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  • New Progress in the Study of Interpersed Repeated Sequences (SINEs and LINEs) in Cyprinid Genomes
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    On April 29, a paper entitled “Multiple source genes of HAmo SINE actively expanded and ongoing retroposition in cyprinid genomes relying on its partner LINE” (BMC Evolutionary Biology 2010, 10:115) was published in the journal BMC Evolutionary Biology. Supervised by He Shunping, professor of Institute of Hydrobiology, Chinese Academy of Sciences (IHB), the paper was mainly completed by Tong Chaobo, a doctoral student now studying at the Research Group of Fish Phylogenetics and Biogeography in the institute.

    In the previous research published in BMC Genomics (Tong et al, 2009), Tong and his colleagues developed special protocol to apply biotin-streptavidin bead system into isolation of interspersed repeated sequences rapidly and efficiently. Isolation of a pair of young SINE family (HAmo SINE) and its partner HAmo LINE family in two carp fishes 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.

    To reveal the species distribution and evolutionary history of SINEs and LINEs in more cyprinid genomes, they performed a multi-species search for HAmo SINE and its partner LINE in almost all subfamilies of Cyprinidae, as well as in distantly related fishes using the bead-probe capture and internal-SINE-primer polymerase chain reaction (PCR) techniques. 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. The results manifested that 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.

    Related link: http://www.biomedcentral.com/1471-2148/10/115

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