Current Status and Future Development of the Plant Genome Duplication Database (PGDD)

Explosive growth in the availability of angiosperm genome sequences is necessitating the development of powerful software to gain maximum benefit from these sequences.  Angiosperm comparative genomics is especially challenging, in that genome duplications are more recent and more abundant than in most other eukaryotes. The availability of intra- and inter-genome alignments utilizing all available genomes, based on uniform standards that have been validated by empirical studies, is of central importance to angiosperm comparative genomics. PGDD is a public database to identify and catalog intra- or inter-genome syntenic relationships among plant genes, determined using MCscan which can simultaneously scan multiple genomes to identify homologous chromosomal regions and align these regions using genes as anchors.  In the PGDD, syntenic relationship are shown in various ways such as dot plots between (pseudo-) chromosomes, lists of syntenic genes, and figures depicting alignment of syntenic regions. The database also supports various ways to search specific syntenic regions. PGDD currently contains synteny data for 22 plants with available whole genome sequences (preferably assembled pseudomolecules with ordered gene models), including Brassica rapa published August 28 2011. In a recent 12-month period, PGDD was accessed 432,949 times, from 4,931 unique IP addresses in at least 81 countries. To better satisfy the opportunity to archive and compare many genomes, and to meet demands for new analysis functions and user interfaces, we have redesigned the database schema and are rewriting the program in Django web framework and jQuery. We will also add new functions such as multiple alignments of syntenic regions of intra- or inter-genomes, and color-coding of gene pairs in dot plots based on Ks.