Tracking the origin of two genetic components associated with transposable element bursts in domesticated rice

• DOI: 10.1038/s41467-019-08451-3
• Publication Date: 2019-02-07T11:05:41Z
• Authors: Jinfeng Chen; Lu Lu; Jazmine Benjamin; Stephanie Diaz; C. Nathan Hancock; Jason E. Stajich; Susan R. Wessler
• Keywords: 0301 basic medicine; 570; Genome; Science; Human Genome; Q; Oryza; Plant; Biological Sciences; Article; Epigenesis, Genetic; Domestication; 03 medical and health sciences; Genetic; Genetics; DNA Transposable Elements; Generic health relevance; Genome, Plant; Biotechnology; Epigenesis

AbstractTransposable elements (TEs) shape genome evolution through periodic bursts of amplification. In this study prior knowledge of themPing/Ping/PongTE family is exploited to track their copy numbers and distribution in genome sequences from 3,000 accessions of domesticatedOryza sativa(rice) and the wild progenitorOryza rufipogon. We find thatmPingbursts are restricted to recent domestication and is likely due to the accumulation of two TE components,Ping16AandPing16A_Stow, that appear to be critical formPinghyperactivity.Ping16Ais a variant of the autonomous element with reduced activity as shown in a yeast transposition assay. Transposition ofPing16Ainto aStowawayelement generatedPing16A_Stow, the onlyPinglocus shared by all bursting accessions, and shown here to correlate with highmPingcopies. Finally, we show that sustained activity of themPing/Pingfamily in domesticated rice produced the components necessary formPingbursts, not the loss of epigenetic regulation.