4月29日，BMC  Evolutionary  Biology发表了研究论文报道了鲤科鱼类散在重复序列研究取得的新进展。该文章是由中国科学院水生生物研究所鱼类系统学与生物地理学学科组博士研究生童超波等人在何舜平研究员的指导下完成的。

童超波等之前在BMC  Genomics  (Tong  et  al.，2009)  发表的论文中，报道了一种将磁珠分选系统应用于散在重复序列的分离的方法，在鲢和鳙中分离了一个年轻的SINE家族（HAmoSINE）及其反转座所依附的LINE家族（HAmoLINE2），发现该SINE家族借助于其基因组内HAmo  LINE2编码的反转座酶系统实现自身近期的不断增殖。

本篇论文承接之前的研究，进一步研究HAmoSINE和HAmoLINE在整个鲤科鱼类12个亚科的17个代表物种基因组中的进化模式。基于磁珠分选技术大规模捕获鲤科鱼类17个代表物种基因组中的散在重复序列，根据特征性的诊断性核苷酸的存在，发现四个HAmoSINE源基因（亚家族）活跃增殖于整个鲤科鱼类或特定谱系中，HAmoSINE在这些鱼类中的拷贝数从104到106不等。探讨了这些亚家族在斑马鱼基因组中的情况及其物种分布情况。该论文的结果表明，HAmoSINE在整个鲤科鱼类中通过反转座寄生于HAmoLINE得到了大规模的扩张。

原文出处：

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.