PGDD: a database of gene and genome duplication in plants

By Tae-Ho Lee, Haibao Tang, Xiyin Wang, Andrew H. Paterson. Nucleic Acids Res., 2012

558 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/3c6f5e21e46ccdb21a47f02feeb743d0331d618c

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. B. Mueller‐Roeber
2. Melissa D. Lehti-Shiu
3. Y. Van de Peer
4. Nicholas Panchy
5. Shin-Han Shiu

In Plant Science

1. Melissa D. Lehti-Shiu
2. Y. Van de Peer
3. Nicholas Panchy
4. Shin-Han Shiu

Citations in the corpus

• Evolution of Gene Duplication in Plants1[OPEN] (2016, background): “…(WGD) has occurred multiple times over the past 200 million years of angiosperm evolution (Lyons et al., 2008; Soltis et al., 2009, 2014; Lee et al., 2013; Renny-Byfield andWendel, 2014), and genomic sequencing continues to reveal new events (Velasco et al., 2010; D’Hont et al., 2012;…”
• PLAZA 3.0: an access point for plant comparative genomics (2014, background): “The latter are usually remnants of large-scale duplication events and various studies have revealed that traces of WGDs are present in all plant genomes sequenced to date (49).”