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; Susan R Wessler

doi:10.1038/s41467-019-08451-3

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

Nat Commun. 2019 Feb 7;10(1):641. doi: 10.1038/s41467-019-08451-3.

Authors

Jinfeng Chen^{1

2

3}, Lu Lu^{2

3}, Jazmine Benjamin⁴, Stephanie Diaz⁴, C Nathan Hancock⁴, Jason E Stajich^{5

6}, Susan R Wessler^{7

8}

Affiliations

¹ Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA.
² Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
³ Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
⁴ Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC, 29801, USA.
⁵ Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA. jason.stajich@ucr.edu.
⁶ Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA. jason.stajich@ucr.edu.
⁷ Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA. susan.wessler@ucr.edu.
⁸ Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA. susan.wessler@ucr.edu.

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.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

DNA Transposable Elements / genetics*
Domestication*
Epigenesis, Genetic / genetics
Genome, Plant / genetics*
Oryza / genetics*

Substances

DNA Transposable Elements

Grants and funding

S10 OD016290/OD/NIH HHS/United States