Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon

Stritt, Christoph; Gordon, Sean P.; Wicker, Thomas; Vogel, John P.; Roulin, Anne C.

doi:10.1093/gbe/evx276

Title: Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon

Abstract

Transposable element (TE) activity has emerged as a major cause of variation in genome size and structure among species. To what extent TEs contribute to genetic variation and divergence within species, however, is much less clear, mainly because population genomic data have so far only been available for the classical model organisms. In this study, we use the annual Mediterranean grass Brachypodium distachyon to investigate TE dynamics in natural populations. Using whole-genome sequencing data for 53 natural accessions, we identified more than 5,400 TE polymorphisms across the studied genomes. We found, first, that while population bottlenecks and expansions have shaped genetic diversity in B. distachyon, these events did not lead to lineage-specific activations of TE families, as observed in other species. Instead, the same families have been active across the species range and TE activity is homogeneous across populations, indicating the presence of conserved regulatory mechanisms. Second, almost half of the TE insertion polymorphisms are accession-specific, most likely because of recent activity in expanding populations and the action of purifying selection. And finally, although TE insertion polymorphisms are underrepresented in and around genes, more than 1,000 of them occur in genic regions and could thus contribute to functional divergence. Ourmore »« less

Authors:

Stritt, Christoph ^[1]; Gordon, Sean P. ^[2]; Wicker, Thomas ^[1]; Vogel, John P. ^[2]; Roulin, Anne C. ^[1]

Univ. of Zurich (Switzerland). Inst. for Plant and Microbial Biology
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Publication Date:: Thu Dec 21 00:00:00 EST 2017

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC)

OSTI Identifier:: 1543957

Grant/Contract Number:: AC02-05CH11231

Resource Type:: Accepted Manuscript

Journal Name:: Genome Biology and Evolution

Additional Journal Information:: Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 1759-6653

Publisher:: Society for Molecular Biology and Evolution

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; Evolutionary Biology; Genetics & Heredity

Citation Formats


                    Stritt, Christoph, Gordon, Sean P., Wicker, Thomas, Vogel, John P., and Roulin, Anne C. Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon.  United States: N. p., 2017. 
Web.  doi:10.1093/gbe/evx276.

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                    Stritt, Christoph, Gordon, Sean P., Wicker, Thomas, Vogel, John P., & Roulin, Anne C. Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon.  United States.  https://doi.org/10.1093/gbe/evx276

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                    Stritt, Christoph, Gordon, Sean P., Wicker, Thomas, Vogel, John P., and Roulin, Anne C. Thu .  
"Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon".  United States.  https://doi.org/10.1093/gbe/evx276.  https://www.osti.gov/servlets/purl/1543957.

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@article{osti_1543957,

  title        = {Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon},

  author       = {Stritt, Christoph and Gordon, Sean P. and Wicker, Thomas and Vogel, John P. and Roulin, Anne C.},

  abstractNote = {Transposable element (TE) activity has emerged as a major cause of variation in genome size and structure among species. To what extent TEs contribute to genetic variation and divergence within species, however, is much less clear, mainly because population genomic data have so far only been available for the classical model organisms. In this study, we use the annual Mediterranean grass Brachypodium distachyon to investigate TE dynamics in natural populations. Using whole-genome sequencing data for 53 natural accessions, we identified more than 5,400 TE polymorphisms across the studied genomes. We found, first, that while population bottlenecks and expansions have shaped genetic diversity in B. distachyon, these events did not lead to lineage-specific activations of TE families, as observed in other species. Instead, the same families have been active across the species range and TE activity is homogeneous across populations, indicating the presence of conserved regulatory mechanisms. Second, almost half of the TE insertion polymorphisms are accession-specific, most likely because of recent activity in expanding populations and the action of purifying selection. And finally, although TE insertion polymorphisms are underrepresented in and around genes, more than 1,000 of them occur in genic regions and could thus contribute to functional divergence. Our study shows that while TEs in B. distachyon are “well-behaved” compared with TEs in other species with larger genomes, they are an abundant source of lineage-specific genetic variation and may play an important role in population divergence and adaptation.},

  doi          = {10.1093/gbe/evx276},

  journal      = {Genome Biology and Evolution},

  number       = 1,

  volume       = 10,

  place        = {United States},

  year         = {Thu Dec 21 00:00:00 EST 2017},

  month        = {Thu Dec 21 00:00:00 EST 2017}

}

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