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PGDD: a database of gene and genome duplication in plants.

TitlePGDD: a database of gene and genome duplication in plants.
Publication TypeJournal Article
Year of Publication2013
AuthorsLee, T. - H., Tang H., Wang X., & Paterson A. H.
JournalNucleic acids research
Volume41
IssueDatabase issue
PaginationD1152-8
Date Published2013 Jan
ISSN1362-4962
KeywordsAngiosperms, Chromosome Mapping, Databases, Genetic, Genes, Duplicate, Genes, Plant, Genome, Plant, Internet
Abstract

Genome duplication (GD) has permanently shaped the architecture and function of many higher eukaryotic genomes. The angiosperms (flowering plants) are outstanding models in which to elucidate consequences of GD for higher eukaryotes, owing to their propensity for chromosomal duplication or even triplication in a few cases. Duplicated genome structures often require both intra- and inter-genome alignments to unravel their evolutionary history, also providing the means to deduce both obvious and otherwise-cryptic orthology, paralogy and other relationships among genes. The burgeoning sets of angiosperm genome sequences provide the foundation for a host of investigations into the functional and evolutionary consequences of gene and GD. To provide genome alignments from a single resource based on uniform standards that have been validated by empirical studies, we built the Plant Genome Duplication Database (PGDD; freely available at http://chibba.agtec.uga.edu/duplication/), a web service providing synteny information in terms of colinearity 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.

DOI10.1093/nar/gks1104
Alternate JournalNucleic Acids Res.
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