• Comparative analysis of codon...

Treffer: Comparative analysis of codon usage bias and phylogenetic relationships in chloroplast genomes across 49 Dendrobium species.

Title:
Comparative analysis of codon usage bias and phylogenetic relationships in chloroplast genomes across 49 Dendrobium species.
Authors:
Wu C; College of Pharmaceutical Science, Dali University, Dali, 671000, China.; International Joint Laboratory for the Development and Utilization of Traditional Chinese Medicine Resources in Yunnan Province, Baoshan, 678300, China.; International Joint Laboratory for the Development and Utilization of Traditional Chinese Medicine Resources in Yunnan Province, Dali, 671000, China., Liu R; College of Pharmaceutical Science, Dali University, Dali, 671000, China.; International Joint Laboratory for the Development and Utilization of Traditional Chinese Medicine Resources in Yunnan Province, Baoshan, 678300, China.; International Joint Laboratory for the Development and Utilization of Traditional Chinese Medicine Resources in Yunnan Province, Dali, 671000, China., Li C; College of Pharmaceutical Science, Dali University, Dali, 671000, China.; International Joint Laboratory for the Development and Utilization of Traditional Chinese Medicine Resources in Yunnan Province, Baoshan, 678300, China.; International Joint Laboratory for the Development and Utilization of Traditional Chinese Medicine Resources in Yunnan Province, Dali, 671000, China., Shang M; College of Pharmaceutical Science, Dali University, Dali, 671000, China.; International Joint Laboratory for the Development and Utilization of Traditional Chinese Medicine Resources in Yunnan Province, Baoshan, 678300, China.; International Joint Laboratory for the Development and Utilization of Traditional Chinese Medicine Resources in Yunnan Province, Dali, 671000, China., Zhang Y; College of Pharmaceutical Science, Dali University, Dali, 671000, China.; International Joint Laboratory for the Development and Utilization of Traditional Chinese Medicine Resources in Yunnan Province, Baoshan, 678300, China.; International Joint Laboratory for the Development and Utilization of Traditional Chinese Medicine Resources in Yunnan Province, Dali, 671000, China., Bai K; College of Pharmaceutical Science, Dali University, Dali, 671000, China.; International Joint Laboratory for the Development and Utilization of Traditional Chinese Medicine Resources in Yunnan Province, Baoshan, 678300, China.; International Joint Laboratory for the Development and Utilization of Traditional Chinese Medicine Resources in Yunnan Province, Dali, 671000, China., Wang Y; College of Pharmaceutical Science, Dali University, Dali, 671000, China.; International Joint Laboratory for the Development and Utilization of Traditional Chinese Medicine Resources in Yunnan Province, Baoshan, 678300, China.; International Joint Laboratory for the Development and Utilization of Traditional Chinese Medicine Resources in Yunnan Province, Dali, 671000, China., Zhou Y; College of Pharmaceutical Science, Dali University, Dali, 671000, China., Lin Y; College of Pharmaceutical Science, Dali University, Dali, 671000, China. 531172419@qq.com.; International Joint Laboratory for the Development and Utilization of Traditional Chinese Medicine Resources in Yunnan Province, Baoshan, 678300, China. 531172419@qq.com.; International Joint Laboratory for the Development and Utilization of Traditional Chinese Medicine Resources in Yunnan Province, Dali, 671000, China. 531172419@qq.com., Duan B; College of Pharmaceutical Science, Dali University, Dali, 671000, China. bzduan@126.com.; International Joint Laboratory for the Development and Utilization of Traditional Chinese Medicine Resources in Yunnan Province, Baoshan, 678300, China. bzduan@126.com.; International Joint Laboratory for the Development and Utilization of Traditional Chinese Medicine Resources in Yunnan Province, Dali, 671000, China. bzduan@126.com.
Source:
BMC plant biology [BMC Plant Biol] 2025 Oct 21; Vol. 25 (1), pp. 1411. Date of Electronic Publication: 2025 Oct 21.
Publication Type:
Journal Article; Comparative Study
Language:
English
Journal Info:
Publisher: BioMed Central Country of Publication: England NLM ID: 100967807 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2229 (Electronic) Linking ISSN: 14712229 NLM ISO Abbreviation: BMC Plant Biol Subsets: MEDLINE
Imprint Name(s):
Original Publication: London : BioMed Central, [2001-
MeSH Terms:
Dendrobium*/genetics , Dendrobium*/classification , Codon Usage*/genetics , Genome, Chloroplast*/genetics , Phylogeny*, Selection, Genetic ; Evolution, Molecular ; Codon ; Base Composition
References:
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Grant Information:
202205AF150026 Yunnan academician expert workstation; 202302AA310029 biomedical major special project of Yunnan province
Contributed Indexing:
Keywords: Dendrobium genus; Codon usage bias; Complete chloroplast genome; Optimal codons
Substance Nomenclature:
0 (Codon)
Entry Date(s):
Date Created: 20251022 Date Completed: 20251022 Latest Revision: 20251025
Update Code:
20251025
PubMed Central ID:
PMC12538735
DOI:
10.1186/s12870-025-07395-9
PMID:
41120874
Database:
MEDLINE

Weitere Informationen

Background: Dendrobium is the second-largest genus in the Orchidaceae family. However, research on codon usage bias (CUB) in Dendrobium genus remains relatively limited. This knowledge gap impedes progress in genetic engineering and the breeding of superior varieties, making it challenging to meet the growing demand for higher yield and quality of Dendrobium.
Results: The cp genomes of Dendrobium species exhibited codon composition biased toward A/T bases, with GC content below 50% (GC1 > GC2 > GC3). Eleven to nineteen optimal codons were identified across these species, with the third base of most codons predominantly ending with A/U. Parity rule 2-bias plots, effective number of codons plots, and neutrality plot analysis further revealed that natural selection serves as the primary driver of CUB variation, while mutation pressure played a secondary role. Notably, the positions of some species were different in the phylogenetic topologies from cp genomes and cp CDS.
Conclusions: CUB is an effective tool for investigating the phylogenetic evolution of Dendrobium. The CUB in Dendrobium species is primarily driven by natural selection, while mutation pressure plays a secondary role.
(© 2025. The Author(s).)

Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.