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Multiple source genes of HAmo SINE actively expanded and ongoing retroposition in cyprinid genomes relying on its partner LINE
Tong, Chaobo; Gan, Xiaoni; He, Shunping; He, SP, Chinese Acad Sci, Lab Fish Phylogenet & Biogeog, Inst Hydrobiol, Wuhan 430072, Hubei, Peoples R China
2010
Source PublicationBMC EVOLUTIONARY BIOLOGY
ISSN1471-2148
Volume10Pages:-
AbstractBackground: 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.
KeywordEuropean Cyprinids Evolution Sequences Elements Methylation Phylogeny Inference Mrbayes Ends Rna
Department[Tong, Chaobo; Gan, Xiaoni; He, Shunping] Chinese Acad Sci, Lab Fish Phylogenet & Biogeog, Inst Hydrobiol, Wuhan 430072, Hubei, Peoples R China; [Tong, Chaobo; Gan, Xiaoni] Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China
Subject AreaEvolutionary Biology ; Genetics & Heredity
Funding OrganizationNational Natural Science Foundation of China [30530120, 30225008]; Major State Basic Research Development Program of China (973 Program) [2007CB411601] ; National Natural Science Foundation of China [30530120, 30225008]; Major State Basic Research Development Program of China (973 Program) [2007CB411601] ; National Natural Science Foundation of China [30530120, 30225008]; Major State Basic Research Development Program of China (973 Program) [2007CB411601] ; National Natural Science Foundation of China [30530120, 30225008]; Major State Basic Research Development Program of China (973 Program) [2007CB411601]
Indexed BySCI
Language英语
WOS IDWOS:000277851600001
Funding OrganizationNational Natural Science Foundation of China [30530120, 30225008]; Major State Basic Research Development Program of China (973 Program) [2007CB411601] ; National Natural Science Foundation of China [30530120, 30225008]; Major State Basic Research Development Program of China (973 Program) [2007CB411601] ; National Natural Science Foundation of China [30530120, 30225008]; Major State Basic Research Development Program of China (973 Program) [2007CB411601] ; National Natural Science Foundation of China [30530120, 30225008]; Major State Basic Research Development Program of China (973 Program) [2007CB411601]
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Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/13479
Collection水生生物多样性与资源保护研究中心_期刊论文
Corresponding AuthorHe, SP, Chinese Acad Sci, Lab Fish Phylogenet & Biogeog, Inst Hydrobiol, Wuhan 430072, Hubei, Peoples R China
Recommended Citation
GB/T 7714
Tong, Chaobo,Gan, Xiaoni,He, Shunping,et al. 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,&He, SP, Chinese Acad Sci, Lab Fish Phylogenet & Biogeog, Inst Hydrobiol, Wuhan 430072, Hubei, Peoples R China.(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):-.
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