Transposable elements contribute to dynamic genome content in maize

Sarah N. Anderson; Michelle C. Stitzer; Alex B. Brohammer; Peng Zhou; Jaclyn M. Noshay; Christine H. O'Connor; Cory D. Hirsch; Jeffrey Ross-Ibarra; Candice N. Hirsch; Nathan M. Springer

doi:10.1111/tpj.14489

Transposable elements contribute to dynamic genome content in maize

Sarah N. Anderson, Michelle C. Stitzer, Alex B. Brohammer, Peng Zhou, Jaclyn M. Noshay, Christine H. O'Connor, Cory D. Hirsch, Jeffrey Ross-Ibarra, Candice N. Hirsch, Nathan M. Springer

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Abstract

Transposable elements (TEs) are ubiquitous components of eukaryotic genomes and can create variation in genome organization and content. Most maize genomes are composed of TEs. We developed an approach to define shared and variable TE insertions across genome assemblies and applied this method to four maize genomes (B73, W22, Mo17 and PH207) with uniform structural annotations of TEs. Among these genomes we identified approximately 400 000 TEs that are polymorphic, encompassing 1.6 Gb of variable TE sequence. These polymorphic TEs include a combination of recent transposition events as well as deletions of older TEs. There are examples of polymorphic TEs within each of the superfamilies of TEs and they are found distributed across the genome, including in regions of recent shared ancestry among individuals. There are many examples of polymorphic TEs within or near maize genes. In addition, there are 2380 gene annotations in the B73 genome that are located within variable TEs, providing evidence for the role of TEs in contributing to the substantial differences in annotated gene content among these genotypes. TEs are highly variable in our survey of four temperate maize genomes, highlighting the major contribution of TEs in driving variation in genome organization and gene content. Open Research Badges: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://github.com/SNAnderson/maizeTE_variation; https://mcstitzer.github.io/maize_TEs.

Original language	English (US)
Pages (from-to)	1052-1065
Number of pages	14
Journal	Plant Journal
Volume	100
Issue number	5
DOIs	https://doi.org/10.1111/tpj.14489
State	Published - Dec 1 2019

Bibliographical note

Funding Information:
We are grateful to Peter Crisp for helpful suggestions on this manuscript. The Minnesota Supercomputing Institute (MSI) at the University of Minnesota provided computational resources that contributed to this research. SNA, CDH, and NMS are supported by a grant from USDA‐NIFA (2016‐67013‐24747). Research on this project was supported by grants from the NSF Plant Genome Research Program (IOS‐1238014 for JRI and MCS; IOS‐1546727 for ABB, CHO and CNH; IOS‐1546899 for PZ and NMS) JMN is supported by a Hatch grant from the Minnesota Agricultural Experiment Station (MIN 71‐068). ABB is supported by the DuPont Pioneer Bill Kuhn Honorary Fellowship and the University of Minnesota MnDRIVE Global Food Ventures Graduate Fellowship.

Funding Information:
We are grateful to Peter Crisp for helpful suggestions on this manuscript. The Minnesota Supercomputing Institute (MSI) at the University of Minnesota provided computational resources that contributed to this research. SNA, CDH, and NMS are supported by a grant from USDA-NIFA (2016-67013-24747). Research on this project was supported by grants from the NSF Plant Genome Research Program (IOS-1238014 for JRI and MCS; IOS-1546727 for ABB, CHO and CNH; IOS-1546899 for PZ and NMS) JMN is supported by a Hatch grant from the Minnesota Agricultural Experiment Station (MIN 71-068). ABB is supported by the DuPont Pioneer Bill Kuhn Honorary Fellowship and the University of Minnesota MnDRIVE Global Food Ventures Graduate Fellowship.

Publisher Copyright:
© 2019 The Authors The Plant Journal © 2019 John Wiley & Sons Ltd

Keywords

Zea mays
comparative genomics
gene content variation
transposable elements

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title = "Transposable elements contribute to dynamic genome content in maize",

abstract = "Transposable elements (TEs) are ubiquitous components of eukaryotic genomes and can create variation in genome organization and content. Most maize genomes are composed of TEs. We developed an approach to define shared and variable TE insertions across genome assemblies and applied this method to four maize genomes (B73, W22, Mo17 and PH207) with uniform structural annotations of TEs. Among these genomes we identified approximately 400 000 TEs that are polymorphic, encompassing 1.6 Gb of variable TE sequence. These polymorphic TEs include a combination of recent transposition events as well as deletions of older TEs. There are examples of polymorphic TEs within each of the superfamilies of TEs and they are found distributed across the genome, including in regions of recent shared ancestry among individuals. There are many examples of polymorphic TEs within or near maize genes. In addition, there are 2380 gene annotations in the B73 genome that are located within variable TEs, providing evidence for the role of TEs in contributing to the substantial differences in annotated gene content among these genotypes. TEs are highly variable in our survey of four temperate maize genomes, highlighting the major contribution of TEs in driving variation in genome organization and gene content. Open Research Badges: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://github.com/SNAnderson/maizeTE_variation; https://mcstitzer.github.io/maize_TEs.",

keywords = "Zea mays, comparative genomics, gene content variation, transposable elements",

author = "Anderson, {Sarah N.} and Stitzer, {Michelle C.} and Brohammer, {Alex B.} and Peng Zhou and Noshay, {Jaclyn M.} and O'Connor, {Christine H.} and Hirsch, {Cory D.} and Jeffrey Ross-Ibarra and Hirsch, {Candice N.} and Springer, {Nathan M.}",

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Transposable elements contribute to dynamic genome content in maize

Abstract

Bibliographical note

Keywords

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