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

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, suggest...

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Autores principales: Pereira, Wendell J., Knaack, Sara, Chakraborty, Sanhita, Conde, Daniel, Folk, Ryan A., Triozzi, Paolo M., Balmant, Kelly M., Dervinis, Christopher, Schmidt, Henry W., Ané, Jean‐Michel, Roy, Sushmita, Kirst, Matias
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9302667/
https://www.ncbi.nlm.nih.gov/pubmed/35092309
http://dx.doi.org/10.1111/nph.18006
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author Pereira, Wendell J.
Knaack, Sara
Chakraborty, Sanhita
Conde, Daniel
Folk, Ryan A.
Triozzi, Paolo M.
Balmant, Kelly M.
Dervinis, Christopher
Schmidt, Henry W.
Ané, Jean‐Michel
Roy, Sushmita
Kirst, Matias
author_facet Pereira, Wendell J.
Knaack, Sara
Chakraborty, Sanhita
Conde, Daniel
Folk, Ryan A.
Triozzi, Paolo M.
Balmant, Kelly M.
Dervinis, Christopher
Schmidt, Henry W.
Ané, Jean‐Michel
Roy, Sushmita
Kirst, Matias
author_sort Pereira, Wendell J.
collection PubMed
description 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.
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spelling pubmed-93026672022-07-22 Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen‐fixing clade Pereira, Wendell J. Knaack, Sara Chakraborty, Sanhita Conde, Daniel Folk, Ryan A. Triozzi, Paolo M. Balmant, Kelly M. Dervinis, Christopher Schmidt, Henry W. Ané, Jean‐Michel Roy, Sushmita Kirst, Matias New Phytol Research 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. John Wiley and Sons Inc. 2022-02-21 2022-04 /pmc/articles/PMC9302667/ /pubmed/35092309 http://dx.doi.org/10.1111/nph.18006 Text en © 2022 The Authors New Phytologist © 2022 New Phytologist Foundation https://creativecommons.org/licenses/by-nc/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
spellingShingle Research
Pereira, Wendell J.
Knaack, Sara
Chakraborty, Sanhita
Conde, Daniel
Folk, Ryan A.
Triozzi, Paolo M.
Balmant, Kelly M.
Dervinis, Christopher
Schmidt, Henry W.
Ané, Jean‐Michel
Roy, Sushmita
Kirst, Matias
Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen‐fixing clade
title Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen‐fixing clade
title_full Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen‐fixing clade
title_fullStr Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen‐fixing clade
title_full_unstemmed Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen‐fixing clade
title_short Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen‐fixing clade
title_sort functional and comparative genomics reveals conserved noncoding sequences in the nitrogen‐fixing clade
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9302667/
https://www.ncbi.nlm.nih.gov/pubmed/35092309
http://dx.doi.org/10.1111/nph.18006
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