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The New phytologist
04, 2022;234 (2): 634-649.

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

Wendell J Pereira, Sara Knaack, Sanhita Chakraborty, Daniel Conde, Ryan A Folk, Paolo M Triozzi, Kelly M Balmant, Christopher Dervinis, Henry W Schmidt, Jean-Michel Ané, Sushmita Roy, Matias Kirst
Author Information
  1. Wendell J Pereira: School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL, 32611, USA. ORCID
  2. Sara Knaack: Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA. ORCID
  3. Sanhita Chakraborty: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA. ORCID
  4. Daniel Conde: School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL, 32611, USA. ORCID
  5. Ryan A Folk: Department of Biological Sciences, Mississippi State University, Starkville, MS, 39762, USA. ORCID
  6. Paolo M Triozzi: School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL, 32611, USA. ORCID
  7. Kelly M Balmant: School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL, 32611, USA.
  8. Christopher Dervinis: School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL, 32611, USA. ORCID
  9. Henry W Schmidt: School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL, 32611, USA. ORCID
  10. Jean-Michel Ané: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA. ORCID
  11. Sushmita Roy: Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA. ORCID
  12. Matias Kirst: School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL, 32611, USA. ORCID
PMID: 35092309 DOI: 10.1111/nph.18006

Abstract

Nitrogen is one of the most inaccessible plant nutrients, but certain species have overcome this limitation by establishing symbiotic interactions with nitrogen-fixing bacteria in the root nodule. This root-nodule symbiosis (RNS) is restricted to species within a single clade of angiosperms, suggesting a critical, but undetermined, evolutionary event at the base of this clade. To identify putative regulatory sequences implicated in the evolution of RNS, we evaluated the genomes of 25 species capable of nodulation and identified 3091 conserved noncoding sequences (CNS) in the nitrogen-fixing clade (NFC). We show that the chromatin accessibility of 452 CNS correlates significantly with the regulation of genes responding to lipochitooligosaccharides in Medicago truncatula. These included 38 CNS in proximity to 19 known genes involved in RNS. Five such regions are upstream of MtCRE1, Cytokinin Response Element 1, required to activate a suite of downstream transcription factors necessary for nodulation in M. truncatula. Genetic complementation of an Mtcre1 mutant showed a significant decrease of nodulation in the absence of the five CNS, when they are driving the expression of a functional copy of MtCRE1. CNS identified in the NFC may harbor elements required for the regulation of genes controlling RNS in M. truncatula.

Keywords

Medicago truncatula MtCRE1 comparative genomics conserved noncoding sequences (CNS) nitrogen fixation nodulation

Associated Data

figshare | 10.6084/m9.figshare.17124287

References

Science. 2018 Jul 13;361(6398): [PMID: 29794220]
Nature. 2019 Oct;574(7780):679-685 [PMID: 31645766]
Nucleic Acids Res. 2020 Jan 8;48(D1):D1104-D1113 [PMID: 31701126]
Plant Physiol. 2012 Dec;160(4):2155-72 [PMID: 23077241]
Plant Cell. 2020 Jan;32(1):15-41 [PMID: 31649123]
Curr Biol. 2019 Nov 4;29(21):3657-3668.e5 [PMID: 31543454]
Plant Cell. 2014 Mar;26(3):946-61 [PMID: 24681619]
Plant Mol Biol. 2000 Jan;42(1):181-94 [PMID: 10688136]
Curr Opin Plant Biol. 2009 Apr;12(2):126-32 [PMID: 19249238]
Plant Physiol. 2016 Jul;171(3):2256-76 [PMID: 27217496]
Plant J. 2011 Feb;65(4):622-33 [PMID: 21244535]
Nat Commun. 2014 Jun 10;5:4087 [PMID: 24912610]
PLoS One. 2011;6(12):e28819 [PMID: 22205972]
Nature. 2010 Jan 14;463(7278):178-83 [PMID: 20075913]
Genome Res. 2021 Jul;31(7):1245-1257 [PMID: 34045362]
PLoS One. 2011 Feb 18;6(2):e16765 [PMID: 21364738]
Development. 2010 Dec;137(24):4317-25 [PMID: 21098572]
Genome Res. 2005 Aug;15(8):1034-50 [PMID: 16024819]
Sci Rep. 2017 Aug 24;7(1):9384 [PMID: 28839170]
Nucleic Acids Res. 1985 Aug 26;13(16):5965-76 [PMID: 2994020]
Nat Plants. 2018 Dec;4(12):1017-1025 [PMID: 30397259]
Plant Signal Behav. 2011 Oct;6(10):1510-4 [PMID: 21904113]
BMC Biol. 2022 Nov 9;20(1):252 [PMID: 36352404]
New Phytol. 2020 Jul;227(2):513-528 [PMID: 32187696]
Proc Natl Acad Sci U S A. 2018 May 15;115(20):E4700-E4709 [PMID: 29717040]
Nucleic Acids Res. 2011 Mar;39(4):e23 [PMID: 21109538]
Am J Bot. 2018 Mar;105(3):291-301 [PMID: 29603143]
Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9 [PMID: 14500911]
Mol Plant Microbe Interact. 2021 Aug;34(8):904-921 [PMID: 33819071]
Plant J. 2005 Nov;44(3):505-15 [PMID: 16236159]
Genome Res. 2011 Mar;21(3):487-93 [PMID: 21209072]
Plant Cell. 2014 Jul;26(7):2729-45 [PMID: 24989046]
Plant Signal Behav. 2019;14(6):1598730 [PMID: 30931725]
New Phytol. 2021 Mar;229(5):2525-2534 [PMID: 33067828]
Plant Cell. 2014 Dec;26(12):4680-701 [PMID: 25527707]
Plant Physiol. 2018 Apr;176(4):3003-3026 [PMID: 29440269]
Methods Mol Biol. 2019;1962:227-245 [PMID: 31020564]
Genome Biol Evol. 2018 Feb 1;10(2):473-488 [PMID: 29378032]
Nat Genet. 2013 Aug;45(8):891-8 [PMID: 23817568]
ACS Synth Biol. 2014 Nov 21;3(11):839-43 [PMID: 24933124]
Plant Physiol. 2015 Sep;169(1):233-65 [PMID: 26175514]
Nature. 2020 Nov;587(7833):246-251 [PMID: 33177663]
Mol Plant Microbe Interact. 2001 Jun;14(6):695-700 [PMID: 11386364]
Plant Cell. 2019 Jan;31(1):68-83 [PMID: 30610167]
Proc Natl Acad Sci U S A. 1995 Mar 28;92(7):2647-51 [PMID: 7708699]
Science. 2006 Nov 3;314(5800):786 [PMID: 17082449]
Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):7383-8 [PMID: 12771380]
Nucleic Acids Res. 2012 Jan;40(Database issue):D1178-86 [PMID: 22110026]
Genome Biol. 2015 May 21;16:106 [PMID: 25994148]
Nucleic Acids Res. 2018 Jan 4;46(D1):D1190-D1196 [PMID: 29069403]
PLoS Genet. 2006 Oct 13;2(10):e168 [PMID: 17040131]
Plant Cell. 2006 Oct;18(10):2680-93 [PMID: 17028204]
Nucleic Acids Res. 2017 Jan 4;45(D1):D1040-D1045 [PMID: 27924042]

MeSH Term

Gene Expression Regulation, Plant
Genomics
Medicago truncatula
Nitrogen
Nitrogen Fixation
Plant Proteins
Plant Root Nodulation
Root Nodules, Plant
Sinorhizobium meliloti
Symbiosis

Chemicals

Plant Proteins
Nitrogen
Journal Article Research Support, U.S. Gov't, Non-P.H.S.

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