Dissection of symbiosis and organ development by integrated transcriptome analysis of lotus japonicus mutant and wild-type plants

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  • Niels Høgslund, Denmark
  • Simona Radutoiu
  • Lene Krusell, Denmark
  • Vera Voroshilova, Max-Planck-Institute for Molecular Plant Physiology, Germany
  • Matthew A Hannah, Max-Planck-Institute for Molecular Plant Physiology, Germany
  • Nicolas Goffard, ARC Centre of Excellence for Integrative Legume Research, Genomic Interactions Group, Research School of Biological Sciences, Australian National University, Australia
  • Diego H Sanchez, Max-Planck-Institute for Molecular Plant Physiology, Germany
  • Felix Lippold, Max-Planck-Institute for Molecular Plant Physiology, Germany
  • Thomas Ott, Max-Planck-Institute for Molecular Plant Physiology, Germany
  • Shusei Sato, Kazusa DNA Research Institute, Japan
  • Satoshi Tabata, Kazusa DNA Research Institute, Japan
  • Poul Liboriussen, Denmark
  • Gitte Vestergaard Lohmann, Denmark
  • Leif Schauser, Denmark
  • Georg F Weiller, ARC Centre of Excellence for Integrative Legume Research, Genomic Interactions Group, Research School of Biological Sciences, Australian National University, Australia
  • Michael K Udvardi, Max-Planck-Institute for Molecular Plant Physiology, Germany
  • Jens Stougaard
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.
Original languageEnglish
JournalP L o S One
Volume4
Issue8
Pages (from-to)e6556
Number of pages14
ISSN1932-6203
DOIs
Publication statusPublished - 7 Aug 2009

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