Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The...
To survive winter, many perennial plants become endodormant, a state of suspended growth maintained even in favorable growing environments. To understand vegetative bud endodormancy, we collected paradormant, endodormant, and ecodormant axillary buds from Populus trees growing under natural conditions. Of 44,441 Populus gene models analyzed using NimbleGen microarrays, we found...
BACKGROUND: Circadian clocks provide an adaptive advantage through anticipation of daily and seasonal environmental
changes. In plants, the central clock oscillator is regulated by several interlocking feedback loops. It was shown that a
substantial proportion of the Arabidopsis genome cycles with phases of peak expression covering the entire day.
Synchronized...
Now in its 10th year, the Gramene database (http://www.gramene.org) has grown from its primary focus on rice, the first fully-sequenced grass genome, to become a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice. Gramene began with...
Eucalypts are the world’s most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have
made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase
genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest...
Gramene (http://www.gramene.org) is a curated
online resource for comparative functional
genomics in crops and model plant species, currently
hosting 27 fully and 10 partially sequenced
reference genomes in its build number 38. Its
strength derives from the application of a phylogenetic
framework for genome comparison and the
use of ontologies...
A framework for understanding the synthesis and catalysis of metabolites and other biochemicals by proteins is crucial for unraveling the physiology of cells. To create such a framework for Zea mays L. subsp. mays (maize), we developed MaizeCyc, a metabolic network of enzyme catalysts, proteins, carbohydrates, lipids, amino acids, secondary...
Background: Functional annotations of large plant genome projects mostly provide information on gene function
and gene families based on the presence of protein domains and gene homology, but not necessarily in
association with gene expression or metabolic and regulatory networks. These additional annotations are necessary
to understand the physiology, development...
Comparative analysis of multiple angiosperm genomes has implicated gene duplication in the expansion and diversification of many gene families. However, empirical data and theory suggest that whole-genome and small-scale duplication events differ with respect to the types of genes preserved as duplicate pairs. We compared gene duplicates resulting from a...
Background: DNA cytosine methylation is an epigenetic modification that has been implicated in many biological processes. However, large-scale epigenomic studies have been applied to very few plant species, and variability in methylation among specialized tissues and its relationship to gene expression is poorly understood.
Results: We surveyed DNA methylation from...