CentriVision: An integrated platform for multiscale centromere analysis in plants

Area of Science:

• Genomics and Bioinformatics
• Molecular Biology
• Plant Science

Background:

• Centromeres are essential for chromosome segregation and genome stability.
• Telomere-to-telomere (T2T) assemblies highlight the importance of centromeric regions in genome-wide studies.
• Understanding centromere structure and evolution is crucial for genome research.

Purpose of the Study:

• To develop CentriVision, a bioinformatics platform for centromere analysis.
• To identify candidate centromeres, assess structural similarity, and decompose DNA repeat units.
• To explore relationships between sequence conservation and functional features, integrating with CENH3 ChIP-seq data.

Main Methods:

• Development of a modular bioinformatics platform, CentriVision.
• Utilized tools including editing-distance dotplots, heatmaps, and repeat monomer scanning.
• Integrated analyses with CENH3 ChIP-seq data for functional insights.

Main Results:

• CentriVision accurately identified diverse centromere organizational patterns in plants.
• Arabidopsis thaliana centromeres show conserved repeats potentially representing pre-centromeric sequences.
• Oryza sativa has two dominant repeat classes, Zea mays evolves a single dominant repeat unit, and Papaver setigerum exhibits a three-layered nested structure.

Conclusions:

• CentriVision provides a framework to connect repeat evolution, structural variation, and epigenomics.
• The study reveals species-specific centromere evolutionary trajectories.
• Findings advance understanding of plant centromere architecture, diversification, and function.