PGDD: A Database for Investigations into the Functional and Evolutionary Consequences of Gene and Genome Duplication, using Angiosperms as a Model

The structure and function of many higher eukaryotic genomes have been shaped by genome duplication (GD). For higher eukaryotes, outstanding models in which to elucidate consequences of genome duplication are the angiosperms (flowering plants), due to their propensity for chromosomal duplication or even triplication in a few cases. To unravel their evolutionary history, both intra- and inter-genome alignments are often used in duplicated genome structures, also providing the means to deduce both obvious and otherwise-cryptic orthology, paralogy, and other relationships among genes. Since the full genome sequence of Arabidopsis thaliana was determined, the burgeoning sets of angiosperm genome sequences provide the foundation for a host of investigations into the functional and evolutionary consequences of gene and genome duplication. To provide genome alignments based on uniform standards that have been validated by empirical studies, we built the Plant Genome Duplication Database (PGDD), a web service providing synteny information in terms of collinearity between chromosomes. At present, PGDD contains data for 26 plants including bryophytes and chlorophyta as well as angiosperms with draft genome sequences. In addition to the inclusion of new genomes as they become available, we are preparing new functions to enhance PGDD. The database is freely available at http://chibba.agtec.uga.edu/duplication/. For the last one year, PGDD has been utilized by researchers from 109 countries with a total of 762,365 accession logs (after removing those due to Web Bots).