Comparative Transcriptomics Reveals Distinct Transcription Factors and Hormone Action Pathways in Nodules and Lateral Roots of Soybean

Symbiotic legume nodules and lateral roots arise away from the root meristem via dedifferentiation events. While these organs share some morphological and developmental similarities, whether legume nodules are modified lateral roots is an open question. We identified genes enriched in emerging nodules, mature nodules, emerging lateral roots and young lateral roots in soybean by comparing global gene expression profiles between each of these organs and adjacent root segments. There was very little overlap in transcription factor expression profiles between emerging nodules and emerging lateral roots. Indeed, singular enrichment analysis indicated that cell division was the most common biological process between these organs. Expression profiles of key hormone biosynthesis and signaling genes were also distinct between nodules and lateral roots. While local auxin biosynthesis appeared to be active in both nodules and lateral roots, auxin signaling was markedly enriched in lateral roots. Conversely, genes associated with cytokinin biosynthesis and signaling were enriched in nodules compared to lateral roots. In addition, expression profiles of genes associated with gibberellin metabolism indicated that active gibberellin biosynthesis might occur in nodules. Members of genes families associated with shoot axillary meristem formation were enriched in nodules, but not lateral roots. These observations suggested that hormonal and developmental signaling pathways active during nodule development are more similar to that of shoot axillary meristems than lateral roots. In addition, we identified a number of novel transcribed regions in soybean and report an accurate set of nodule-specific genes using adjacent root tissues as control.