Differences in activity and stability drive transposable element variation in tropical and temperate maize

Area of Science:

• Genomics
• Plant Science
• Bioinformatics

Background:

• Transposable elements (TEs) are major drivers of genome variation across species.
• Understanding within-species TE variation is crucial for crop improvement.

Purpose of the Study:

• To develop and apply an algorithm for de novo transposable element annotation in a pangenome context.
• To investigate the extent and drivers of TE variation within maize species.

Main Methods:

• Developed panEDTA, an open-source algorithm for de novo TE annotation.
• Generated a unified TE annotation for a maize pangenome using 26 high-quality genomes.
• Analyzed methylome, transcriptome, LTR age, and insertional polymorphism data.

Main Results:

• Identified an excess of 35.1 Mb TE sequences per genome in tropical maize compared to temperate maize.
• Found that young, less methylated, and more expressed LTR retrotransposon families drive 64.7% of this variation.
• Observed enrichment of young LTR families near nucleotide-binding and leucine-rich repeat (NLR) clusters.

Conclusions:

• TEs, particularly LTR retrotransposons, significantly contribute to genome content variation between maize populations.
• TE activity, especially of young LTR families, is associated with differences in methylation and expression, and may play a role in maize disease resistance.