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

CORC > 水生生物研究所 > 中科院水生所知识产出（2009年前） > 水生生物多样性与资源保护研究中心 > 期刊论文

	Multiple source genes of HAmo SINE actively expanded and ongoing retroposition in cyprinid genomes relying on its partner LINE
	Tong, Chaobo 1,2; Gan, Xiaoni 1,2; He, Shunping 1
刊名	BMC EVOLUTIONARY BIOLOGY
	2010-04-29
卷号	10 页码:-
关键词	EUROPEAN CYPRINIDS EVOLUTION SEQUENCES ELEMENTS METHYLATION PHYLOGENY INFERENCE MRBAYES ENDS RNA
ISSN号	1471-2148
通讯作者	He, SP, Chinese Acad Sci, Lab Fish Phylogenet & Biogeog, Inst Hydrobiol, Wuhan 430072, Hubei, Peoples R China
中文摘要	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: Sixty-seven 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.
英文摘要	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.
学科主题	Evolutionary Biology; Genetics & Heredity
WOS标题词	Science & Technology ; Life Sciences & Biomedicine
类目[WOS]	Evolutionary Biology ; Genetics & Heredity
研究领域[WOS]	Evolutionary Biology ; Genetics & Heredity
关键词[WOS]	EUROPEAN CYPRINIDS ; EVOLUTION ; SEQUENCES ; ELEMENTS ; METHYLATION ; PHYLOGENY ; INFERENCE ; MRBAYES ; ENDS ; RNA
收录类别	SCI
资助信息	National Natural Science Foundation of China [30530120, 30225008]; Major State Basic Research Development Program of China (973 Program) [2007CB411601]
语种	英语
WOS记录号	WOS:000277851600001
公开日期	2010-12-23
内容类型	期刊论文
源URL	[http://ir.ihb.ac.cn/handle/342005/13479]
专题	水生生物研究所_水生生物多样性与资源保护研究中心_期刊论文
作者单位	1.Chinese Acad Sci, Lab Fish Phylogenet & Biogeog, Inst Hydrobiol, Wuhan 430072, Hubei, Peoples R China 2.Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China
推荐引用方式 GB/T 7714	Tong, Chaobo,Gan, Xiaoni,He, Shunping. Multiple source genes of HAmo SINE actively expanded and ongoing retroposition in cyprinid genomes relying on its partner LINE[J]. BMC EVOLUTIONARY BIOLOGY,2010,10:-.
APA	Tong, Chaobo,Gan, Xiaoni,&He, Shunping.(2010).Multiple source genes of HAmo SINE actively expanded and ongoing retroposition in cyprinid genomes relying on its partner LINE.BMC EVOLUTIONARY BIOLOGY,10,-.
MLA	Tong, Chaobo,et al."Multiple source genes of HAmo SINE actively expanded and ongoing retroposition in cyprinid genomes relying on its partner LINE".BMC EVOLUTIONARY BIOLOGY 10(2010):-.