Transposable elements contribute to dynamic genome content in maize.

Area of Science:

• Genomics
• Molecular Biology
• Plant Science

Background:

• Transposable elements (TEs) are major components of eukaryotic genomes, influencing genome structure and content.
• Maize genomes are largely composed of TEs, making them a key focus for understanding genome variation.

Purpose of the Study:

• To develop and apply a method for identifying shared and variable transposable element insertions across multiple maize genome assemblies.
• To quantify the extent of TE-driven variation in genome organization and gene content among different maize genotypes.

Main Methods:

• Developed a novel approach for defining shared and variable TE insertions.
• Applied this method to four diverse maize genome assemblies (B73, W22, Mo17, PH207) with uniform TE structural annotations.
• Analyzed approximately 400,000 polymorphic TEs across the surveyed genomes.

Main Results:

• Identified approximately 400,000 polymorphic transposable elements (TEs), comprising 1.6 Gb of variable TE sequence across four maize genomes.
• Documented both recent transposition events and deletions of older TEs, distributed throughout the genome, including near genes.
• Found 2380 gene annotations in the B73 genome located within variable TEs, indicating TEs' role in gene content differences.

Conclusions:

• Transposable elements exhibit high variability in temperate maize genomes, significantly contributing to differences in genome organization and gene content.
• The identified polymorphic TEs provide insights into the dynamic nature of maize genomes and their evolution.
• This study highlights the critical role of TEs in shaping genomic diversity within maize populations.