Evidence map›Paper›PMID 40380089›Full record

ArticleBMC genomics2025

Common bean pan-genome reveals abundant variation patterns and relationships of stress response genes and pathways.

Xu Wang, Ming Yan, Shanshan Cui, Fang Li, Qingqing Zhao, Qingnan Wang, Bin Jiang, Yixin Huang, Yang Sun, Xiangdong Kong

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2025. 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
–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

3 citing papers in PubMed.

  1. Genome evolution through polyploidy: Enhancing plant stress resilience in agriculture.Proceedings of the National Academy of Sciences of the United States of America · 2026
    Review
  2. Review
  3. Integration of crop modeling and sensing into molecular breeding for nutritional quality and stress tolerance.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025
    Review
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

10 authors.

Xu WangAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China.
Ming YanAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China.
Shanshan CuiAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China.
Fang LiAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China.
Qingqing ZhaoAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China.
Qingnan WangAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China.
Bin JiangAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China.
Yixin HuangCollaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Founded By Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui, China.
Yang SunAnhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China. 2018259@ahnu.edu.cn.
Xiangdong KongJiguangGene Biotechnology Co. Ltd, Nanjing, China. xdkong@zju.edu.cn.

Funding

Major Science and Technology Projects in Anhui Province 202003a06020009National Natural Science Foundation of China 32100352, 32100355, 31871964National Science & Technology Fundamental Resources Investigation Program of China 2019FY101800Natural Science Foundation of Universities of Anhui Province KJ2020A0094Natural Science Fund of Anhui Province 1908085QC93
6 · The paper itself

Abstract

Long-term geographical isolation and the different directions of domestication can cause a large number of genome variations. Population genetic analysis based on a single reference genome cannot capture all the variation information. Pan-genome construction is an effective way to overcome this problem. Resequencing data from 683 common bean landraces and breeding lines provided a pan-genome construction data resource. For the first time, for common bean pan-genome construction, 305 Mb non-reference contigs and 10,452 novel genes were identified. Among these new genes, 373 resistance gene analogs containing 372 variable genes were identified and used to narrow down the candidate genes in Pseudomonas syringae pv. phaseolicola resistance quantitative trait locus interval of the common bean. Transcriptome analysis of multiple biotic and abiotic stresses reveals that gene expression patterns are organ-, stress-, and gene conservation-specific. Core and shell genes may be co-expressed in all samples and may have functional complementarity to maintain the stability of plant growth. Within pathways, 8990 and 30,272 mutual exclusivity and co-occurrence gene presence-absence variations (PAVs) were discovered respectively, providing further insights into the functional complementarity of genes. In conclusion, our study provides a comprehensive genome resource, which will be useful for further common bean breeding and study.

Indexed as

Genetic VariationGenome, PlantPhaseolusStress, PhysiologicalDisease ResistanceGene Expression ProfilingGene Expression Regulation, PlantPseudomonas syringaeQuantitative Trait LociCommon beanMutual exclusivityPan-genomePresence-absence variationsResistance gene analogs

Identifiers

PMID40380089
PMCPMC12084947

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.