Introducing LocalSynteny in PGDD 2.0
March 30, 2026
We are excited to introduce LocalSynteny, a new feature in PGDD 2.0 that makes exploring gene collinearity across plant genomes more intuitive, flexible, and interactive. This tool allows users to analyze conserved genomic neighborhoods by simply entering a gene ID or uploading their own genome data, with built-in validation to ensure consistency between protein and annotation files . Powered by DIAMOND and MCScanX, LocalSynteny delivers fast and reliable synteny analysis across a wide range of species.
The platform provides a seamless workflow, enabling users to configure collinearity parameters, select multiple target genomes, and run analyses efficiently. Results are presented through an interactive visualization interface that supports features such as dark/light mode, adjustable spacing between genome tracks, alignment of colinear regions, and the ability to hide non-colinear genes for clearer interpretation . Users can also toggle links and labels to customize the display according to their needs and export high-quality figures in PNG or SVG format for downstream use.
By combining ease of use with powerful analytical capabilities, LocalSynteny enhances the ability to study gene evolution, duplication events, and functional conservation. This release represents a significant step forward in making synteny analysis more accessible and visually informative for the plant genomics community.