PGDD 2.0: Plant Genome Duplication Database with updated content and tools

Polyploidy and small–scale duplication have repeatedly reshaped plant genomes, making synteny and colinearity indispensable for evolutionary inference. We present PGDD 2.0 (accessible at chibba.agtec.uga.edu and pgdd2.org), a major update to the Plant Genome Duplication Database (PGDD) that now aggregates >120 complete telomere-to-telomere (T2T) assemblies, including many chromosome–scale genomes spanning all major Viridiplantae lineages. Each genome sequence is processed with a standardized pipeline to call intra– and intergenomic colinear (syntenic) blocks, estimate Ks, and block score metrics and age distributions. PGDD 2.0 introduces (i) interactive synteny networks for pattern discovery across taxa, (ii) a “riparian” or synteny alignment view for visualizing mesosynteny and rearrangements, and (iii) an embedded SynVisio module for rendering user–supplied or PGDD-downloaded MCScanX results directly in the browser. Together, these advances support tasks from resolving ancient whole-genome duplication signatures to tracing the postduplication fates of specific gene families with T2T–level precision and beyond. PGDD 2.0 delivers an up–to–date, uniform, and user–centered platform for plant comparative genomics, accelerating discovery regarding polyploidy, gene duplication, and genome evolution.