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

Summary 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,...

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Veröffentlicht in:The New phytologist 2022-04, Vol.234 (2), p.634-649
Hauptverfasser: 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
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container_issue 2
container_start_page 634
container_title The New phytologist
container_volume 234
creator 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
description Summary 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.
doi_str_mv 10.1111/nph.18006
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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. 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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. 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source Wiley Free Content; MEDLINE; Wiley Online Library Journals Frontfile Complete; EZB-FREE-00999 freely available EZB journals
subjects Alfalfa
Angiosperms
Chromatin
comparative genomics
Complementation
conserved noncoding sequences (CNS)
Cytokinins
Fixing
Gene Expression Regulation, Plant
Gene regulation
Genes
Genomes
Genomics
Identification
Medicago truncatula
Medicago truncatula - microbiology
MtCRE1
Nitrogen
Nitrogen - metabolism
nitrogen fixation
Nitrogen Fixation - genetics
Nitrogen-fixing bacteria
Nodulation
Nutrients
Plant growth substances
Plant Proteins - genetics
Plant Proteins - metabolism
Plant Root Nodulation - genetics
Plant Sciences
Regulatory sequences
Root Nodules, Plant - microbiology
Sinorhizobium meliloti
Species
Symbionts
Symbiosis
Symbiosis - genetics
Transcription
Transcription factors
title Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen‐fixing clade
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