Evidence map›Paper›PMID 41009973›Full record

ArticleGenes2025

Comparative Chloroplast Genomics of Ten Collabieae Species Including Three Novel Genomes.

Shuangshuang Xie, Xingyou Jiang, Wenting Yang, Kunlin Wu, Lin Fang, Songjun Zeng, Jingjue Zeng, Lin Li

Abstract readComparative Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Genes, 2025. 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

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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

8 authors.

Shuangshuang XieKey Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
Xingyou JiangKey Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
Wenting YangKey Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.ORCID 0000-0002-4784-8776
Kunlin WuKey Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
Lin FangKey Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.ORCID 0000-0002-9971-4569
Songjun ZengKey Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.ORCID 0000-0001-7446-333X
Jingjue ZengKey Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
Lin LiKey Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.ORCID 0000-0001-7091-9686

Funding

National Natural Science Foundation of China 32070224Science and Technology Program of For-estry Administration of Guangdong Province Grant No. E5360800
6 · The paper itself

Abstract

backgroundCollabieae is a medium-sized group within the orchid subfamily Epidendroideae that is distributed primarily across tropical Asia. Most Collabieae species are known for their considerable ornamental and medicinal merits. However, habitat destruction and overharvesting have led to severe decline in their wild populations. Chloroplast (cp) genomes are highly valued in evolutionary studies, due to comparative conservation and accumulation of genomic variations. Elucidating the structure of chloroplast genome is instrumental in conserving genetic diversity within the Collabieae.

methodswe explored the chloroplast genome characteristics of Collabieae. We incorporated three newly sequenced genomes from species (

resultsall analyzed cp genomes displayed a typical quadripartite circular structure. The total lengths ranged from 157,036 bp to 158,321 bp. Each genome contained 136 genes: 88 protein-coding genes, 38 tRNA genes, eight rRNA genes, and two pseudogenes. Across the ten Collabieae species, gene number, order, orientation, GC content, and codon usage bias were highly consistent, indicative of strong sequence conservation. However, notable structural divergence was observed at the plastome junctions, alongside variations in SSR and repetitive element frequencies. Moreover, six hypervariable regions were identified. Noncoding regions exhibited higher variability compared to protein-coding regions. Phylogenetic analysis indicated that

conclusionsthis overall phylogenetic framework aligns well with previous findings. Our study provides valuable cp genomic resources and advances evolutionary research in Collabieae.

Indexed as

ChloroplastsGenome, ChloroplastOrchidaceaeBase CompositionEvolution, MolecularGenomicsPhylogenychloroplast genomesCollabieaecomparative genomicsOrchidaceaephylogenetic analysis

Identifiers

PMID41009973
PMCPMC12469772

What Socratic holds

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LicenceCC BY
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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 Socratic graph.