Transposable elements contribute to dynamic genome content in maize

The Plant Journal : for Cell and Molecular Biology
Sarah N AndersonNathan M. Springer

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 driv...Continue Reading

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Citations

Sep 12, 2019·G3 : Genes - Genomes - Genetics·Sarah N AndersonNathan M Springer
Oct 2, 2019·The New Phytologist·Philippa Borrill
Jan 23, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Jia YuLi Pu
Mar 18, 2020·G3 : Genes - Genomes - Genetics·Stefania VendraminKaren M McGinnis
Jul 8, 2020·Genome Biology·Rajiv K ParvathaneniAndrea L Eveland
Nov 27, 2020·Nature·Murukarthick JayakodiNils Stein
Jan 8, 2021·Journal of Plant Physiology·Mahendar ThudiRajeev K Varshney
Nov 21, 2020·The Plant Genome·Muhammad Tahir Ul QamarLing-Ling Chen
Jan 6, 2021·Genome Biology·Rafael Della ColettaCandice N Hirsch
Feb 3, 2020·Current Opinion in Plant Biology·Saima Shahid, R Keith Slotkin
Apr 2, 2021·G3 : Genes - Genomes - Genetics·Peri A TobiasRobert F Park
Jun 5, 2021·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Anahí Mara Yañez-SantosJuan Domingo Urdampilleta
Sep 23, 2021·Nucleic Acids Research·David RoquisEtienne Bucher

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