章 Gene Order Viewer 43
4-1 處理流程 45
4-2 結果與討論 49
4-5-1 Gene Order Viewer數據分析 49
4-5-2 頁面介紹 50
4-5-3 實例探討 54
第五章 結論與未來展望 57
5-1 結論 57
5-2 未來展望 57
附錄
參考文獻
參考文獻 [1] Angiosperm Phylogeny Group. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society. 2009, 161 (2): 105–121 [26 June 2013]
[2] Cai, J., Liu, X., Vanneste, K. et al. The genome sequence of the orchid Phalaenopsis equestris. Nat Genet 47, 65–72 (2015) doi:10.1038/ng.3149
[3] Zhang, G., Xu, Q., Bian, C. et al. The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution. Sci Rep 6, 19029 (2016) doi:10.1038/srep19029
[4] Zhang, G., Liu, K., Li, Z. et al. The Apostasia genome and the evolution of orchids. Nature 549, 379–383 (2017) doi:10.1038/nature23897
[5] Fu, C. H., Chen, Y. W., Hsiao, Y. Y., Pan, Z. J., Liu, Z. J., Huang, Y. M., ... Chen, H. H. (2011). OrchidBase: A collection of sequences of the transcriptome derived from orchids. Plant and Cell Physiology, 52(2), 238-243.
[6] Cui H, Zhai J, Ma C. miRLocator: Machine Learning-Based Prediction of Mature MicroRNAs within Plant Pre-miRNA Sequences. PLoS One. 2015;10(11):e0142753. Published 2015 Nov 11. doi:10.1371/journal.pone.0142753
[7] Eric Bonnet, Ying He, Kenny Billiau, Yves Van de Peer, TAPIR, a web server for the prediction of plant microRNA targets, including target mimics, Bioinformatics, Volume 26, Issue 12, 15 June 2010, Pages 1566–1568, https://doi.org/10.1093/bioinformatics/btq233
[8] Ambros, V. The functions of animal microRNAs. Nature. Sep 16, 2004, 431 (7006): 350–5. PMID 15372042. doi:10.1038/nature02871.
[9] Bartel, DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. Jan 23, 2004, 116 (2): 281–97. PMID 14744438. doi:10.1016/S0092-8674(04)00045-5.
[10] Lee, Rosalind & Feinbaum, Rhonda & Ambros, Victor. (1994). The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell. 75. 843-54. 10.1016/0092-8674(93)90529-Y.
[11] Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell. January 2009, 136 (2): 215–33. PMC 3794896. PMID 19167326. doi:10.1016/j.cell.2009.01.002.
[12] Liu WW, Meng J, Cui J, Luan YS. Characterization and Function of MicroRNA∗s in Plants. Front Plant Sci. 2017;8:2200. Published 2017 Dec 22. doi:10.3389/fpls.2017.02200
[13] LC Sciences miRNA sequencing report
https://www.lcsciences.com/documents/sample_data/microrna_sequencing/miRNA_sequencing_report_DEMO.html#1.%20Introduction
[14] Allen E, et al. microRNA-directed phasing during trans-acting siRNA biogenesis in plants, Cell , 2005, vol. 121 (pg. 207-221)
[15] Srivastava, P.K., Moturu, T.R., Pandey, P. et al. A comparison of performance of plant miRNA target prediction tools and the characterization of features for genome-wide target prediction. BMC Genomics 15, 348 (2014) doi:10.1186/1471-2164-15-348
[16] Rehmsmeier M, et al. Fast and effective prediction of microRNA/target duplexes, Rna , 2004, vol. 10 (pg. 1507-1517)
[17] Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. Rfam: an RNA family database. Nucleic Acids Res. 2003;31(1):439–441. doi:10.1093/nar/gkg006

[18] Leijten W, Koes R, Roobeek I, Frugis G. Translating Flowering Time From Arabidopsis thaliana to Brassicaceae and Asteraceae Crop Species. Plants (Basel). 2018;7(4):111. Published 2018 Dec 16. doi:10.3390/plants7040111
[19] Wang Y, Tang H, Debarry JD, et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012;40(7):e49. doi:10.1093/nar/gkr1293
[20] JCVI (Mcscan) https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)
[21] Schnable JC . 2015 . Genome evolution in maize: from genomes back to genes . Annu Rev Plant Biol. 66 : 329 – 343 .
[22] Myers, P. (2008) Synteny: Inferring ancestral genomes. Nature Education 1(1):47
[23] Citrus Genome Database (http://www.citrusgenomedb.org/
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