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研究生:莊博舜
研究生(外文):Po-Shun Chuang
論文名稱:亞目魚類毒素基因解序及演化分析
論文名稱(外文):Venom gene determination and evolution in Scorpaenoidei
指導教授:蕭仁傑蕭仁傑引用關係
指導教授(外文):Jen-Chieh Hsiao
口試委員:黃登福湯森林廖德裕
口試委員(外文):Deng-Fwu HwangSen-Lin TangTe-Yu Liao
口試日期:2014-01-22
學位類別:碩士
校院名稱:國立臺灣大學
系所名稱:海洋研究所
學門:自然科學學門
學類:海洋科學學類
論文種類:學術論文
論文出版年:2014
畢業學年度:102
語文別:英文
論文頁數:93
中文關鍵詞:&;#39819;形目&;#39819;亞目石狗公毒素基因
外文關鍵詞:ScorpaeniformesScorpaenoideiscorpionfishrockfishvenom gene
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棘鰭魚首目中有超過1200種的魚類被認定為具有毒性。其中&;#39819;亞目(Scorpaenoidei)為這些有毒物種的主要類群之一,因此也被認定具有高度潛力可從中發現具有生物活性之分子。在本研究中,我們解序&;#39819;亞目中三個物種的毒素基因,並且參考資料庫已有之序列,重建出此毒素基因可能的演化過程。根據cDNA推導出來之蛋白質序列,眉鬚鱗頭&;#39819;(Sebastapistes strongia)、尖頭擬&;#39819;(Scorpaenopsis oxycephala)及石狗公(Sebastiscus marmoratus)毒素的兩個次單元(subunit)長度約為700個胺基酸(698~703),與過去在毒&;#39819;屬(Synanceja)及簑&;#39819;屬(Pterois)所發現之毒素相似。演化親緣關係的分析顯示,此毒素次單元的複製與分化應早於&;#39819;亞目之分化,且此毒素基因可能普遍存在於整個&;#39819;形目(Scorpaeniformes)的種類。除此之外,在簑&;#39819;屬物種分化之前,可能發生了另外一次基因複製事件&;not;而產生了簑&;#39819;屬的兩種毒素次單元。利用斑馬短鰭簑&;#39819;(Dendrochirus zebra)的基因體,我們發現了三種不同的毒素基因序列,此結果暗示了在簑&;#39819;亞科中假基因(pseudogene)存在的可能。此外,反轉錄定量聚合&;#37238;連鎖反應(RT-qPCR)的結果顯示,石狗公(Se. marmoratus)的背鰭硬棘具有相對最高的毒素基因表現,其他鰭的毒素表現則相對較少,而其表現量在各個不同組織的差異對應了其防禦性的功能─越容易受到攻擊的區域具有越高的毒素表現量。

More than 1200 fish species among acanthomorpha might be venomous. Scorpaenoidei, a diverse suborder of ray-finned fish, is a hotspot of venomous fish and possesses a large pool of potential bioactive molecules. In the present study we determined the venom genes from three scorpaenoid fishes and reconstructed their evolutionary relationship. The deduced amino acid sequences of two venom subunits in Sebastapistes strongia, Scorpaenopsis oxycephala, and Sebastiscus marmoratus are about 700 a.a. (698~703 a.a.), corresponding to the size of stonefish and lionfish venoms. Phylogenetic analysis shows that the two gene subunits were duplicated prior to the speciation of Scorpaenoidei and may be common to the whole Scorpaeniform family. In addition, another gene duplication event occurred before the speciation of lionfish (Pteroinae), thus generating the two venom subunits in the genus Pterois. The venom genes determined from the genomic DNA of Dendrochirus zebra show three types of venom genes in the genome, implying that a pseudogene may present in Pteroinae. The expression pattern of the venom genes in different tissues of Se. marmoratus were evaluated by RT-qPCR, respectively. The dorsal spines were found to be the most venomous part of the fish, while lesser amounts of the venom genes were detected in other fins. The venom expression pattern seems to reflect the defensive purpose of the venom, with the most easily attacked part expressing the highest venom levels.

中文摘要…………………………………………………………………………………I
Abstract.…………………………………………………………………………………II
Table of contents………………………………………………………………………. III
Table list………………………………………………………………………………..VI
Figure list……………………………………………………………………………...VII
Appendix list………………………………………………………………………….VIII
Introduction……………………………………………………………………………...1
1.1 Applications of venom study……………………………………………….…..1
1.2 Venom studies on scorpaenoid fishes…………………………………………..2
1.3 The distribution of venom……………………………..……………………….5
1.4 Aims of this study………………………..……………………………………..6
Materials and Methods…………………………………………………………………..7
2.1 Sample collection and species identification………………...…………………7
2.2 Venom extraction and western blotting………………………………………...7
2.3 RNA and DNA extraction………………………………………………...…….9
2.3.1 RNA extraction………………………………………………………….9
2.3.2 DNA extraction………………..……………………………………….10
2.4 Reverse transcription-polymerase chain reaction (RT-PCR) and 3’ and 5’ Rapid Amplification of cDNA ends (3’ RACE and 5’ RACE)……………………….….11
2.4.1 RT-PCR……………………………………….………………………..12
2.4.2 5’ RACE-PCR……….…………………………………………………13
2.4.3 3’ RACE-PCR………………….………………………………………14
2.5 Polymerase chain reaction (PCR) and cloning……………………..…………14
2.5.1 PCR for cox1 gene……………………………………………………..14
2.5.2 PCR for the venom gene……………………………………………….15
2.5.3 PCR product cloning………………………….……………………….17
2.6 Sequence analysis………………………..……………………………………20
2.7 Phylogenic analysis…………...………………………………………………21
2.8 Reverse transcription-quantitative polymerase chain reaction (RT-qPCR)…...21
2.9. Whole genome sequencing (WGS)…………………………………………..23
Results………………………………………………………………………………….24
1. Western blotting……..……………………………………………………….24
2. Determination and differential gene expression of putative venom genes..…24
2.1 Venom genes determination from cDNA templates….………………….24
2.2 Venom genes determination from genomic DNA templates………...…..26
2.3 Open reading frames and deduced amino acid sequences analysis...……29
3. Phylogenetic analysis……………….……………………………………….30
3.1 Outgroup searching...…………………………………………………….30
3.2 Phylogenetic trees construction………………………………………….31
4. Venom gene expression pattern in Se. marmoratus………………...………..32
5. Whole genome sequencing in Se. strongia…………………………………..33
Discussion……………………………………………………………………………....36
1. High similarity among the venoms in Scorpaenoidei………………………..36
2. Conservative nature of intron positions……………..……………………….39
3. Precedence of venom gene duplication to scorpaenoid speciation….……….40
4. Defending weapons reinforcement by selection pressure…………………...44
5. Functional unit of the venom protein………………………………………..46
6. Whole genome sequencing………………….……………………………….47
Conclusion……………………………………………………………………………...48
References……………………………………………………………………………...50
Table ………………………………………………………...…………………………57
Figure…………………………………………………………………………………...65
Appendix……………………………………………………………………………….78


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