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

Jinfeng Chen,Jazmine Benjamin,C Nathan Hancock,Stephanie Diaz,Jason E Stajich,Lu Lu,Susan R Wessler

doi:10.1038/s41467-019-08451-3

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.

Highlights

Transposable elements (TEs) shape genome evolution through periodic bursts of amplification
Because the vast majority of TE bursts have been inferred after the fact—via computational analysis of whole-genome sequence—the stealth features they require for success have remained largely undiscovered[2,4]
Insertion sites and copy numbers for mPing, Ping, and Pong were identified from genome sequences of 3000 rice accessions using RelocaTE219

Summary

Introduction

Transposable elements (TEs) shape genome evolution through periodic bursts of amplification. 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. Because the vast majority of TE bursts have been inferred after the fact—via computational analysis of whole-genome sequence—the stealth features they require for success have remained largely undiscovered[2,4]. Ongoing bursts of mPing were discovered in four temperate japonica accessions: EG4, HEG4, A119, and A123, whose genomes were sequenced, and insertion sites and epigenetic landscape determined[6,7,8]. These analyses uncovered two features of successful mPing bursts.

Methods

Results

Conclusion