Advances in single-cell and spatial omics for studying symbiotic nitrogen fixation: comparative cellular and evolutionary perspectives.

Yan Shi, Huiru Liu, Weicai Yang, Jixian Zhai, Haifeng Wang

Abstract readReview

In one paragraph

Review in Genome biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing papers in PubMed

–field-weighted citation impact

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

5 authors.

Yan Shi *Yazhouwan National Laboratory, Sanya, Hainan, 572025, China.

Huiru Liu *Yazhouwan National Laboratory, Sanya, Hainan, 572025, China.

Weicai YangYazhouwan National Laboratory, Sanya, Hainan, 572025, China. yangweicai@yzwlab.cn.

Jixian ZhaiDepartment of Biology, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China. zhaijx@sustech.edu.cn.

Haifeng WangYazhouwan National Laboratory, Sanya, Hainan, 572025, China. wanghaifeng@yzwlab.cn.

Funding

Biological Breeding-National Science and Technology Major Project 2024ZD04079

6 · The paper itself

Abstract

Single-cell and spatial transcriptomics have revolutionized studies of symbiotic nitrogen fixation by resolving cellular heterogeneity, spatial gene-expression, and regulatory dynamics within root nodules. Recent investigations in model legumes have revealed conserved and species-specific programs controlling immune recognition, nodule development, and nitrogen-fixation metabolism. Integrating these datasets with single-cell epigenomic profiles, such as chromatin accessibility and three-dimensional genome architecture, provides new insight into epigenetic mechanisms that regulate key symbiotic genes. Comparative single-cell analyses across legumes and non-legumes elucidate phenotypic diversity and core regulatory networks of symbiotic nitrogen fixation at the cellular level, offering critical frameworks for engineering this process in non-legume crops.

Indexed as

Nitrogen FixationSingle-Cell AnalysisSymbiosisFabaceaeMultiomicsSingle-Cell Gene Expression AnalysisSpatial TranscriptomicsComparative multi-omicsNodulation-based nitrogen fixationSingle-cell transcriptomicsSpatial transcriptomics

Identifiers

PMID41814406

DOI10.1186/s13059-026-04024-y

PMCPMC13088453

What OpenQuestion holds

Textmetadata

LicenceCC BY-NC-ND

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.