Evidence map›Paper›PMID 39901356›Full record

ArticlePlant biotechnology journal2025

Haplotype-resolved genome assembly provides new insights into the genomic origin of purple colour in Prunus mume.

Juan Meng, Ziwei Li, Haoning Wang, Runtian Miao, Xu Liu, Dapeng Miao, Chunxu Zhao, Guijia Wang, Tangren Cheng, Qixiang Zhang and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Plant biotechnology journal, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. A 32-bp deletion inHorticulture research · 2026
    Article
  2. Allele-specific methylation, and InDels ofHorticulture research · 2026
    Article
  3. Graph statistics theory of individualized quantitative genetics under haplotype-resolved genome assembly.Proceedings of the National Academy of Sciences of the United States of America · 2026
    Article
  4. A NAC family geneHorticulture research · 2025
    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

11 authors.

Juan Meng *State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China.
Ziwei Li *State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China.
Haoning WangState Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China.
Runtian MiaoState Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China.
Xu LiuState Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China.
Dapeng MiaoState Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China.
Chunxu ZhaoState Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China.
Guijia WangState Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China.
Tangren ChengState Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China.
Qixiang ZhangState Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China.ORCID https://orcid.org/0000-0001-5690-0065
Lidan SunState Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China.ORCID https://orcid.org/0000-0001-9577-7282

Funding

Beijing High-Precision Discipline Project, Discipline of Ecological Environment of Urban and Rural Human SettlementsForestry and Grassland Science and Technology Innovation Youth Top Talent Project of China 2020132608Fundamental Research Funds for the Central Universities QNTD202306
6 · The paper itself

Abstract

Prunus mume, an important ornamental woody plant in the Rosaceae family, contains many interspecific hybridizations. Purple colour is a breeding trait of aesthetic value for P. mume, but little is known about the origin and genetic architecture of this trait. Here we address these issues by producing a haplotype-resolved genome from an interspecific hybrid cultivar of P. mume (M) and P. cerasifera 'Pissardii' (C), named P. mume 'Meiren', followed by a detailed molecular characterization. The final length of the diploid genome is 499.47 Mb, with 250.66 Mb of haplotype M (HM) and 248.79 Mb of haplotype C (HC). Approximately 95.42% (476.61 Mb) of the phased assembly is further anchored to 16 homologous chromosomes. Based on the genomic variation, we identify a 1.8 Mb large-fragmented inversion (INV) on chromosome 1b of HC, which co-segregates with purple colour traits of 'Meiren' inherited from its purple C parent 'Pissardii'. We find that a MYB transcription factor, PmmMYB10.5b, resides at the distal breakpoint of the INV, which displays consistent allele-specific expression (ASE). By directly binding to the promoter of anthocyanin synthetic alleles, PmmMYB10.5b serves as a co-activator to promote anthocyanin accumulation in 'Meiren' organs. Notably, the INV identified in 'Meiren' is generated from 'Pissardii' rather than P. cerasifera, which alters the promoter sequence of PmmMYB10.5b, activates its expression and results in the purple colour trait. Results from this study shed light on the evolutionary origin of purple colour in 'Meiren' and could potentially provide guidance on the genetic improvement of colour traits in ornamental woody plants.

Indexed as

Genome, PlantHaplotypesPigmentationPrunusAnthocyaninsChromosomes, PlantColorPlant ProteinsAnthocyaninsPlant Proteinsgenetic architecturehaplotype genome assemblyinversionornamental plantPrunus mumepurple colour

Identifiers

PMID39901356
PMCPMC12018819

What Socratic 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 Socratic graph.