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

Nucleic Acids Res. 2026 Jan 6;54(D1):D1753-D1760. doi: 10.1093/nar/gkaf1287.

ABSTRACT

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.

PMID:41296551 | PMC:PMC12807773 | DOI:10.1093/nar/gkaf1287