A roadmap of cell-type specific gene expression during sequential stages of AM. Expression patterns of 1392 M. truncatula genes during four AM stages. Activated genes are shown in pink, repressed genes in green. Selected transcription factor genes (Figure 6) are highlighted. Group A: Genes with equal expression in APP and NAP that are induced by Myc-LCOs , thus probably activated before contact (stage I). Genes which were also expressed in mature mycorrhizal roots are listed. Group B: Genes induced in APP in comparison to NAP, thus being activated during initial intracellular infection (stage II). Genes also transcribed in mature mycorrhizal roots are listed. Group C: Genes with equal expression in all cell-types from mature mycorrhizal roots (ARB~CMR~EPI), induced in ARB and CMR alike (ARB+CMR) or being CMR-induced. Since these were not activated by Myc-LCOs or during appressorium formation, but induced in whole mycorrhizal roots (AM core set, ), they are probably activated during intraradical hyphal spread (stage III) and needed for general root colonization. Group D: Genes preferentially expressed in ARB. Whereas transcripts of 125 genes were not found in APP or NAP, 81 genes were only weakly expressed in APP or NAP, indicating specific or predominant activation during arbuscule formation (stage IV). Group E: Genes induced in ARB, and equally expressed in APP and NAP, thus undergoing an expression shift towards arbusculated cells. Group F: Genes induced in NAP in comparison to APP, thus being repressed upon infection. Group G: Genes exclusively induced in CMR or in CMR as well as EPI, thus being repressed during arbuscule formation. Abbreviations: LCOs, lipo-chitooligosaccharides; APP, appressorial areas; NAP, non-appressorial areas; ARB, cortical cells containing arbuscules; CMR, cortical cells from mycorrhizal roots; EPI, epidermal cells from mycorrhizal roots; ~, equal expression; ind, induced; exp, expressed; ne, not expressed.