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

Jinfeng Chen, Lu Lu, Jazmine Benjamin, Stephanie Diaz, C. Nathan Hancock, Jason E. Stajich () and Susan R. Wessler ()
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Jinfeng Chen: University of California
Lu Lu: University of California
Jazmine Benjamin: University of South Carolina Aiken
Stephanie Diaz: University of South Carolina Aiken
C. Nathan Hancock: University of South Carolina Aiken
Jason E. Stajich: University of California
Susan R. Wessler: University of California

Nature Communications, 2019, vol. 10, issue 1, 1-10

Abstract: Abstract Transposable elements (TEs) shape genome evolution through periodic bursts of amplification. In this study prior knowledge of the mPing/Ping/Pong TE family is exploited to track their copy numbers and distribution in genome sequences from 3,000 accessions of domesticated Oryza sativa (rice) and the wild progenitor Oryza rufipogon. We find that mPing bursts are restricted to recent domestication and is likely due to the accumulation of two TE components, Ping16A and Ping16A_Stow, that appear to be critical for mPing hyperactivity. Ping16A is a variant of the autonomous element with reduced activity as shown in a yeast transposition assay. Transposition of Ping16A into a Stowaway element generated Ping16A_Stow, the only Ping locus shared by all bursting accessions, and shown here to correlate with high mPing copies. Finally, we show that sustained activity of the mPing/Ping family in domesticated rice produced the components necessary for mPing bursts, not the loss of epigenetic regulation.

Date: 2019
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DOI: 10.1038/s41467-019-08451-3

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