MedicCyc: a biochemical pathway database for Medicago truncatula

Recent Advances in Medicago truncatula Genomics

Legume rotation has allowed a consistent increase in crop yield and consequently in human population since the antiquity. Legumes will also be instrumental in our ability to maintain the sustainability of our agriculture while facing the challenges of increasing food and biofuel demand. Medicago truncatula and Lotus japonicus have emerged during the last decade as two major model systems for legume biology. Initially developed to dissect plant-microbe symbiotic interactions and especially legume nodulation, these two models are now widely used in a variety of biological fields from plant physiology and development to population genetics and structural genomics. This review highlights the genetic and genomic tools available to the M. truncatula community. Comparative genomic approaches to transfer biological information between model systems and legume crops are also discussed.

Challenges in plant cellular pathway reconstruction based on gene expression profiling

Microarrays are used to profile transcriptional activity, providing global cell biology insight. Particularly for plants, interpretation of transcriptional profiles is challenging because many genes have unknown functions. Furthermore, many plant gene sequences do not have clear homologs in other model organisms. Fortunately, over the past five years, various tools that assist plant scientists have been developed. Here, we evaluate the currently available in silico tools for reconstruction of cellular (metabolic, biochemical and signal transduction) pathways based on plant gene expression datasets. Furthermore, we show how expression-profile comparison at the level of these various cellular pathways contributes to the postulation of novel hypotheses which, after experimental verification, can provide further insight into decisive elements that have roles in cellular processes.