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

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...

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Bibliographic Details
Published in:Nature communications 2019-02, Vol.10 (1), p.641-641, Article 641
Main Authors: Chen, Jinfeng, Lu, Lu, Benjamin, Jazmine, Diaz, Stephanie, Hancock, C. Nathan, Stajich, Jason E., Wessler, Susan R.
Format: Article
Language:English
Subjects:
45/23
631/181/2474
631/208/182
631/208/212/2305
Bursts
DNA Transposable Elements - genetics
Domestication
Epigenesis, Genetic - genetics
Gene sequencing
Genome, Plant - genetics
Genomes
Humanities and Social Sciences
Hyperactivity
multidisciplinary
Oryza - genetics
Oryza sativa
Science
Science (multidisciplinary)
Tracking
Transposition
Transposons
Yeast
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Summary: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. Transposable element (TE) bursts shape genome evolution but their origin remains unclear. Here, the authors show that a burst is restricted to only a few domesticated rice accessions and is associated with the acquisition of two TE variants, Ping16A and Ping16A_Stow, not the loss of TE silencing.
ISSN:2041-1723
2041-1723
DOI:10.1038/s41467-019-08451-3