農業部-水產試驗所全球資訊網農業部-水產試驗所全球資訊網

在粒線體DNA序列上產生的適應性突變(adaptive mutations)，對於確認生物體的生 命歷史而言，是非常重要的潛力標的，線粒體基因體的細胞色素c氧化酶 1（COX1）基因，常被選擇應用在分析族群及物種上的遺傳結構和親緣關係。本研究 選用澎湖支庫中可進行繁殖6種觀賞蝦為樣本，利用次世代定序的取得原始序列數據 ，利用CLC Genomics Workbench進行de novo assembly的組裝分析，透過BLAST比對 分析找出含有粒線體基因序列的contig片段，可找到單一含有粒線體基因片段的種 類及長度為：亨氏活額蝦16,532 bp、油彩蠟膜蝦15,659 bp、德斑氏活額蝦16,837 bp、花斑掃帚蝦16,637 bp及網紋活額蝦15,159 bp，並利用MITOS及DOGMA進行粒線 體基因位置及數量之預測。以COX1基因的核酸序列全長進行親源性的分析，總共有 16分支結點(node)，其中4出現頻率大於70%、2個為98%及7個為100%，顯示此演化樹 之分析具有高重複性。組裝出的contig序列片段以misa v1.0進行SSR的預測分析 ，從6種蝦類預測出含有SSR序列的區域數量為：亨氏活額蝦10,092個、油彩蠟膜蝦 17,530個、德斑氏活額蝦47,839個、花斑掃帚蝦2,559個、安波多蝦4,437個及網紋 活額蝦33,067個，後續將利用SSR區域兩端的flanking region中設計出可進行PCR的 引子對，進行再現性及多型性的驗證。

Adaptive mitochondrial DNA mutations have the potential to be of great importance in determining aspects of the life history of an organism. The cytochrome c oxidase 1 (COX1) gene, have been used for examining genetic structuring and phylogenetic relationships at both the population and species level. Six shrimps were used for next generation sequencing. After de novo assembling and prediction of MITOS and GOGMA, the candidate of mitogenome is 16,532 bp inCinetorhynchus reticulatus , 15,659 bp inHymenocera picta , 16,837 bp inRhynchocinetes durbanensis , 16,637 bp inSaron marmoratusand 15,159 bp inCinetorhynchus hendersoni , respectively. We reconstructed the phylogenetic relationships of Cyprinodontiform species based on COX1 gene with maximum likelihood (ML) criteria. Bootstrap values (1000 replications) greater than 70% are shown at the branch nodes. The majority of nodes had support values higher than 70% and 7 were 100% supported. The number of SSR candidate is 33,067 in Cinetorhynchus reticulatus , 17,530 in Hymenocera picta , 47,839 in Rhynchocinetes durbanensis , 2,559 in Saron marmoratus , 4,437 in Thor amboinesisand 10,092 in Cinetorhynchus hendersoni.