臺灣博碩士論文加值系統

本論文以絲珊瑚科石珊瑚的基因體來探討：(1) 石珊瑚粒線體基因體結構在跨洋性石珊瑚科中的差異；(2) 細胞色素I介入子在石珊瑚粒線體中的演化。
絲珊瑚科共有7個物種涵蓋三大洋的分佈，本研究完成了絲珊瑚科 6物種的粒線體基因體定序與基因註解，以釐清跨洋性石珊瑚粒線體基因體的差異。絲珊瑚粒線體基因的排列順序與大部分石珊瑚粒線體基因相似，絲珊瑚有現生石珊瑚物種最大的粒線體基因體， 主要來自於其非編碼區域（non-coding region）所產生的片段重複或插入，特別是控制區 (control region) 上的結構變異。絲珊瑚粒線體基因體的控制區位在cytb及nad2之間，與同屬石珊瑚演化基部的類群–多孔珊瑚科 (Poritidae) 的粒線體基因體控制區一致。本研究也發線絲珊瑚粒線體基因體共有5個tRNA基因，而其中tRNA-Ser、tRNA-Pro及tRNA-Tyr的 DHU loop較一般tRNA基因短很多，可能是無法表現功能的偽基因 (pseudogene) 。與多孔珊瑚一樣，絲珊瑚也有兩個介入子(intron)，其中位於細胞色素I (cox1)的介入子內還具有核酸內切酶基因 (endonuclease) 的插入，可能來自於水平基因轉移 (horizontal gene transfer)。
粒線體基因的排列順序在絲珊瑚科內並沒有太大差異，主要變異則來自於三大洋間的遺傳距離相對於其他科的石珊瑚大。此外，除了西太平洋的兩個擬絲珊瑚物種 (Pseudosiderastrea) ，其他絲珊瑚在另外兩個洋區內物種的遺傳距離則相對接近，此一現象表示西太平洋絲珊瑚物種的分歧時間可能遠早於其他洋區。
絲珊瑚的親緣關係分析則顯示西太平洋類群為最早出現的絲珊瑚，類群內兩個擬絲珊瑚屬物種–田山擬絲珊瑚 (P. tayamai) 及福爾摩沙擬絲珊瑚 (P. formosa) 間具有較大的遺傳距離，顯示西太平洋區相對於其他兩大洋區，有較悠久的演化歷史，得以累積較多的變異。
絲珊瑚內的細胞色素I介入子相較於其他石珊瑚來說並非特例，過去研究便發現該介入子存在於部分的石珊瑚類群，包括複雜類群 (Complexa) 及堅實類群 (Robusta)。細胞色素I介入子主要分佈在複雜類群的演化基部物種，該介入子甚至與擬珊瑚海葵 (Corallimorpharia) 的細胞色素I介入子頗為相似。在比較過細胞色素I的外顯子(exon) 與介入子之間的共演化關係後，本研究認為複雜類群的介入子應與擬珊瑚海葵的介入子同源。
然而，堅實類群的細胞色素I介入子則完全與複雜類群及擬珊瑚海葵不同。藉由介入子的序列與結構的比較，過去的研究認為堅實類群的介入子可能來自於海綿或其他微生物的水平基因轉移。本研究也重新檢驗了選汰壓力對介入子的影響，結果顯示相對於複雜類群，堅實類群的介入子承受較大的淨化選汰(purifying selection)壓力，此一結果使得堅實類群的介入子為新進入侵的可能性大為增加。而外顯子與介入子的共演化分析也顯示堅實類群的細胞色素I介入子可能是後來多次插入粒線體基因體的結果。

In this dissertation, I focused on the study of mitochondrial genomes (mitogenomes) of a scleractinian family, Siderastreidae, to address their evolutionary pattern of mitogenome changes. The genomic structure and variations of mitochondria (mt) DNA among siderastreids from different biogeographic provinces were studied. Then, the gain and loss of cox1 introns in scleractinians and its implication on the evolutionary history of scleractinians were addressed.
The mitochondrial genomes of 6 out of 7 species in Siderastreidae were first sequenced and annotated to verify the changes of mitogenomes across the three ocean provinces. The gene arrangement of siderastreids mitogenomes was similar to those of scleractinians in general, while their mitogenomes were the largest among those of scleractinians. A putative control region located between cytb and nad2 were at the same location as that in Poritidae, the family which also located on the basal of scleractinian phylogeny. Five tRNAs instead of two were prediceted in Siderastreidae based on previous studies in hexacorallians. However, tRNA-Ser, tRNA-Pro and tRNA-Tyr were thought to be false positive due to their relatively short DHU loops. Moreover, introns with novel open reading frame recognized as homing endonuclease were discovered in the cox1 of both Siderastreidae and Poritidae, suggesting possible horizontal gene transfers among lineages.
Although there was no difference in gene arrangement among Siderastreidae species, the genetic distance among species from three ocean provinces was larger than that in other families. However, the genetic distance between species from the same ocean was very small except that of the Pacific lineages, which implied that the Pacific lineage might have an earlier divergence. Besides, the differences of genome sizes among species from three ocean provinces is mainly due to the fragment insertions or deletions of inter-genic spacers, especially in putative control regions. The phylogeny of siderastreids also showed that the Pacific lineage was the ancestral group and large divergence between Pseudosiderastrea tayamai and P. formosa, implied that they might have a long evolutionary history to accumulate genetic variations in the Pacific Ocean.
Intron insertions of cox1 were not exclusive in siderastreids. Cox1 intron could be found sporadically in species of scleractinians among the complex clade (Complexa) and the robust clade (Robusta). The distribtution of cox1 intron in Complexa was concentrated on the basal lineages of phylogeny which could even be traced to that in Corallimorpharia. Co-speciation comparison of cox1 introns and exons among species in Complexa and Corallimorpharia implied that they showed homologus from their ancestors.
However, intron in Robusta have completely different origin from that in Complexa and Corallimorpharia. Previous study proposed that cox1 intron in Robusta might come from Porifera or other microbials due to the sequences and structure similarities instead of that with Complexa and Corallimorpharia. The examination of selection forces on cox1 intron of scleractinians showed that introns in Robusta afford relatively purifying selection than that in Complexa, which implied the possibility of new invasion to cox1 in Robusta. Co-speciation comparison of exons and introns in Robusta also suggested that multiple lateral insertions from similar organisms might have happened in the evolution of mitogenomes in Robusta.

Chapter 1 General Introduction 1
1.1 Biological function of mitochondrion 1
1.2 Mitochondrial genome of metazoans 2
1.3 Mitochondrial genomes in anthozoans 3
1.4 MtDNA as molecular markers and gene rearrangements 3
1.5 Siderastreidae and the status of Scleractinia evolution 4
1.6 Aim of this study 5
Chapter 2 Mitochondrial genome of Siderastreidae and phylogenetic application 7
2.1 Introduction 7
2.2 Materials and Methods 10
2.2.1 DNA extraction, PCR amplification and sample location 10
2.2.2 Mitochondrial genome analyses and gene annotation 11
2.2.3 Phylogenetic analyses of the mitochondrial genomes 12
2.3 Results 14
2.3.1 Gene content and order of siderastreid mtgenome 14
2.3.2 Intron, inter-genic spacer and putative control region 15
2.3.3 Mitochondrial genomic differences among siderastreids 16
2.3.4 Genetic variations in siderastreids 17
2.3.5 Phylogeny inference of siderastreids 18
2.4 Discussion 19
2.4.1 Genome size evolution in scleractinians 19
2.4.2 tRNA and putative control region 20
2.4.3 Intron insertions 21
2.4.4 Divergences and phylogeography in siderasreids 21
Chapter 3 Loss and Gain of Group I Introns in the Mitochondrial Cox1 Gene of the Scleractinia (Cnidaria; Anthozoa) 33
3.1 Introduction 33
3.2 Materials & Methods 36
3.2.1 Cox1 exon and group I intron sequences 36
3.2.2 Sequence analysis, open reading frame (ORF), and secondary structure prediction of cox1 group I introns 36
3.2.3 Phylogeny construction and comparisons 37
3.2.4 Molecular dating of the cox1 exon tree 39
3-3 Results 40
3.3.1 Molecular characteristics of the group I introns in the cox1 loci 40
3.3.2 Evolutionary rates of exon and HEG 42
3.3.3 Co-evolution of the cox1 exon and intron in scleractinians and corallimorpharians 42
3.3.4 Molecular clock estimates for intron loss and gain events 44
3-4 Discussion 46
3.4.1 Evolutionary history of group I introns in scleractinian corals 46
3.4.2 Hypothesis: Intron loss and gain might be corroborated with major extinction events 50
Chapter 4 General discussion and conclusion 67
4.1 Mitogenomic features of the siderastreid corals 67
4.2 Gain and loss of cox1 introns in Scleractinia 68
4.3 Summary and perspectives of mitogenome and cox1 introns evolution 69
References 71

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