BMC：鱼类重复序列研究*新成果

领导这一研究的是水生生物研究所学术带头人何舜平研究员，其2002年获得国家杰出青年基金，现任中国科学院水生生物标本馆馆长、中国科学院水生生物研究所生物多样性及资源保护中心主任等，主要研究方向是鱼类系统学与生物地理学，曾在国际上率先使用分子系统学方法对亚洲鲇类及相关类群开展系统发育研究。

在之前的研究中，何舜平研究组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HAmoLINE2编码的反转座酶系统实现自身近期的不断增殖。

在这一基础上，研究人员进一步研究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。

分类学研究在全世界范围内都处于下滑阶段。在中国，情形也不乐观，其实在上世纪80年代末之前，分类学一直是很多中国植物学家研究的重点领域。**版《中国植物志》由312位植物分类学家一同编写。但是多年以来，分类学研究领域流失了很多人才。做分类学的科学家中很多人都已经转向其他方向的研究，而不做分类学了。

为了发展分类学，国内开始鼓励分类学家们必须将触角伸向分子生物学领域，何舜平研究员就是一个成功的例子，他使用DNA条形码技术 —物种特异性 DNA线粒体序列—以确定鱼的种类。因此他遇到的经费问题比较少：以DNA为基础的分类学研究为他赢得了国外广泛的合作网络和稳定的科研经费。

目前国内正在策划进行中国生物多样性的综合调查，这项为期数年的项目将需要一个庞大的分类学家团队，也许还需要分子生物学方面专家们的配合。希望这一项目将为分类学领域的复兴带来希望。

原文检索：

Multiple source genes of HAmo SINE actively expanded and ongoingretroposition in cyprinid genomes relying on its partner LINE

Background
We recently characterized HAmo SINE and its partner LINE in silvercarp and bighead carp based on hybridization capture of repetitiveelements from digested genomic DNA in solution using a bead-probe[1]. To reveal the distribution and evolutionary history of SINEsand LINEs in cyprinid genomes, we performed a multi-species searchfor HAmo SINE and its partner LINE using the bead-probe capture andinternal-primer-SINE polymerase chain reaction (PCR)techniques.

Results
67 full-size and 125 internal-SINE sequences (as well as 34full-size and 9 internal sequences previously reported in bigheadcarp and silver carp) from 17 species of the family Cyprinidae werealigned as well as 14 new isolated HAmoL2 sequences. Foursubfamilies (type I, II, III and IV), which were divided based ondiagnostic nucleotides in the tRNA-unrelated region, expandedpreferentially within a certain lineage or within the whole familyof Cyprinidae as multiple active source genes. The copy numbers ofHAmo SINEs were estimated to vary from 104 to 106 in cyprinidgenomes by quantitative RT-PCR. Over one hundred type IV memberswere identified and characterized in the primitive cyprinid Daniorerio genome but only tens of sequences were found to be similarwith type I, II and III since the type IV was the oldest subfamilyand its members dispersed in almost all investigated cyprinidfishes. 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 inother families of order Cypriniforms but absent in other orders ofbony fishes: Siluriformes, Polypteriformes, Lepidosteiformes,Acipenseriformes and Osteoglossiforms.

Conclusions
Depending on HAmo LINE2, multiple source genes (subfamilies) ofHAmo SINE actively expanded and underwent retroposition in acertain lineage or within the whole family of Cyprinidae. From thisperspective, HAmo SINE should provide useful phylogenetic makersfor future analyses of the evolutionary relationships among speciesin the family Cyprinidae.