Evidence map›Paper›PMID 35092309›Full record

ArticleThe New phytologist2022

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 and 2 more

Open access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in The New phytologist, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
1.3field-weighted citation impact, top 18% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed, 7 citations in OpenAlex.

  1. Article
  2. Article
  3. Identification of clade-wide putativeHorticulture research · 2023
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors at 3 institutions in 1 country.

Wendell J PereiraSchool of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL, 32611, USA.ORCID 0000-0003-1019-6281
Sara KnaackWisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA.ORCID 0000-0002-1178-2517
Sanhita ChakrabortyDepartment of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.ORCID 0000-0001-7991-3977
Daniel CondeSchool of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL, 32611, USA.ORCID 0000-0001-8362-4190
Ryan A FolkDepartment of Biological Sciences, Mississippi State University, Starkville, MS, 39762, USA.ORCID 0000-0002-5333-9273
Paolo M TriozziSchool of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL, 32611, USA.ORCID 0000-0003-0192-3336
Kelly M BalmantSchool of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL, 32611, USA.
Christopher DervinisSchool of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL, 32611, USA.ORCID 0000-0002-2176-4232
Henry W SchmidtSchool of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL, 32611, USA.ORCID 0000-0003-3917-3219
Jean-Michel AnéDepartment of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.ORCID 0000-0002-3128-9439
Sushmita RoyWisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA.ORCID 0000-0002-3694-1705
Matias KirstSchool of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, FL, 32611, USA.ORCID 0000-0002-8186-3945
University of Florida · USUniversity of Wisconsin–Madison · USMississippi State University · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

Medicago truncatulaSinorhizobium melilotiGene Expression Regulation, PlantGenomicsNitrogenNitrogen FixationPlant ProteinsPlant Root NodulationRoot Nodules, PlantSymbiosisNitrogenPlant Proteinscomparative genomicsconserved noncoding sequences (CNS)Medicago truncatulaMtCRE1nitrogen fixationnodulation

Identifiers

PMID35092309
PMCPMC9302667
OpenAlexW4210519461

What OpenQuestion holds

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LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.