PGDD: a database of gene and genome duplication in plants - PubMed (original) (raw)
. 2013 Jan;41(Database issue):D1152-8.
doi: 10.1093/nar/gks1104. Epub 2012 Nov 24.
Affiliations
- PMID: 23180799
- PMCID: PMC3531184
- DOI: 10.1093/nar/gks1104
PGDD: a database of gene and genome duplication in plants
Tae-Ho Lee et al. Nucleic Acids Res. 2013 Jan.
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.
Figures
Figure 1.
Diagram of current PGDD server. (A) Diagram of pipeline to update PGDD with new genome data (in blue box). The boxes in the diagram represent four major steps of the pipeline, consisting of 18 in-house scripts. Insets in some boxes contain the name of a major program in the process. (B) Layers diagram of PGDD structure (in green polygon).
Figure 2.
Homepage and examples of three major functions of PGDD. (A) The homepage of PGDD and functions supported by the database. (B) Web page of Dot plot function and a plot applying a Ks filter of 0.4–0.7 between rice and sorghum as an example, representing colinear blocks between the plants. (C) Example of Locus-search result for AT1G25460 loci in Arabidopsis. A blue line in alignment image represents same orientations of paired genes, whereas the red line represents opposite orientations of the genes. (D) Example of Map-view function. The grey vertical bars represent chromosomes, and green arrows on the bars represent the position of locus, which are similar to input sequences. The detailed loci information page, the inset, shows protein and nucleotide sequences of gene in the loci and a description of the gene.
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