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Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen-fixing clade.

Wendell J Pereira1, Sara Knaack2, Sanhita Chakraborty3

  • 1School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL, 32611, USA.

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|January 29, 2022
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Summary

Researchers identified conserved noncoding sequences (CNS) crucial for root-nodule symbiosis (RNS) evolution in nitrogen-fixing plants. These CNS regulate key genes, like MtCRE1, essential for establishing nitrogen-fixing bacterial interactions.

Keywords:
Medicago truncatulaMtCRE1comparative genomicsconserved noncoding sequences (CNS)nitrogen fixationnodulation

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Area of Science:

  • Plant biology
  • Evolutionary genetics
  • Microbial symbiosis

Background:

  • Nitrogen is a key nutrient, but its fixation by plants is limited to specific species via root-nodule symbiosis (RNS).
  • The evolutionary origins of RNS are linked to a specific angiosperm clade, suggesting a critical genetic event.
  • Understanding the genetic regulation of RNS is vital for improving nitrogen utilization in agriculture.

Purpose of the Study:

  • To identify conserved noncoding sequences (CNS) involved in the evolution of RNS.
  • To investigate the regulatory role of CNS in genes essential for nodulation.

Main Methods:

  • Genomic analysis of 25 nodulating species to identify conserved noncoding sequences (CNS) within the nitrogen-fixing clade (NFC).
  • Chromatin accessibility assays to correlate CNS with gene regulation in response to lipochitooligosaccharides (LCOs) in Medicago truncatula.
  • Genetic complementation experiments to assess the function of specific CNS in regulating the MtCRE1 gene.

Main Results:

  • Identified 3091 CNS in the NFC, with 452 showing significant correlation with LCO-responsive gene regulation.
  • Discovered 38 CNS near 19 known RNS genes, including five upstream of MtCRE1, a key nodulation regulator.
  • Demonstrated that these five CNS are essential for MtCRE1 expression and nodulation, as shown by genetic complementation of an Mtcre1 mutant.

Conclusions:

  • Conserved noncoding sequences in the NFC harbor regulatory elements critical for the evolution and function of root-nodule symbiosis.
  • The identified CNS, particularly those near MtCRE1, play a vital role in regulating gene expression necessary for establishing nitrogen-fixing symbioses.
  • These findings provide insights into the genetic underpinnings of RNS and could inform strategies for enhancing nitrogen fixation in crops.