請用此 Handle URI 來引用此文件:
http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/71749
完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 王俊能(Chun-Neng Wang) | |
dc.contributor.author | Goang-Jiun Wang | en |
dc.contributor.author | 王廣鈞 | zh_TW |
dc.date.accessioned | 2021-06-17T06:08:33Z | - |
dc.date.available | 2020-11-12 | |
dc.date.copyright | 2020-11-12 | |
dc.date.issued | 2020 | |
dc.date.submitted | 2020-11-04 | |
dc.identifier.citation | The Angiosperm Phylogeny G, Chase MW, Christenhusz MJM, Fay MF, Byng JW, Judd WS, Soltis DE, Mabberley DJ, Sennikov AN, Soltis PS et al: An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Botanical Journal of the Linnean Society 2016, 181(1):1-20. Clark J, Weber A, Moeller M: A new formal classification of Gesneriaceae. Selbyana 2013, 31:68-94. Wang C-N, xd, Ller M, Cronk QCB: Population Genetic Structure of Titanotrichum oldhamii (Gesneriaceae), a Subtropical Bulbiliferous Plant with Mixed Sexual and Asexual Reproduction. Ann Bot 2004, 93(2):201-209. Wang C-N, Cronk QCB: Meristem fate and bulbil formation in Titanotrichum (Gesneriaceae). American Journal of Botany 2003, 90(12):1696-1707. Wang C-N, Möller M, Cronk QCB: Aspects of sexual failure in the reproductive processes of a rare bulbiliferous plant, Titanotrichum oldhamii (Gesneriaceae), in subtropical Asia. Sexual Plant Reproduction 2004, 17(1):23-31. Hasing T, Rinaldi E, Manrique S, Colombo L, Haak DC, Zaitlin D, Bombarely A: Extensive phenotypic diversity in the cultivated Florist’s Gloxinia, Sinningia speciosa (Lodd.) Hiern, is derived from the domestication of a single founder population. PLANTS, PEOPLE, PLANET 2019, 1(4):363-374. Dong Y, Liu J, Li P-W, Li C-Q, Lü T-F, Yang X, Wang Y-Z: Evolution of Darwin’s Peloric Gloxinia (Sinningia speciosa) Is Caused by a Null Mutation in a Pleiotropic TCP Gene. Molecular Biology and Evolution 2018, 35(8):1901-1915. Yang B, Ding H-B, Fu K-C, Yuan Y-K, Yang H-Y, Li J-W, Zhang L-X, Tan Y-H: Four new species of Gesneriaceae from Yunnan, Southwest China. PhytoKeys 2019, 130:183-203. Kuo W-H, Hung Y-L, Wu H-W, Pan Z-J, Hong C-Y, Wang C-N: Shoot regeneration process and optimization of Agrobacterium-mediated transformation in Sinningia speciosa. Plant Cell, Tissue and Organ Culture (PCTOC) 2018, 134(2):301-316. Hsu H-C, Wang C-N, Liang C-H, Wang C-C, Kuo Y-F: Association between Petal Form Variation and CYC2-like Genotype in a Hybrid Line of Sinningia speciosa. Front Plant Sci 2017, 8(558). Hsu H-C, Chen C-Y, Lee T-K, Weng L-K, Yeh D-M, Lin T-T, Wang C-N, Kuo Y-F: Quantitative analysis of floral symmetry and tube dilation in an F2 cross of Sinningia speciosa. Scientia Horticulturae 2015, 188:71-77. Wang C-N, Hsu H-C, Wang C-C, Lee T-K, Kuo Y-F: Quantifying floral shape variation in 3D using microcomputed tomography: a case study of a hybrid line between actinomorphic and zygomorphic flowers. Front Plant Sci 2015, 6(724). Xiao L, Yang G, Zhang L, Yang X, Zhao S, Ji Z, Zhou Q, Hu M, Wang Y, Chen M et al: The resurrection genome of Boea hygrometrica: A blueprint for survival of dehydration. Proc Natl Acad Sci U S A 2015, 112(18):5833-5837. Zaitlin D, Pierce AJ: Nuclear DNA content in Sinningia (Gesneriaceae); intraspecific genome size variation and genome characterization in S. speciosa. Genome 2010, 53(12):1066-1082. Rhoads A, Au KF: PacBio Sequencing and Its Applications. Genomics, Proteomics Bioinformatics 2015, 13(5):278-289. Lu H, Giordano F, Ning Z: Oxford Nanopore MinION Sequencing and Genome Assembly. Genomics, Proteomics Bioinformatics 2016, 14(5):265-279. Li-Yaung K, Fay-Wei L: A Roadmap for Fern Genome Sequencing. American Fern Journal 2019, 109(3):212-223. Tan G, Opitz L, Schlapbach R, Rehrauer H: Long fragments achieve lower base quality in Illumina paired-end sequencing. Sci Rep 2019, 9(1):2856. Doležel J, Greilhuber J, Suda J: Estimation of nuclear DNA content in plants using flow cytometry. Nature Protocols 2007, 2(9):2233-2244. Kuo L-Y, Huang Y-M: Determining Genome Size from Spores of Seedless Vascular Plants. Bio-protocol 2017, 7(11):e2322. Greilhuber J, Temsch E, Loureiro J: Nuclear DNA Content Measurement. In.; 2007: 67-101. Mayjonade B, Gouzy J, Donnadieu C, Pouilly N, Marande W, Callot C, Langlade N, Muños S: Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules. BioTechniques 2016, 61(4):203-205. Jordon-Thaden IE, Chanderbali AS, Gitzendanner MA, Soltis DE: Modified CTAB and TRIzol protocols improve RNA extraction from chemically complex Embryophyta. Appl Plant Sci 2015, 3(5):apps.1400105. Tyler AD, Mataseje L, Urfano CJ, Schmidt L, Antonation KS, Mulvey MR, Corbett CR: Evaluation of Oxford Nanopore's MinION Sequencing Device for Microbial Whole Genome Sequencing Applications. Sci Rep 2018, 8(1):10931-10931. Ewing B, Green P: Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998, 8(3):186-194. Sichtig H, Minogue T, Yan Y, Stefan C, Hall A, Tallon L, Sadzewicz L, Nadendla S, Klimke W, Hatcher E et al: FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science. Nature Communications 2019, 10(1):3313. Simpson JT, Durbin R: Efficient de novo assembly of large genomes using compressed data structures. Genome Res 2012, 22(3):549-556. Zerbino DR, Birney E: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18(5):821-829. Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA: The MaSuRCA genome assembler. Bioinformatics 2013, 29(21):2669-2677. Li Z, Chen Y, Mu D, Yuan J, Shi Y, Zhang H, Gan J, Li N, Hu X, Liu B et al: Comparison of the two major classes of assembly algorithms: overlap–layout–consensus and de-bruijn-graph. Briefings in Functional Genomics 2011, 11(1):25-37. Sharma N, Jung C-H, Bhalla PL, Singh MB: RNA Sequencing Analysis of the Gametophyte Transcriptome from the Liverwort, Marchantia polymorpha. PLOS ONE 2014, 9(5):e97497. Hölzer M, Marz M: De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers. Gigascience 2019, 8(5):giz039. The UniProt C: UniProt: a worldwide hub of protein knowledge. Nucleic Acids Research 2018, 47(D1):D506-D515. Dierckxsens N, Mardulyn P, Smits G: NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Research 2016, 45(4):e18-e18. Greiner S, Lehwark P, Bock R: OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Research 2019, 47(W1):W59-W64. Rozewicki J, Li S, Amada KM, Standley DM, Katoh K: MAFFT-DASH: integrated protein sequence and structural alignment. Nucleic Acids Research 2019, 47(W1):W5-W10. Trifinopoulos J, Nguyen L-T, von Haeseler A, Minh BQ: W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research 2016, 44(W1):W232-W235. Kuo L-Y, Qi X, Ma H, Li F-W: Order-level fern plastome phylogenomics: new insights from Hymenophyllales. American Journal of Botany 2018, 105(9):1545-1555. Guerriero G, Berni R, Muñoz-Sanchez JA, Apone F, Abdel-Salam EM, Qahtan AA, Alatar AA, Cantini C, Cai G, Hausman J-F et al: Production of Plant Secondary Metabolites: Examples, Tips and Suggestions for Biotechnologists. Genes 2018, 9(6):309. Endrullat C, Glökler J, Franke P, Frohme M: Standardization and quality management in next-generation sequencing. Applied Translational Genomics 2016, 10:2-9. Francis WR, Christianson LM, Kiko R, Powers ML, Shaner NC, D Haddock SH: A comparison across non-model animals suggests an optimal sequencing depth for de novotranscriptome assembly. BMC Genomics 2013, 14(1):167. Haznedaroglu BZ, Reeves D, Rismani-Yazdi H, Peccia J: Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms. BMC Bioinformatics 2012, 13(1):170. Li F-W, Harkess A: A guide to sequence your favorite plant genomes. Appl Plant Sci 2018, 6(3):e1030-e1030. Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, Yabana M, Harada M, Nagayasu E, Maruyama H et al: Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res 2014. Chikhi R, Medvedev P: Informed and automated k-mer size selection for genome assembly. Bioinformatics 2013, 30(1):31-37. Góngora-Castillo E, Buell CR: Bioinformatics challenges in de novo transcriptome assembly using short read sequences in the absence of a reference genome sequence. Natural Product Reports 2013, 30(4):490-500. Bushmanova E, Antipov D, Lapidus A, Prjibelski AD: rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data. Gigascience 2019, 8(9). Moreno-Santillán DD, Machain-Williams C, Hernández-Montes G, Ortega J: De Novo Transcriptome Assembly and Functional Annotation in Five Species of Bats. Sci Rep 2019, 9(1):6222. Bairoch A, Apweiler R: The SWISS-PROT Protein Sequence Data Bank and Its New Supplement TREMBL. Nucleic Acids Research 1996, 24(1):21-25. Du X-Y, Lu J-M, Lu S-g, Li D: Complete plastome of an endemic fern species from China: Neocheiropteris palmatopedata (Polypodiaceae). Mitochondrial DNA Part B 2019, 4:2394 - 2395. Monfil VO, Casas-Flores S: Chapter 32 - Molecular Mechanisms of Biocontrol in Trichoderma spp. and Their Applications in Agriculture. In: Biotechnology and Biology of Trichoderma. Edited by Gupta VK, Schmoll M, Herrera-Estrella A, Upadhyay RS, Druzhinina I, Tuohy MG. Amsterdam: Elsevier; 2014: 429-453. Suresh Babu, Agilent Technologies, Bangalore: Assessing Integrity of Plant RNA with the Agilent 2100 Bioanalyzer System 2016. Dumschott K, Schmidt MHW, Chawla HS, Snowdon R, Usadel B: Oxford Nanopore sequencing: new opportunities for plant genomics? Journal of Experimental Botany 2020, 71(18):5313-5322. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q et al: Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 2011, 29(7):644-652. | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/71749 | - |
dc.description.abstract | 苦苣苔科花朵具呈現多樣性特色並分布全球,在生態與園藝上具有重要的意義。在苦苣苔科中,俄氏草(Titanotrichum oldhamii)是位於台灣的本土觀賞植物,其具有從有性生殖花反轉成無性繁殖體特性;大岩桐(Sinningia speciosa)是位於巴西並在園藝上廣受歡迎的植物,其花朵的多樣性也讓達爾文為之著迷。俄氏草與大岩桐是未來新興模式植物,在我們實驗室研究俄氏草花反轉與大岩桐花對稱之潛在基因。然而卻沒有高品質的俄氏草與大岩桐之基因體問世,如此嚴重影響到更進一步的研究工作。為了獲得高品質的俄氏草與大岩桐之基因體,我結合三代(TGS; Oxford Nanopore Technology)長片段定序,加上次世代(NGS; Illumina)雙端高質量短序列(150 bp),以長接短策略進行全新混合組裝(de novo hybrid assemble),透過CLC軟體和MaSuRCA組裝。這樣結合長片段與精準Illumina短片段之組裝策略可以解決長片段定序高錯誤率的問題。我也將俄氏草與大岩桐之不同器官轉錄體原始定序資料進行轉錄體組裝,組裝好之轉錄體有高N50值與功能性分析驗證,使其組裝更完備。最後透過組裝葉綠體基因體,結構分析葉綠體基因體編碼區序列,建立分子標記與演化樹,利於推論苦苣苔科的親緣關係。本論文研究中,進行俄氏草與大岩桐基因體與轉錄體之定序與組裝,對於苦苣苔科中這些新興模式植物的科學探索和園藝改良提供了關鍵的見解與和研究資源。 | zh_TW |
dc.description.abstract | Gesnariaceae species displays floral diversity and is distributed globally with ecological and and horticultural significance. Within Gensariaceae, Titanotrichum oldhamii is native ornamental in Taiwan with its sexual flower is capable to reverse into asexual propagules. Sinningia speciosa is a popular Barzilian horticultural plant that Charles Darwin was fascinated on its rich flower diversity upon human slection. Both of them are emerging plant models and well-studied for the underlying genetic of flower reversal and floral symmetry in our lab. However, the lacking of high-quality sequenced genome of both species hinders further research works. In order to obtain the first high-quality sequenced genomes in Gesnariaceae, I combined the long reads from the third-generation sequencing (TGS; Oxford Nanopore Technology) with the high quality pair-end short reads (150 bp) from the next-generation sequencing (NGS; Illumina) to generate de novo hybrid genome assemblies of T. oldhamii and S. speciosa using the QIAGEN CLC genomic workbench and hybrid genome assemlbing by MaSuRCA. This strategy combines long reads with accurate Illumina sequencing short reads to solve the high error rate problem from long reads. I also assembled T. oldhamii and S. speciosa transcriptome from different development organs for best k-mer length to obtain high quality transcriptomes with long N50 with draft annotation. Plastomes of these species were sequenced for their usage of inferring phylogeny of Gesneriaceae species. The genomes and transcriptomes of T. oldhamii and S. speciosa sequenced in this study present pivotal insights into and resources for scientific exploration and horticultural improvement of these emerging plant models in Gesneriaceae. | en |
dc.description.provenance | Made available in DSpace on 2021-06-17T06:08:33Z (GMT). No. of bitstreams: 1 U0001-2110202011002500.pdf: 3822756 bytes, checksum: cfc578d0caba40d8deef88b242164f9b (MD5) Previous issue date: 2020 | en |
dc.description.tableofcontents | 致謝 I 中文摘要 II Abstract III 目錄 V 圖目錄 VI 表目錄 VIII 第一章、前言 1 第二章、材料與方法 5 第三章、結果 27 第四章、討論 59 第五章、參考資料 72 第六章、附錄 79 | |
dc.language.iso | zh-TW | |
dc.title | 結合次世代與長片段定序組裝大岩桐及俄氏草之基因組與轉錄體 | zh_TW |
dc.title | De novo assembly for draft genome and transcriptome sequences of Sinningia speciosa and Titanotrichum oldhamii with Oxford Nanopore and Illumina technologies | en |
dc.type | Thesis | |
dc.date.schoolyear | 109-1 | |
dc.description.degree | 碩士 | |
dc.contributor.oralexamcommittee | 李承叡(Cheng- Ruei Lee),林盈仲(Ying-Chung Jimmy Lin) | |
dc.subject.keyword | 俄氏草,大岩桐,基因體,轉錄體,葉綠體,演化樹, | zh_TW |
dc.subject.keyword | Titanotrichum oldhamii,Sinningia Speciosa,draft genome,transcriptome,plastome,phylogeny, | en |
dc.relation.page | 86 | |
dc.identifier.doi | 10.6342/NTU202004299 | |
dc.rights.note | 有償授權 | |
dc.date.accepted | 2020-11-04 | |
dc.contributor.author-college | 生命科學院 | zh_TW |
dc.contributor.author-dept | 生命科學系 | zh_TW |
顯示於系所單位: | 生命科學系 |
文件中的檔案:
檔案 | 大小 | 格式 | |
---|---|---|---|
U0001-2110202011002500.pdf 目前未授權公開取用 | 3.73 MB | Adobe PDF |
系統中的文件,除了特別指名其著作權條款之外,均受到著作權保護,並且保留所有的權利。