4月29日,，BMC Evolutionary Biology發(fā)表了研究論文報道了鯉科魚類散在重復(fù)序列研究取得的新進展。該文章是由中國科學(xué)院水生生物研究所魚類系統(tǒng)學(xué)與生物地理學(xué)學(xué)科組博士研究生童超波等人在何舜平研究員的指導(dǎo)下完成的,。
童超波等之前在BMC Genomics (Tong et al.,，2009) 發(fā)表的論文中，報道了一種將磁珠分選系統(tǒng)應(yīng)用于散在重復(fù)序列的分離的方法,，在鰱和鳙中分離了一個年輕的SINE家族（HAmoSINE）及其反轉(zhuǎn)座所依附的LINE家族（HAmoLINE2）,，發(fā)現(xiàn)該SINE家族借助于其基因組內(nèi)HAmo LINE2編碼的反轉(zhuǎn)座酶系統(tǒng)實現(xiàn)自身近期的不斷增殖。
本篇論文承接之前的研究,，進一步研究HAmoSINE和HAmoLINE在整個鯉科魚類12個亞科的17個代表物種基因組中的進化模式,。基于磁珠分選技術(shù)大規(guī)模捕獲鯉科魚類17個代表物種基因組中的散在重復(fù)序列,，根據(jù)特征性的診斷性核苷酸的存在,，發(fā)現(xiàn)四個HAmoSINE源基因（亞家族）活躍增殖于整個鯉科魚類或特定譜系中，HAmoSINE在這些魚類中的拷貝數(shù)從104到106不等,。探討了這些亞家族在斑馬魚基因組中的情況及其物種分布情況,。該論文的結(jié)果表明，HAmoSINE在整個鯉科魚類中通過反轉(zhuǎn)座寄生于HAmoLINE得到了大規(guī)模的擴張,。（生物谷Bioon.com）
生物谷推薦原文出處：
BMC Evolutionary Biology doi:10.1186/1471-2148-10-115
Multiple source genes of HAmo SINE actively expanded and ongoing retroposition in cyprinid genomes relying on its partner LINE
Chaobo Tong , Xiaoni Gan and Shunping He
Background
We recently characterized HAmo SINE and its partner LINE in silver carp and bighead carp based on hybridization capture of repetitive elements from digested genomic DNA in solution using a bead-probe [1]. To reveal the distribution and evolutionary history of SINEs and LINEs in cyprinid genomes, we performed a multi-species search for HAmo SINE and its partner LINE using the bead-probe capture and internal-primer-SINE polymerase chain reaction (PCR) techniques.
Results
67 full-size and 125 internal-SINE sequences (as well as 34 full-size and 9 internal sequences previously reported in bighead carp and silver carp) from 17 species of the family Cyprinidae were aligned as well as 14 new isolated HAmoL2 sequences. Four subfamilies (type I, II, III and IV), which were divided based on diagnostic nucleotides in the tRNA-unrelated region, expanded preferentially within a certain lineage or within the whole family of Cyprinidae as multiple active source genes. The copy numbers of HAmo SINEs were estimated to vary from 104 to 106 in cyprinid genomes by quantitative RT-PCR. Over one hundred type IV members were identified and characterized in the primitive cyprinid Danio rerio genome but only tens of sequences were found to be similar with type I, II and III since the type IV was the oldest subfamily and its members dispersed in almost all investigated cyprinid fishes. For determining the taxonomic distribution of HAmo SINE, inter-primer SINE PCR was conducted in other non-cyprinid fishes, the results shows that HAmo SINE- related sequences may disperse in other families of order Cypriniforms but absent in other orders of bony fishes: Siluriformes, Polypteriformes, Lepidosteiformes, Acipenseriformes and Osteoglossiforms.
Conclusions
Depending on HAmo LINE2, multiple source genes (subfamilies) of HAmo SINE actively expanded and underwent retroposition in a certain lineage or within the whole family of Cyprinidae. From this perspective, HAmo SINE should provide useful phylogenetic makers for future analyses of the evolutionary relationships among species in the family Cyprinidae.
