• Chloroplast Genome Evolution a...

Treffer: Chloroplast Genome Evolution and Codon Usage In the Medicinal Plant Pothos chinensis (Araceae).

Title:
Chloroplast Genome Evolution and Codon Usage In the Medicinal Plant Pothos chinensis (Araceae).
Authors:
Chen H; Liaoning Key Laboratory of Development and Utilization for Natural Products Active Molecules, Anshan Normal University, Anshan 114000, China., Zhang J; Liaoning Key Laboratory of Development and Utilization for Natural Products Active Molecules, Anshan Normal University, Anshan 114000, China.
Source:
Genes [Genes (Basel)] 2025 Aug 28; Vol. 16 (9). Date of Electronic Publication: 2025 Aug 28.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: MDPI Country of Publication: Switzerland NLM ID: 101551097 Publication Model: Electronic Cited Medium: Internet ISSN: 2073-4425 (Electronic) Linking ISSN: 20734425 NLM ISO Abbreviation: Genes (Basel) Subsets: MEDLINE
Imprint Name(s):
Original Publication: Basel : MDPI
MeSH Terms:
Genome, Chloroplast*/genetics , Codon Usage*/genetics , Plants, Medicinal*/genetics , Evolution, Molecular* , Araceae*/genetics , Araceae*/classification, Phylogeny ; Codon/genetics ; Chloroplasts/genetics
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Grant Information:
sszx077 Funding of Special Project for Applying for Master's Degree during the 14th Five-Year Plan of Anshan Normal University
Contributed Indexing:
Keywords: Pothos chinensis; chloroplast genome; codon usage bias; phylogeny
Substance Nomenclature:
0 (Codon)
Entry Date(s):
Date Created: 20250927 Date Completed: 20250927 Latest Revision: 20250930
Update Code:
20250930
PubMed Central ID:
PMC12470003
DOI:
10.3390/genes16091017
PMID:
41009963
Database:
MEDLINE

Weitere Informationen

Background/objectives: Pothos chinensis is commonly used as traditional medicine in China and India. Codon usage analysis is a good way to understand plants' evolution. However, there is no report about the codon usage bias of chloroplast genomes in P. chinensis .
Methods: In this study, the chloroplast genome of the medicinal plant P. chinensis was newly obtained. Comparative analyses, DNA barcoding investigation, codon usage bias, and phylogenetic reconstruction were conducted to reveal the chloroplast genome characteristics of P. chinensis .
Results: The length of the chloroplast genome of P. chinensis was 165,165 bp. A total of 134 genes were annotated, i.e., 90 protein-coding genes, 36 transfer RNA genes, and eight ribosomal RNA genes. Compared to its sister group Anthurium andraeanum , the length of the large single-copy region (LSC) had been expanded, while the small single-copy region (SSC) had been contracted. Within P. chinensis and P. scandens there were no obvious differences in the length of LSC, SSC, and two inverted repeat regions. Based on Pi values, seven hypervariable regions of whole plastomes were identified. The analysis of codons showed that an average frequency of the 50 candidate genes was 35.30%, and these genes preferred A/U-ending codons. The average effective number of codon (ENC) value was 45.49, which indicated weak codon usage bias. ENCs had a highly significant positive correlation with GC3. Fourteen optimal codons had been identified, 11 of which ended with A/U. The results of the neutrality plot, ENC-plot, and PR2-plot analysis indicated that natural selection might have a significant impact on codon usage patterns.
Conclusions: Taken together, our study unraveled the codon usage patterns in P. chinensis and provided valuable genetic information for the genus Pothos .