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

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 rearrangem

SUBMITTER: Sharma A 

PROVIDER: S-EPMC12807773 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature