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Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation
Tong, Chaobo1,2; Guo, Baocheng1,2; He, Shunping1; He, SP, Chinese Acad Sci, Inst Hydrobiol, Lab Fish Phylogenet & Biogeog, Wuhan 430072, Peoples R China
2009-02-19
Source PublicationBMC GENOMICS
ISSN1471-2164
Volume10Issue:0
AbstractBackground: Short and long interspersed elements (SINEs and LINEs, respectively), two types of retroposons, are active in shaping the architecture of genomes and powerful tools for studies of phylogeny and population biology. Here we developed special protocol to apply biotin-streptavidin bead system into isolation of interspersed repeated sequences rapidly and efficiently, in which SINEs and LINEs were captured directly from digested genomic DNA by hybridization to bead-probe complex in solution instead of traditional strategy including genomic library construction and screening. Results: A new couple of SINEs and LINEs that shared an almost identical 3'tail was isolated and characterized in silver carp and bighead carp of two closely related species. These SINEs (34 members), designated HAmo SINE family, were little divergent in sequence and flanked by obvious TSD indicated that HAmo SINE was very young family. The copy numbers of this family was estimated to 2 x 10(5) and 1.7 x 10(5) per haploid genome by Real-Time qPCR, respectively. The LINEs, identified as the homologs of LINE2 in other fishes, had a conserved primary sequence and secondary structures of the 3'tail region that was almost identical to that of HAmo SINE. These evidences suggest that HAmo SINEs are active and amplified recently utilizing the enzymatic machinery for retroposition of HAmoL2 through the recognition of higher-order structures of the conserved 42-tail region. We analyzed the possible structures of HAmo SINE that lead to successful amplification in genome and then deduced that HAmo SINE, SmaI SINE and FokI SINE that were similar in sequence each other, were probably generated independently and created by LINE family within the same lineage of a LINE phylogeny in the genomes of different hosts. Conclusion: The presented results show the advantage of the novel method for retroposons isolation and a pair of young SINE family and its partner LINE family in two carp fishes, which strengthened the hypotheses containing the slippage model for initiation of reverse transcription, retropositional parasitism of SINEs on LINEs, the formation of the stem loop structure in 3'tail region of some SINEs and LINEs and the mechanism of template switching in generating new SINE family.; Background: Short and long interspersed elements (SINEs and LINEs, respectively), two types of retroposons, are active in shaping the architecture of genomes and powerful tools for studies of phylogeny and population biology. Here we developed special protocol to apply biotin-streptavidin bead system into isolation of interspersed repeated sequences rapidly and efficiently, in which SINEs and LINEs were captured directly from digested genomic DNA by hybridization to bead-probe complex in solution instead of traditional strategy including genomic library construction and screening.
SubtypeArticle
KeywordInterspersed Repetitive Elements Ltr Retrotransposable Elements Eukaryotic Genomes Transcribable Sequences Molecular Systematics Short Retroposons Rna Evolution Transcription Superfamily
Department[Tong, Chaobo; Guo, Baocheng; He, Shunping] Chinese Acad Sci, Inst Hydrobiol, Lab Fish Phylogenet & Biogeog, Wuhan 430072, Peoples R China; [Tong, Chaobo; Guo, Baocheng] Chinese Acad Sci, Grad Univ, Beijing 100039, Peoples R China
Subject AreaBiotechnology & Applied Microbiology ; Genetics & Heredity
DOI10.1186/1471-2164-10-83
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
Funding OrganizationNational Natural Science Foundation of China [30530120, 30225008] ; National Natural Science Foundation of China [30530120, 30225008] ; National Natural Science Foundation of China [30530120, 30225008] ; National Natural Science Foundation of China [30530120, 30225008]
Indexed BySCI
Language英语
WOS Research AreaBiotechnology & Applied Microbiology ; Genetics & Heredity
WOS SubjectBiotechnology & Applied Microbiology ; Genetics & Heredity
WOS IDWOS:000264124200001
WOS KeywordINTERSPERSED REPETITIVE ELEMENTS ; LTR RETROTRANSPOSABLE ELEMENTS ; EUKARYOTIC GENOMES ; TRANSCRIBABLE SEQUENCES ; MOLECULAR SYSTEMATICS ; SHORT RETROPOSONS ; RNA ; EVOLUTION ; TRANSCRIPTION ; SUPERFAMILY
Funding OrganizationNational Natural Science Foundation of China [30530120, 30225008] ; National Natural Science Foundation of China [30530120, 30225008] ; National Natural Science Foundation of China [30530120, 30225008] ; National Natural Science Foundation of China [30530120, 30225008]
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Cited Times:2[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/152342/7838
Collection期刊论文
Corresponding AuthorHe, SP, Chinese Acad Sci, Inst Hydrobiol, Lab Fish Phylogenet & Biogeog, Wuhan 430072, Peoples R China
Affiliation1.Chinese Acad Sci, Inst Hydrobiol, Lab Fish Phylogenet & Biogeog, Wuhan 430072, Peoples R China
2.Chinese Acad Sci, Grad Univ, Beijing 100039, Peoples R China
Recommended Citation
GB/T 7714
Tong, Chaobo,Guo, Baocheng,He, Shunping,et al. Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation[J]. BMC GENOMICS,2009,10(0).
APA Tong, Chaobo,Guo, Baocheng,He, Shunping,&He, SP, Chinese Acad Sci, Inst Hydrobiol, Lab Fish Phylogenet & Biogeog, Wuhan 430072, Peoples R China.(2009).Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation.BMC GENOMICS,10(0).
MLA Tong, Chaobo,et al."Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation".BMC GENOMICS 10.0(2009).
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