無共生藻石珊瑚和有共生藻石珊瑚粒線體基因組之演化比較研究

Abstract

近年來利用分子親緣研究顯示無共生藻石珊瑚的演化關係仍需進一步探討。 本論文以Fungiacyathus stephanus和Madrepora oculata兩種無共生藻石珊瑚，以及Polycyathus sp.和Euphyllia ancora兩種有共生藻石珊瑚作為研究材料，比較無共生藻石珊瑚和有共生藻石珊瑚粒線體基因組中的差異，並和已知石珊瑚粒線體基因比較，加以分析其親緣關係。 研究結果發現，無共生藻石珊瑚粒線體基因組和有共生藻石珊瑚基因組相似，但個別支序中擁有許多獨立的特徵: （一）本研究首度發現珊瑚粒線體基因組內基因間的排列重組。在Madrepora粒線基因組中，細胞色素氧化酶第二次單元基因 (cytochrome oxidase subunit II, cox2) 和細胞色素氧化酶第三次單元基因 (cytochrome oxidases subunit III, cox3) 之間發生基因重新排列。另外，NADH脫氫酶第四次單元基因 (NADH dehydrogenase subunit 4, nad4) 的五撇端具有胸腺嘧啶的細胞間異質性現象 (heteroplasm) ; (二) Fungiacyathus具有較長的基因間區且在細胞色素氧化酶第一次單元基因 (cytochrome oxidase subunit I, cox1) 中發現第一型介入子 (group I intron) 插入，而造成其基因體結構較為鬆散 (> 19 kb)；（三）相反的，因基因間區較短，使得Polycyathus則為目前已知珊瑚粒線體中基因排列最緊密的粒線體 (< 16 kb)；（四）在Euphyllia中發現目前石珊瑚中已知最長的cox1基因。 以粒線體基因片段序列親緣關係分析也支持這四個粒線體基因組的特徵演化。Madrepora在石珊瑚中呈現獨立分支，對應了在其基因重組的特殊性；而具有第一型介入子的Fungiacyathus和一群也具有第一型介入子的複雜珊瑚群 (complex clade)有較相近的關係，顯示無共生藻石珊瑚和有共生藻石珊瑚可能具有相同的第一型介入子來源；而Polycyathus和Euphyllia的分據親緣樹上的強壯珊瑚系群 (robust clade) 和複雜珊瑚系群，則支持了葵珊瑚亞目 (suborder Caryophylliina) 為非單一起源。

Because only a few studies of azooxanthellate scleractinians exist and results of 16S rDNA analyses of coral phylogeny are ambiguous, a mitochondrial genomics study can provide further understanding of scleractinian evolution. Both Euphyllia ancora and Polycyathus sp. which contain zooxanthellae belong to the suborder Caryophylliina and were previously separated into the robust subclade with family-level debates. The genera, Fungiacyathus and Madrepora, have also been the subject of taxonomic debate after radioimmunoassay and mitochondrial sequence analyses. Four mitochondrial (mt) genomes, two from azooxanthallate corals, Fungiacyathus stephanus and Madrepora oculata, and two from zooxanthellate corals, Euphyllia ancora and Polycyathus sp., were sequenced in this study. Three major features were discovered in the azooxanthellate mt genomes. First, gene rearrangement of cytochrome oxidase subunit II (COII) and cytochrome oxidase subunit III (COIII) and a poly (T) variation in the nad4 protein-coding gene were found in the mt genome of M. oculata. These characters are discussed in the Scleractinia for the first time. Second, F. stephanus presented a loose genome (19,381 bp) with a group I intron in the cox1 gene. In contrast, the zooxanthellate coral, Polycyathus sp., had the most compact mt genome (15,356 bp) among all the scleractinians known to date. Euphyllia ancora presented an extremely long cox1 gene. Phylogenetic analyses also showed unique information of these four mt genomes in the evolutionary trees, and M. oculata formed a single lineage with robust clade corals, supporting the result of rearrangement of the COII and COIII genes. Fungiacyathus stephanus grouped with the Poritidae. The cox1 group I intron occurs in the Fungiacyathus-Poritidae lineage. The high sequence similarity of cox1 intron nucleotides between Fungicyathus and the Poritidae indicates that azooxanthellate and zooxanthellate corals have the same origin of cox1 group I intron. The two Caryophylliina corals, Polycyathus and Euphyllia, were respectively grouped with the robust and complex clades. This suggests that Caryophylliina corals are not monophyletic. In conclusion, based on a mitogenomic approach, this study provides some insights into the phylogenetic relationships and evolution of mitochondrial genomes among these taxonomically ambiguous taxa.