Data from: Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses

  • Robin van Velzen (Creator)
  • Rens Holmer (Creator)
  • F. Bu (Creator)
  • L.J.J. Rutten (Creator)
  • A.L. van Zeijl (Creator)
  • W. Liu (Creator)
  • L. Santuari (Creator)
  • Q. Cao Beijing University of Agriculture (Creator)
  • Trupti Sharma (Creator)
  • D. Shen (Creator)
  • Yuda Roswanjaya (Creator)
  • Titis Wardhani (Creator)
  • M. Seifi Kalhor (Creator)
  • joelle jansen (Creator)
  • D.J. van den Hoogen (Creator)
  • Berivan Gungor (Creator)
  • Marijke Hartog (Creator)
  • Jan Hontelez (Creator)
  • J.W.G. Verver (Creator)
  • Wei-Cai Yang (Creator)
  • Elio Schijlen (Creator)
  • rimi repin (Creator)
  • M. Schilthuizen (Creator)
  • Eric Schranz (Creator)
  • Renze Heidstra (Creator)
  • Kana Miyata (Creator)
  • E. Fedorova (Creator)
  • Wouter Kohlen (Creator)
  • Ton Bisseling (Creator)
  • Sandra Smit (Creator)
  • Rene Geurts (Creator)



Nodules harboring nitrogen-fixing rhizobia are a well-known trait of legumes, but nodules also occur in other plant lineages, with rhizobia or the actinomycete Frankia as microsymbiont. It is generally assumed that nodulation evolved independently multiple times. However, molecular-genetic support for this hypothesis is lacking, as the genetic changes underlying nodule evolution remain elusive. We conducted genetic and comparative genomics studies by using Parasponia species (Cannabaceae), the only nonlegumes that can establish nitrogen-fixing nodules with rhizobium. Intergeneric crosses between Parasponia andersonii and its nonnodulating relative Trema tomentosa demonstrated that nodule organogenesis, but not intracellular infection, is a dominant genetic trait. Comparative transcriptomics of P. andersonii and the legume Medicago truncatula revealed utilization of at least 290 orthologous symbiosis genes in nodules. Among these are key genes that, in legumes, are essential for nodulation, including NODULE INCEPTION (NIN) and RHIZOBIUM-DIRECTED POLAR GROWTH (RPG). Comparative analysis of genomes from three Parasponia species and related nonnodulating plant species show evidence of parallel loss in nonnodulating species of putative orthologs of NIN, RPG, and NOD FACTOR PERCEPTION. Parallel loss of these symbiosis genes indicates that these nonnodulating lineages lost the potential to nodulate. Taken together, our results challenge the view that nodulation evolved in parallel and raises the possibility that nodulation originated ∼100 Mya in a common ancestor of all nodulating plant species, but was subsequently lost in many descendant lineages. This will have profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants
Date made available3 May 2018
PublisherWageningen University & Research

Research Output

Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses

van Velzen, R., Holmer, R., Bu, F., Rutten, L. J. J., van Zeijl, A. L., Liu, W., Santuari, L., Cao, Q., Sharma, T., Shen, D., Purwana Roswanjaya, Y., Wardhani, T., Seifi Kalhor, M., Jansen, J., van den Hoogen, D. J., Güngör, B., Hartog, M. V., Hontelez, J., Verver, J., Yang, W-C. & 11 others, Schijlen, E. G. W. M., Repin, R., Schilthuizen, M., Schranz, M. E., Heidstra, R., Miyata, K., Fedorova, E., Kohlen, W., Bisseling, A. H. J., Smit, S. & Geurts, R., 15 May 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 20, p. E4700-E4709

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
  • 56 Citations (Scopus)

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    van Velzen, R. (Creator), Holmer, R. (Creator), Bu, F. (Creator), Rutten, L. J. J. (Creator), van Zeijl, A. L. (Creator), Liu, W. (Creator), Santuari, L. (Creator), Cao, Q. (Creator), Sharma, T. (Creator), Shen, D. (Creator), Roswanjaya, Y. (Creator), Wardhani, T. (Creator), Seifi Kalhor, M. (Creator), Jansen, J. (Creator), van den Hoogen, D. J. (Creator), Gungor, B. (Creator), Hartog, M. V. (Creator), Hontelez, J. (Creator), Verver, J. W. G. (Creator), Yang, W. (Creator), Schijlen, E. G. W. M. (Creator), Repin, R. (Creator), Schilthuizen, M. (Creator), Schranz, M. E. (Creator), Heidstra, R. (Creator), Miyata, K. (Creator), Fedorova, E. (Creator), Kohlen, W. (Creator), Bisseling, A. H. J. (Creator), Smit, S. (Creator), Geurts, R. (Creator) (3 May 2018). Data from: Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses. Wageningen University & Research. 10.5061/dryad.fq7gv88