A novel composite retrotransposon derived from or generated independently of the SVA (SINE/VNTR/Alu) transposon has undergone proliferation in gibbon genomes

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The superfamily Hominoidea (hominoids) comprises two families: Hominidae (hominids) and Hylobatidae (gibbons, also called small apes). The SVA transposon is a composite retrotransposon that occurs widely in hominoids and is considered to have been generated by stepwise fusions of three genetic elements: SINE-R, a variable number of tandem repeat (VNTR) sequence, and <i>Alu</i>. We identified a novel transposon whose basic structure is the same as that of SVA, with one prominent difference being the presence of part of <i>prostaglandin reductase 2</i> (<i>PTGR2</i>) in place of SINE-R. We designate this composite transposon as PVA and propose two possible mechanisms regarding its generation. One is the derivation of PVA from SVA: the SINE-R region of SVA was replaced with a <i>PTGR2</i> fragment by template switching. The other is the formation of PVA independently of SVA: a <i>PTGR2</i> fragment was fused to an evolutionary intermediate comprising the VNTR and <i>Alu</i> regions. The nucleotide sequence of the junction between the VNTR and <i>PTGR2</i> regions supports the second hypothesis. We identified PVA in the white-cheeked gibbon <i>Nomascus leucogenys</i> by analysis of genome sequence databases, and subsequent experimental analysis revealed its presence in all four gibbon genera. The white-cheeked gibbon harbors at least 93 PVA copies in its haploid genome. Another SVA-like composite transposon carrying parts of the LINE1 and <i>Alu</i> transposons in place of SINE-R, designated as LAVA, has recently been reported. The significance of the discovery of PVA is that its substituted fragment originates not from a transposon but from a single-copy gene. PVA should provide additional insights into the transposition mechanism of this type of composite transposon; the transposition activity is conferred even if the substituted fragment is not related to a transposon.


  • Genes & Genetic Systems

    Genes & Genetic Systems 87(3), 181-190, 2012-06-25

    The Genetics Society of Japan

References:  27

Cited by:  1


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