Abstract
Many plant physiological and developmental processes are controlled at the transcriptional level, and the differential expression of genes in specific organs/conditions can give clues about their function. Transcriptome analyses can be conducted in the absence of a complete reference genome, for example by sequencing expressed sequence tags or RNA sequencing. To enhance Medicago truncatula as model system Benedito et al. generated a gene expression atlas that provides a global view of gene expression in all major organ systems of this species, with special emphasis on nodule and seed development. The Atlas reveals massive differences in gene expression of key regulatory genes, such as transcription factor genes, which presumably orchestrate genetic reprogramming during development and differentiation. Bioinformatic and statistical analyses enabled in‐depth comparison, at a whole‐genome level, of gene expression in specific nodule zones. Lang and Long analyzed gene expression in nodules formed by wild‐type bacteria on six plant mutants with defects in nitrogen fixation.