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Two key events associated with a transposable element burst occurred during rice domestication

View ORCID ProfileJinfeng Chen, Lu Lu, Jazmine Benjamin, Stephanie Diaz, View ORCID ProfileC. Nathan Hancock, View ORCID ProfileJason E. Stajich, View ORCID ProfileSusan R. Wessler
doi: https://doi.org/10.1101/405290
Jinfeng Chen
aDepartment of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA
bDepartment of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
cInstitute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
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Lu Lu
bDepartment of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
cInstitute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
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Jazmine Benjamin
dDepartment of Biology and Geology, University of South Carolina Aiken, Aiken, SC 29801, USA
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Stephanie Diaz
dDepartment of Biology and Geology, University of South Carolina Aiken, Aiken, SC 29801, USA
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C. Nathan Hancock
dDepartment of Biology and Geology, University of South Carolina Aiken, Aiken, SC 29801, USA
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Jason E. Stajich
aDepartment of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA
cInstitute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
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  • For correspondence: jason.stajich@ucr.edu susan.wessler@ucr.edu
Susan R. Wessler
bDepartment of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
cInstitute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
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  • For correspondence: jason.stajich@ucr.edu susan.wessler@ucr.edu
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Abstract

Transposable elements shape genome evolution through periodic bursts of amplification. In this study we exploited knowledge of the components of the mPing/Ping/Pong TE family in four rice strains undergoing mPing bursts to track their copy numbers and distribution in a large collection of genomes from the wild progenitor Oryza rufipogon and domesticated Oryza sativa (rice). We characterized two events that occurred to the autonomous Ping element and appear to be critical for mPing hyperactivity. First, a point mutation near the end of the element created a Ping variant (Ping16A) with reduced transposition. The proportion of strains with Ping16A has increased during domestication while the original Ping (Ping16G) has been dramatically reduced. Second, transposition of Ping16A into a Stowaway element generated a locus (Ping16A_Stow) whose presence correlates with strains that have high mPing copies. Finally, demonstration that Pong elements have been stably silenced in all strains analyzed indicates that sustained activity of the mPing/Ping family during domestication produced the components necessary for the mPing burst, not the loss of epigenetic regulation.

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Posted August 31, 2018.
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Two key events associated with a transposable element burst occurred during rice domestication
Jinfeng Chen, Lu Lu, Jazmine Benjamin, Stephanie Diaz, C. Nathan Hancock, Jason E. Stajich, Susan R. Wessler
bioRxiv 405290; doi: https://doi.org/10.1101/405290
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Two key events associated with a transposable element burst occurred during rice domestication
Jinfeng Chen, Lu Lu, Jazmine Benjamin, Stephanie Diaz, C. Nathan Hancock, Jason E. Stajich, Susan R. Wessler
bioRxiv 405290; doi: https://doi.org/10.1101/405290

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