Abstract
Genetic analyses of plant symbiotic mutants has led to the identification of key genes involved in Rhizobium-legume communication as well as in development and function of nitrogen fixing root nodules. However, the impact of these genes in coordinating the transcriptional programs of nodule development has only been studied in limited and isolated studies. Here, we present an integrated genome-wide analysis of transcriptome landscapes in Lotus japonicus wild-type and symbiotic mutant plants. Encompassing five different organs, five stages of the sequentially developed determinate Lotus root nodules, and eight mutants impaired at different stages of the symbiotic interaction, our data set integrates an unprecedented combination of organ- or tissue-specific profiles with mutant transcript profiles. In total, 38 different conditions sampled under the same well-defined growth regimes were included. This comprehensive analysis unravelled new and unexpected patterns of transcriptional regulation during symbiosis and organ development. Contrary to expectations, none of the previously characterized nodulins were among the 37 genes specifically expressed in nodules. Another surprise was the extensive transcriptional response in whole root compared to the susceptible root zone where the cellular response is most pronounced. A large number of transcripts predicted to encode transcriptional regulators, receptors and proteins involved in signal transduction, as well as many genes with unknown function, were found to be regulated during nodule organogenesis and rhizobial infection. Combining wild type and mutant profiles of these transcripts demonstrates the activation of a complex genetic program that delineates symbiotic nitrogen fixation. The complete data set was organized into an indexed expression directory that is accessible from a resource database, and here we present selected examples of biological questions that can be addressed with this comprehensive and powerful gene expression data set.
Highlights
Legumes constitute the third largest family (Fabaceae) of flowering plants and they are second only to grasses in their economic and nutritional importance
Mesorhizobium loti (M. loti) derived probe sets, each representing a known or predicted open reading frame (ORF) or miRNA. We used this platform to profile the transcriptome of roots, root nodules, stems, leaves and flowers and to identify Lotus genes defining the identity of the main legume organs
A special effort was devoted towards profiling the symbiotic interaction with the microsymbiont, M. loti, and development of root nodules
Summary
Legumes constitute the third largest family (Fabaceae) of flowering plants and they are second only to grasses in their economic and nutritional importance. Amino acid and ammonium exchange between the plant host and bacteria is important for symbiotic nitrogen fixation, and analyses of our data showed regulation of genes encoding proteins involved in glutamate and asparagine biosynthesis in 21 dpi nodules.
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