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研究生:陳章輝
研究生(外文):Edi Sudianto
論文名稱:松科和羅漢松的質體基因組演化和親緣關係與裸子植物中乙酰輔酶A羧化酶基因的演化
論文名稱(外文):Plastid genome evolution and phylogenomics of Pinaceae and Podocarpaceae and the evolution of acetyl-CoA carboxylase genes in gymnosperms
指導教授:趙淑妙趙淑妙引用關係
指導教授(外文):Chaw, Shu-Miaw
學位類別:博士
校院名稱:國立臺灣師範大學
系所名稱:生命科學系
學門:生命科學學門
學類:生物學類
論文種類:學術論文
論文出版年:2018
畢業學年度:107
語文別:英文
論文頁數:151
中文關鍵詞:plastomegymnospermsPinaceaePodocarpaceaeconifersevolutionplastidchloroplastsplastid-to-nucleus gene transfersaccDacetyl-CoA carboxylase
外文關鍵詞:plastomegymnospermsPinaceaePodocarpaceaeconifersevolutionplastidchloroplastsplastid-to-nucleus gene transfersaccDacetyl-CoA carboxylase
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Plastid genomes (plastomes) serve as valuable and cost-effective genomic resources for plants and algae. More than 2,500 complete plastomes (as of December 2018) are now publicly available on GenBank, and they provide critical information on the evolution and phylogeny of plastid-bearing organisms. In this dissertation, I will focus on the plastome evolution of non-flowering seed plants (gymnosperms). Gymnosperms comprise ca. 1,000 species in five groups, including cycads, ginkgo, gnetophytes, Pinaceae (conifers I), and cupressophytes (conifers II). Cupressophytes may be further divided into five families: Cupressaceae, Taxaceae, Sciadopityaceae, Araucariaceae, and Podocarpaceae. Previous studies have highlighted that gymnosperm plastomes are highly variable. However, our understanding of the plastome evolution within gymnosperm families is incomplete because not all 12 families are equally represented. In this study, I aimed to investigate (1) the plastome evolution and plastid phylogenomics of the two largest conifer families, Pinaceae and Podocarpaceae, and (2) the evolution of acetyl-CoA carboxylase (ACCase) genes in all five groups of gymnosperms.
This dissertation has four chapters. In chapter one, I reviewed the available literature on gymnosperm plastids, plastome evolution, and ACCase. In chapter two, I reconstructed the complete plastid phylogenomics of Pinaceae by sequencing two Pinaceous genera, Pseudolarix and Tsuga. The intergeneric relationships among members of the Abietoideae subfamily were resolved with Cedrus as sister to the clade containing Pseudolarix-Tsuga and Abies-Keteleeria, which refutes previous phylogenetic studies. I also documented accD elongation in Pinaceae for the first time.
In chapter three, I examined plastome evolution in the Podocarpaceae and expanded the number of available Podocarpaceae plastomes from 5 to 13. This addition enabled me to gain more insights into plastome evolution within the family. I found an exceptionally enlarged plastome in Lagarostrobos franklinii (Huon pine), a species endemic to Tasmania. Subsequent analyses revealed that the Lagarostrobos plastome is enriched with repetitive sequences, pseudogenes, and intergenic spacers that were not observed in other Podocarpaceae. In addition, plastid phylogenomic trees were also built to resolve problematic nodes in the Podocarpaceae phylogeny.
In chapter four, I investigated the evolutionary history of ACCase genes in the five gymnosperm groups. These genes are the key regulators of fatty acid biosynthesis, and most plants have both heteromeric and homomeric ACCases in plastids and cytosol, respectively. Heteromeric ACCase is composed of four subunits: three nuclear-encoded accA–C and one plastid-encoded accD, while homomeric ACCase is only encoded by one nuclear ACC gene. This study uncovered that: (1) the ACCD subunit in all cupressophytes (except Sciadopitys) are elongated by lineage-specific tandem repeats, (2) Sciadopitys and gnetophytes have functionally transferred their accD from the plastome to the nucleus, (3) Gnetum has two accDs in their nuclear genomes, and (4) one of Gnetum’s accD dually targets plastids and mitochondria, while the other copy only targets plastoglobuli, a microcompartment within the plastid. This is the first study to report the presence of two accDs and their distinct targeting in any green plant.
Acknowledgements iii
Abstract iv
List of Papers vi
Table of Contents viii
List of Tables xii
List of Figures xiv
CHAPTER 1: Literature Review 1
1.1. The origin and function of plastids 1
1.2. Plastome size, structure, and content 2
1.3. Transfer of plastid DNA to the nucleus 4
1.4. Gymnosperms and their plastome evolution 7
1.5. Using the plastome to resolve phylogenetic conundrums in gymnosperms 10
1.6. Factors influencing plastome size variation 12
1.7. Evolution of the acetyl-CoA carboxylase complex in plants 13
1.8. Dissertation outline 15
CHAPTER 2: Revisiting the plastid phylogenomics of Pinaceae with two complete plastomes of Pseudolarix and Tsuga 17
2.1. Introduction 18
2.2. Materials and Methods 19
2.3. Results and Discussion 21
2.3.1. Plastomic features of Pseudolarix amabilis and Tsuga chinensis 21
2.3.2. Expansion of the accD reading frame in Tsuga 22
2.3.3. Phylogeny of ten Pinaceous genera re-visited 23
2.3.4. Pseudolarix and Tsuga are sisters 24
2.3.5. Loss of psaM as a synaphomorphy of Pseudolarix and Tsuga 25
2.4. Conclusions 26
CHAPTER 3: Enlarged and highly repetitive plastome of Lagarostrobos and plastid phylogenomics of Podocarpaceae 27
3.1. Introduction 28
3.2. Materials and Methods 31
3.2.1. Plant materials and DNA extraction 31
3.2.2. Plastome sequencing, assembly, and annotation 31
3.2.3. Sequence alignment and phylogenetic tree reconstruction 32
3.2.4. Identification of locally collinear blocks and reconstruction of ancestral plastomes 32
3.2.5. Estimation of nucleotide substitution rates 33
3.2.6. Analyses of divergence times and absolute substitution rates 33
3.3. Results 34
3.3.1. Lagarostrobos plastome is enlarged with abundant repeats 34
3.3.2. Outburst of duplicate genes and pseudogenes in the Lagarostrobos plastome 35
3.3.3. Plastid phylogenomic analysis resolved two major clades in Podocarpaceae 36
3.3.4. Podocarpaceae plastomes contain extensive inversions and diverse sets of the intermediate-sized repeats 36
3.3.5. Rearrangement frequencies do not coincide with nucleotide substitution rates in Podocarpaceae plastomes 37
3.4. Discussion 38
3.4.1. Insights into the phylogeny of Podocarpaceae 38
3.4.2. Mechanisms underlying the enlarged Lagarostrobos plastome 39
3.4.3. Abundant intermediate-sized repeats are likely responsible for numerous rearrangements in Lagarostrobos 40
CHAPTER 4: Two independent plastid accD transfers to the nuclear genome of Gnetum and other insights on acetyl-CoA carboxylase evolution in gymnosperms 43
4.1. Introduction 44
4.2. Materials and Methods 47
4.2.1. Isolation of nucleic acids and cDNA synthesis 47
4.2.2. Sequence retrieval 47
4.2.3. RNA sequencing, transcriptome assembly, and identification of ACCase transcripts 48
4.2.4. Tandem repeats and transit peptide identification 48
4.2.5. Sequence alignment and phylogenetic reconstruction 48
4.2.6. Identification of ACCase genes in nuclear genomes 49
4.2.7. Protoplast transient expression of nr-ACCDs transit peptides 49
4.2.8. Estimation of nucleotide substitution rates 50
4.3. Results 50
4.3.1. Gymnosperms have both heteromeric and homomeric ACCases 50
4.3.2. Specific tandem repeat insertions influence ACCD length in gymnosperms 51
4.3.3. The plastid accDs of gnetophytes and Sciadopitys were transferred to the nucleus and Gnetum retains two copies of nr-ACCD 52
4.3.4. Nuclear genes encoding two heteromeric ACCase subunits (accA and accB) are duplicated in various lineages of gymnosperms 54
4.3.5. Nucleotide substitution rates of plastid accD are co-elevated with accA–C, but not with ACC 55
4.4. Discussion 56
4.4.1. No homomeric ACCase was found in the plastids of any gymnosperms 56
4.4.2. TR insertions in the plastid accD may elevate substitution rates of heteromeric ACCase in gymnosperms 57
4.4.3. The two nr-accDs of Gnetum were the product of independent transfers rather than gene duplication 58
4.4.4. Distinct localization of Gnetum’s two nr-ACCDs 59
CHAPTER 5: Conclusions and Future Work 61
Tables 64
Figures 77
Appendices 113
References 125
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