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

Research output: Contribution to journalArticle

2 Citations (Scopus)

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 languageEnglish (US)
Pages (from-to)1052-1065
Number of pages14
JournalPlant Journal
Volume100
Issue number5
DOIs
StatePublished - Dec 1 2019

Fingerprint

DNA Transposable Elements
transposons
Zea mays
Genome
genome
corn
genes
Genome Components
Genes
genome assembly
Molecular Sequence Annotation
transposition (genetics)

Keywords

  • Zea mays
  • comparative genomics
  • gene content variation
  • transposable elements

Cite this

Anderson, S. N., Stitzer, M. C., Brohammer, A. B., Zhou, P., Noshay, J. M., O'Connor, C. H., ... Springer, N. M. (2019). Transposable elements contribute to dynamic genome content in maize. Plant Journal, 100(5), 1052-1065. https://doi.org/10.1111/tpj.14489

Transposable elements contribute to dynamic genome content in maize. / Anderson, Sarah N.; Stitzer, Michelle C.; Brohammer, Alex B.; Zhou, Peng; Noshay, Jaclyn M.; O'Connor, Christine H.; Hirsch, Cory D.; Ross-Ibarra, Jeffrey; Hirsch, Candice N.; Springer, Nathan M.

In: Plant Journal, Vol. 100, No. 5, 01.12.2019, p. 1052-1065.

Research output: Contribution to journalArticle

Anderson, SN, Stitzer, MC, Brohammer, AB, Zhou, P, Noshay, JM, O'Connor, CH, Hirsch, CD, Ross-Ibarra, J, Hirsch, CN & Springer, NM 2019, 'Transposable elements contribute to dynamic genome content in maize', Plant Journal, vol. 100, no. 5, pp. 1052-1065. https://doi.org/10.1111/tpj.14489
Anderson SN, Stitzer MC, Brohammer AB, Zhou P, Noshay JM, O'Connor CH et al. Transposable elements contribute to dynamic genome content in maize. Plant Journal. 2019 Dec 1;100(5):1052-1065. https://doi.org/10.1111/tpj.14489
Anderson, Sarah N. ; Stitzer, Michelle C. ; Brohammer, Alex B. ; Zhou, Peng ; Noshay, Jaclyn M. ; O'Connor, Christine H. ; Hirsch, Cory D. ; Ross-Ibarra, Jeffrey ; Hirsch, Candice N. ; Springer, Nathan M. / Transposable elements contribute to dynamic genome content in maize. In: Plant Journal. 2019 ; Vol. 100, No. 5. pp. 1052-1065.
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