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

doi:10.1111/nph.18006

Title: Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen–fixing clade

Journal Article · 27 January 2022 · New Phytologist

DOI: https://doi.org/10.1111/nph.18006 · OSTI ID:1975677

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University of Florida, Gainesville, FL (United States)
University of Wisconsin‐Madison, WI (United States)
Mississippi State University, Starkville, MS (United States)

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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Research Organization:: University of Florida, Gainesville, FL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0018247

OSTI ID:: 1975677

Journal Information:: New Phytologist, Journal Name: New Phytologist Journal Issue: 2 Vol. 234; ISSN 0028-646X

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
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Title: Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen–fixing clade

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