Tag: Computational Biology

Plants produce scores of specialized metabolites (SMs) to attract or repel the organisms around them and to cope with life in a variable environment. For thousands of years, we have been exploiting these compounds to feed, heal, and adorn us. Many more SMs remain to be discovered: the chemical constituents…

A promoter is a region that “determines the position, direction, frequency, and timing of transcription”.  A cell can decode the sequence of the promoter to ensure appropriate transcription, but we still can’t. Tokizawa et al. performed a large-scale survey of promoters by sequencing regions upstream…

Many legumes are important crops, and to date ten legume genomes have been sequenced, including soybean, common bean, mung bean, and two species of wild peanut. Wang et al. used hierarchical comparative genomics analysis of the ten legume genomes, which enabled them to detected gene colinearity between…

Due to its highly repetitive, polyploid genome, wheat genomics has lagged behind that of other cereals, but new tools promise to begin closing that gap.  Uauy reviews these new tools, which include access to full genomes of several wheat varieties, gene expression data from hundreds of publicly available…

The plethora of diverse leaf shapes results from variations of shared molecular mechanisms that govern leaf growth and development. To better understand the molecular underpinnings of diverse leaf morphologies, Runions et al. constructed a computational model of leaf development that included multiple…

The transcriptional response to auxin depends in large part on the interactions between ARF transcription factors and the Aux/IAA transcription inhibitors that interact with them. The crucial role of auxin in embryo patterning is revealed by the embryo patterning defects observed in mutants of ARF and…

A considerable knowledge gap remains between the plant genome and the plant metabolome. To address this, Schläpfer et al. have developed a computational pipeline to identify metabolic enzymes, pathways, and gene clusters. Although metabolic genes are known to cluster in bacteria and fungi, until recently…

The classic art of plant breeding involves carefully examining a genetically segregating population for traits of interest. Increasingly, high-throughput, automated phenotyping systems are being used; for example, robots can carry plants to imaging chambers for data collection. However, growth-chamber…