A gene expression atlas of the model legume Medicago truncatula

Plant J. 2008 Aug;55(3):504-13. doi: 10.1111/j.1365-313X.2008.03519.x. Epub 2008 Apr 12.


Legumes played central roles in the development of agriculture and civilization, and today account for approximately one-third of the world's primary crop production. Unfortunately, most cultivated legumes are poor model systems for genomic research. Therefore, Medicago truncatula, which has a relatively small diploid genome, has been adopted as a model species for legume genomics. To enhance its value as a model, we have 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 between organs that are accompanied by changes in the expression of key regulatory genes, such as transcription factor genes, which presumably orchestrate genetic reprogramming during development and differentiation. Interestingly, many legume-specific genes are preferentially expressed in nitrogen-fixing nodules, indicating that evolution endowed them with special roles in this unique and important organ. Comparative transcriptome analysis of Medicago versus Arabidopsis revealed significant divergence in developmental expression profiles of orthologous genes, which indicates that phylogenetic analysis alone is insufficient to predict the function of orthologs in different species. The data presented here represent an unparalleled resource for legume functional genomics, which will accelerate discoveries in legume biology.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Cluster Analysis
  • Databases, Genetic*
  • Gene Expression Profiling
  • Gene Expression*
  • Genomics
  • Medicago truncatula / genetics*
  • Medicago truncatula / metabolism
  • Medicago truncatula / microbiology
  • Nitrogen Fixation
  • Oligonucleotide Array Sequence Analysis
  • Plant Leaves / genetics
  • Plant Leaves / metabolism
  • Plant Leaves / microbiology
  • Plant Roots / genetics
  • Plant Roots / metabolism
  • Plant Roots / microbiology
  • RNA, Messenger / metabolism
  • Root Nodules, Plant / genetics
  • Root Nodules, Plant / metabolism
  • Root Nodules, Plant / microbiology
  • Sinorhizobium meliloti / physiology
  • Species Specificity
  • Symbiosis


  • RNA, Messenger