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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
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dc.contributor.advisor | 鍾國芳(Kuo-Fang Chung) | |
dc.contributor.author | Chia-Lun Hsieh | en |
dc.contributor.author | 謝佳倫 | zh_TW |
dc.date.accessioned | 2021-05-12T09:35:04Z | - |
dc.date.available | 2019-03-01 | |
dc.date.available | 2021-05-12T09:35:04Z | - |
dc.date.copyright | 2018-03-01 | |
dc.date.issued | 2018 | |
dc.date.submitted | 2018-02-22 | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/handle/123456789/1257 | - |
dc.description.abstract | 分布於中國華南與北越石灰岩地區之苦苣苔科(Gesneriaceae)報春苣苔屬(Primulina)與石山苣苔屬(Petrocodon),擁有特殊的生境偏好與豐富的多樣性,為當地喀斯特物種之代表類群。本研究採用基因體略讀(genome skimming)之定序策略,定序八個報春苣苔屬與兩個石山苣苔屬物種之低覆蓋率(coverage)全基因體資料,獲取在細胞中擁有高副本數(copy number)的葉綠體基因(plastome)、粒線體外顯子體(mitochondria exome)與細胞核核醣體DNA (nuclear ribosomal DNA)之序列,並分別進行親緣關係樹的重建。此法不需透過成本較高的高覆蓋率定序,仍可獲得大量資料,並能夠增加同時定序的樣本數量。此外,八個下載自基因銀行(GenBank)的苦苣苔科物種之完整葉綠體基因體亦被納入基因體比較與親緣關係分析。雖然不同胞器DNA所重建之親緣關係樹存在許多不一致之處,但根據完整葉綠體基因體重建之演化關係具有極高支持度,可作為報春苣苔屬與其近緣屬間演化歷史之骨幹架構。藉由加入其他物種之序列進行比較,可得知所有納入分析之葉綠體基因體於基因組成與基因體的結構上均相當保守。本研究亦藉由排列比對報春苣苔屬與石山苣苔屬之完整葉綠體基因體序列,辨識出數個高變異的基因體區段,可作為未來進行族群遺傳與親緣關係研究所需的高解析力分子標記。 | zh_TW |
dc.description.abstract | Primulina and Petrocodon, two characteristic Gesneriaceae genera of the limestone flora in southern China and northern Vietnam, are featured by their exclusive habitat preference and remarkable diversity. The genome skimming strategy, which sequences genomic DNA in low coverage to recover the high copy portions and to increase the multiplex level of sequencing, was employed to obtain complete plastomes, mitochondrial exomes and nuclear ribosomal DNAs of eight Primulina and two Petrocodon species. Phylogenies based on the data from the three cell compartments were reconstructed and compared. Additional eight Gesneriad plastomes (including five Primulina spp.) accessed online were incorporated in the comparative and phylogenetic analyses. The newly sequenced plastomes are highly conserved in genome structures and gene contents. Although the phylogenies inferred from plastid, mitochondrial and nuclear data are incongruent, the well supported plastome phylogeny represents a backbone relationships of Primulina and its allies. The sequence divergence among plastomes of Primulina and Petrocodon were evaluated to identify variable regions which serve as potentially useful markers for systematic or population studies. | en |
dc.description.provenance | Made available in DSpace on 2021-05-12T09:35:04Z (GMT). No. of bitstreams: 1 ntu-107-R04625013-1.pdf: 3656562 bytes, checksum: 5bf464f07f1e0b2972e609fb88bfbb90 (MD5) Previous issue date: 2018 | en |
dc.description.tableofcontents | Content
國立臺大學碩士學位論文口試委員會審定書 i 謝辭 ii Abstract iii 摘要 iv Content v List of Figure vii List of Table viii 1. Introduction 1 1.1 Gesneriaceae in karst landscape of southern China 1 1.2 Primulina and Petrocodon 2 1.2.1 Primulina Hance 2 1.2.2 Petrocodon Hance 4 1.3 General features of plastome 5 1.4 The application of cpDNA to plant systematics 7 1.5 Next generation sequencing and genome skimming 9 1.6 Goals of this study 12 2. Materials and Methods 13 2.1 Plant materials and taxon sampling 13 2.2 DNA extraction and next generation sequencing 15 2.3 Plastome assembly and validation 16 2.4 Plastome annotation 21 2.5 Plastome comparison 23 2.6 Plastome alignment, sequence divergence comparison and identification of variable regions 24 2.7 Plastome repeat analyses 25 2.8 Phylogenomic analyses based on plastomes 27 2.9 Mitochondrial exome assembly, alignment and phylogenetic reconstruction 28 2.10 Nuclear ribosomal DNA assembly, alignment and phylogenetic analyses 30 3. Results 32 3.1 Sequencing and assembly of plastomes 32 3.2 Characteristics of Primulina and Petrocodon plastomes 33 3.3 Plastome comparison and identification of variable regions 38 3.4 IR/SC boundaries of Gesneriad plastomes 41 3.5 Repeat contents in Primulina and Petrocodon plastome 43 3.6 Chloroplast phylogenomic analyses 47 3.7 Assembly and phylogenetic analysis of mitochondrial exome 48 3.8 Phylogenetic analysis of nuclear ribosomal sequences 49 4. Discussion 50 4.1 Highly conserved Primulina and Petrocodon plastomes 50 4.2 Variable regions identified for Primulina and Petrocodon 51 4.3 Annotation issues in plastome annotations 52 4.4 Incongruences between plastome phylogeny and previous studies 54 4.5 Incongruences among mitochondrial, nuclear and plastid phylogenies 56 4.6 Potential explanations for the incongruences 59 4.7 Utilities of mitochondrial data in plant phylogenetic analyses 63 5. Conclusion 64 6. References 66 7. Appendix 83 | |
dc.language.iso | en | |
dc.title | 中越石灰岩溶植物─報春苣苔屬與石山苣苔屬之葉綠體基因體 | zh_TW |
dc.title | Plastomes of Primulina and Petrocodon ─ Two Characteristic Plant Genera of Sino-Vietnamese Limestone Flora | en |
dc.type | Thesis | |
dc.date.schoolyear | 106-1 | |
dc.description.degree | 碩士 | |
dc.contributor.oralexamcommittee | 劉少倫(Shao-Lun Liu),蘇慧君(Huei-Jiun Su) | |
dc.subject.keyword | 報春苣苔屬,石山苣苔屬,葉綠體基因體,粒線體外顯子體,基因體略讀,喀斯特植物, | zh_TW |
dc.subject.keyword | Genome skimming,Karst flora,Mitochondrial exome,Petrocodon,Plastome,Primulina, | en |
dc.relation.page | 84 | |
dc.identifier.doi | 10.6342/NTU201800388 | |
dc.rights.note | 同意授權(全球公開) | |
dc.date.accepted | 2018-02-22 | |
dc.contributor.author-college | 生物資源暨農學院 | zh_TW |
dc.contributor.author-dept | 森林環境暨資源學研究所 | zh_TW |
顯示於系所單位: | 森林環境暨資源學系 |
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