High-resolution genome assembly reveals retrotransposon-mediated centromere dynamics in rye

Area of Science:

• Plant genomics
• Epigenetics
• Molecular evolution

Background:

• Rye (Secale cereale) genomes feature large repetitive regions, including subtelomeric heterochromatin and retrotransposon-rich centromeres.
• These centromeric structures contrast with satellite-repeat-based centromeres found in most plant genome assemblies.
• Understanding these complex regions is crucial for rye genome architecture and evolution.

Purpose of the Study:

• To decode the architecture and evolution of rye's unique repetitive regions.
• To investigate centromere dynamics and chromatin regulation in rye.
• To provide a high-resolution genome assembly focusing on elusive genomic areas.

Main Methods:

• Utilized PacBio HiFi and Nanopore sequencing for chromosome-scale assembly.
• Generated a high-resolution assembly resolving subtelomeric heterochromatin and complete centromeres.
• Performed cross-species CENH3 ChIP-seq analyses in cultivated and wild rye.

Main Results:

• Identified terminal tandem repeat arrays influencing chromatin environments and retrotransposon deposition.
• Characterized rye centromeres with unique epigenetic signatures, including DNA hypomethylation.
• Found Cereba retrotransposons are key for CENH3 loading, suggesting a centromere evolution feedback loop.

Conclusions:

• Retrotransposons autonomously organize centromere chromatin and identity in rye, challenging satellite-DNA paradigms.
• Retrotransposons play a dual role in maintaining CENH3 recruitment and facilitating genomic innovation.
• This research advances functional genomics in Triticeae crops and opens avenues for centromere engineering.