Evidence map›Paper›PMID 42363061›Full record

ArticleBMC genomics2026

Structural characteristics of the Phoebe hui chloroplast genome and phylogenetic analyses of Phoebe plants.

Liangxin Zhang, Jianghong Qian, Yunjie Gu, Hongying Guo, Jian Peng, Minhao Liu, Xiandan Luo, Xueqin Wan, Lianghua Chen, Fang He and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 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
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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

13 authors.

Liangxin ZhangSichuan Academy of Forestry, Ecological Conservation, Restoration and Resource Utilization in Forest and Wetland Key Laboratory of Sichuan Province, Chengdu, China.
Jianghong QianForest Ecology and Conservation in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Mt. Emei Forest Ecosystem National Observation and Research Station, Sichuan Agricultural University, Chengdu, China.
Yunjie GuSichuan Academy of Forestry, Ecological Conservation, Restoration and Resource Utilization in Forest and Wetland Key Laboratory of Sichuan Province, Chengdu, China. guyunjie7901@163.com.
Hongying GuoSichuan Academy of Forestry, Ecological Conservation, Restoration and Resource Utilization in Forest and Wetland Key Laboratory of Sichuan Province, Chengdu, China.
Jian PengSichuan Academy of Forestry, Ecological Conservation, Restoration and Resource Utilization in Forest and Wetland Key Laboratory of Sichuan Province, Chengdu, China.
Minhao LiuSichuan Academy of Forestry, Ecological Conservation, Restoration and Resource Utilization in Forest and Wetland Key Laboratory of Sichuan Province, Chengdu, China.
Xiandan LuoForest Ecology and Conservation in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Mt. Emei Forest Ecosystem National Observation and Research Station, Sichuan Agricultural University, Chengdu, China.
Xueqin WanForest Ecology and Conservation in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Mt. Emei Forest Ecosystem National Observation and Research Station, Sichuan Agricultural University, Chengdu, China.
Lianghua ChenForest Ecology and Conservation in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Mt. Emei Forest Ecosystem National Observation and Research Station, Sichuan Agricultural University, Chengdu, China.
Fang HeForest Ecology and Conservation in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Mt. Emei Forest Ecosystem National Observation and Research Station, Sichuan Agricultural University, Chengdu, China.
Yi WangSichuan Academy of Forestry, Ecological Conservation, Restoration and Resource Utilization in Forest and Wetland Key Laboratory of Sichuan Province, Chengdu, China.
Jinwu LiSichuan Academy of Forestry, Ecological Conservation, Restoration and Resource Utilization in Forest and Wetland Key Laboratory of Sichuan Province, Chengdu, China.
Hanbo YangForest Ecology and Conservation in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Mt. Emei Forest Ecosystem National Observation and Research Station, Sichuan Agricultural University, Chengdu, China. yanghanbo6@sicau.edu.cn.

Funding

National Key Research and Development Program of China 2024YFD2200103University Student's Innovation and Entrepreneurship Training Program Project 202410626053y Research and Development Project Program of Sichuan Province 2021YFYZ0032
6 · The paper itself

Abstract

In this study, the chloroplast genome of Phoebe hui was sequenced and assembled, and comparative analyses with those of other Phoebe plants were conducted, with a focus on variations in inverted repeat boundary variations, nucleotide diversity, selection pressure, codon usage bias, and phylogenetic relationships. The length of the chloroplast genome of P. hui exhibited a conserved size of 152,831 bp, the GC content was 39%, and the number of genes was 126; all the genes maintained a quadripartite circular structure. Significant interspecific variations in the inverted repeat boundary were observed; ndhF in P. hui resided entirely within the small single-copy region, while the extended ψycf1 of P. zhennan overlapped with ndhF by 637 bp and served as a potential molecular marker for species identification. Noncoding regions showed higher nucleotide diversity, with hypervariable regions identified as valuable tools for population genetics. Ka/Ks analysis revealed strong purifying selection on photosynthesis-related genes (psbA and rbcL), whereas stress-response genes (ndhF and ndhD) exhibited elevated synonymous substitution rates. A preference for A/U-ending codons was noted, although P. hui exhibited unique codon avoidance, suggesting translational optimization. Divergence time estimation indicated that Phoebe diverged from Machilus approximately 42.366 million years ago (Mya), P. hui diverged from its congeners approximately 24.916 Mya, and the most recent divergence occurred between P. bournei and P. chekiangensis at approximately 0.113 Mya. These divergence events may be associated with major geological events and Quaternary climatic fluctuations. This study provides genomic insights into the phylogeny of conserved endangered plants and the development of molecular markers for hybrid breeding.

Indexed as

Genome, ChloroplastPhylogenyBase CompositionCodonCodon UsageEvolution, MolecularGenetic VariationSelection, GeneticCodonChloroplast genomeCodon usage biasPhoebe huiPhylogeneticsSelection pressure

Identifiers

PMID42363061
PMCPMC13584372

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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.