Co-Expression Network Analysis of Nodule Development in Soybean

Symbiotic nitrogen fixation (SNF) provides about 40-60 million tons of nitrogen for agricultural systems each year in an ecofriendly manner. Legumes are not only an important class of world-wide crops but also can form nodules by intimate symbioses with rhizobia to fix atmospheric nitrogen. What happens for SNF during the legume evolution is an outstanding question in evolutionary developmental biology. Systematic biology will focus on the multiple-genes relationship to elaborate the mechanisms at the level of organism. With the era of the high-throughput sequencing, the explosive genomic and transcriptomics data available from public database lay a foundation for systematic biology and comparative genomics.

 Following a rule of “guilt by association”, genes with similar expression patterns are thought to typically function in a similar way or function in the same pathway. We established a global gene co-expression network with the latest and various microarrays and mined a nodule-specific module. Using the genomic-sequencing plants, covering the algae, early land plant, gymnosperms, early flowering plants, monocots and dicots, we demonstrated the route of evolution for the genes from nodule-specific module. Comparative analysis of the co-expression networks from multiple plant species, we found the nodule module specifically exists in the legumes. We also found that there are both conserved co-expressed genes and specific-evolved genes for different legumes, indicating the complex co-evolution of legumes communicated with the rhizobia. These data provide novel insights into the evolution for the leguminous nodulation.