Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.
Nucleic Acids Res. 2013 Jan;41(Database issue):D1152-8. doi: 10.1093/nar/gks1104. Epub 2012 Nov 24.
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.
基因组加倍（GD）永久性地塑造了许多高等真核生物基因组的结构和功能。由于被子植物（开花植物）具有染色体加倍甚至三倍的倾向，因此它们是阐明 GD 对高等真核生物影响的杰出模型。重复的基因组结构通常需要进行基因组内和基因组间的比对，以揭示其进化历史，这也为推断基因之间明显的和隐藏的同源性、旁系同源性和其他关系提供了手段。不断增加的被子植物基因组序列集为一系列研究基因和 GD 的功能和进化后果提供了基础。为了基于经过实证研究验证的统一标准，从单个资源中提供基因组比对，我们构建了植物基因组加倍数据库（PGDD；可在 http://chibba.agtec.uga.edu/duplication/ 免费获得），这是一个提供染色体之间共线性的同线性信息的网络服务。目前，PGDD 包含了 26 种植物的数据，包括苔藓植物和绿藻，以及具有草案基因组序列的被子植物。除了包含新的基因组外，我们还在准备新的功能来增强 PGDD。
