Evidence map›Paper›PMID 41407664›Full record

ArticleNature communications2025

Analysis of a near telomere-to-telomere genome of Phellodendron amurense reveals insights into berberine biosynthesis.

Song Chen, Yue Yu, Xinyu Wang, Qiwen Guo, Wenxuan Liu, Meiqi Lu, Siyuan Li, Yuanfu Liu, Guanzheng Qu, Guohua Wang and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. 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.

Song ChenState Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China.ORCID http://orcid.org/0000-0003-2896-8235
Yue YuState Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China.
Xinyu WangState Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China.
Qiwen GuoInstitute of Forest Ecology, Department of Ecosystem Management, Climate and Biodiversity, University of Natural Resources and Life Sciences, Vienna, Austria.ORCID http://orcid.org/0000-0002-5436-5932
Wenxuan LiuState Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China.
Meiqi LuState Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China.
Siyuan LiState Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China.
Yuanfu LiuState Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China.
Guanzheng QuState Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China.
Guohua WangState Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China. ghwang@nefu.edu.cn.ORCID http://orcid.org/0000-0001-7381-2374
Su ChenState Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China. chensu@nefu.edu.cn.ORCID http://orcid.org/0000-0002-8814-5444

Funding

National Natural Science Foundation of China (National Science Foundation of China) 62072095National Natural Science Foundation of China (National Science Foundation of China) 62225109
6 · The paper itself

Abstract

Phellodendron amurense is a Tertiary relict species with significant ecological and medicinal value. Here, we present a near telomere-to-telomere (T2T) genome assembly for this species. The assembled genome is 2.92 Gb, with a contig N50 length of 65.3 Mb, and contains 59,548 protein coding genes. Evolutionary analysis reveals that P. amurense is a paleooctoploid and the four subgenomes derived from the hybridizations of four parental lineages. We dissect the berberine biosynthesis pathway in the genome and identify the CNMT gene family (PaCNMT), which may contribute to the berberine biosynthesis in P. amurense. The PaCNMT family underwent a gene loss event within the Rutaceae lineage, followed by functional re-emergence in the P. amurense lineage through LTR-mediated gene expansion, which could have shaped the metabolic pathway in P. amurense. Our results provide insights into berberine biosynthesis in woody plants and highlight the role of LTR retrotransposons in driving the evolution of specialized metabolism.

Indexed as

BerberineGenome, PlantPhellodendronTelomereBiosynthetic PathwaysEvolution, MolecularMultigene FamilyPhylogenyPlant ProteinsRetroelementsBerberinePlant ProteinsRetroelements

Identifiers

PMID41407664
PMCPMC12748771

What OpenQuestion holds

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Registered trials

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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.