Comparative analysis of codon usage bias in chloroplast genomes of ten medicinal species of Rutaceae.
Codon usage bias
Natural selection
Optimal codon
Rutaceae family
Journal
BMC plant biology
ISSN: 1471-2229
Titre abrégé: BMC Plant Biol
Pays: England
ID NLM: 100967807
Informations de publication
Date de publication:
20 May 2024
20 May 2024
Historique:
received:
01
04
2023
accepted:
08
04
2024
medline:
20
5
2024
pubmed:
20
5
2024
entrez:
19
5
2024
Statut:
epublish
Résumé
Rutaceae family comprises economically important plants due to their extensive applications in spices, food, oil, medicine, etc. The Rutaceae plants is able to better utilization through biotechnology. Modern biotechnological approaches primarily rely on the heterologous expression of functional proteins in different vectors. However, several proteins are difficult to express outside their native environment. The expression potential of functional genes in heterologous systems can be maximized by replacing the rare synonymous codons in the vector with preferred optimal codons of functional genes. Codon usage bias plays a critical role in biogenetic engineering-based research and development. In the current study, 727 coding sequences (CDSs) obtained from the chloroplast genomes of ten Rutaceae plant family members were analyzed for codon usage bias. The nucleotide composition analysis of codons showed that these codons were rich in A/T(U) bases and preferred A/T(U) endings. Analyses of neutrality plots, effective number of codons (ENC) plots, and correlations between ENC and codon adaptation index (CAI) were conducted, which revealed that natural selection is a major driving force for the Rutaceae plant family's codon usage bias, followed by base mutation. In the ENC vs. CAI plot, codon usage bias in the Rutaceae family had a negligible relationship with gene expression level. For each sample, we screened 12 codons as preferred and high-frequency codons simultaneously, of which GCU encoding Ala, UUA encoding Leu, and AGA encoding Arg were the most preferred codons. Taken together, our study unraveled the synonymous codon usage pattern in the Rutaceae family, providing valuable information for the genetic engineering of Rutaceae plant species in the future.
Identifiants
pubmed: 38764045
doi: 10.1186/s12870-024-04999-5
pii: 10.1186/s12870-024-04999-5
doi:
Types de publication
Journal Article
Comparative Study
Langues
eng
Sous-ensembles de citation
IM
Pagination
424Subventions
Organisme : the Local Walnut R&D Groups in Guizhou Province
ID : ([2019]5643)
Organisme : the Local Walnut R&D Groups in Guizhou Province
ID : ([2019]5643)
Organisme : the Local Walnut R&D Groups in Guizhou Province
ID : ([2019]5643)
Organisme : the National Natural Science Foundation of China
ID : (Grant No. 32260410)
Organisme : the National Natural Science Foundation of China
ID : (Grant No. 32260410)
Organisme : Guizhou science and Technology plan Support Project
ID : (Grant Nos. common projects [ 2022 ] 118 and [2022] 222)
Organisme : Guizhou science and Technology plan Support Project
ID : (Grant Nos. common projects [ 2022 ] 118 and [2022] 222)
Organisme : QianKehe Fundation
ID : ZK [2023] common project 121
Organisme : Guizhou Province Forestry Characteristic Forestry Industry Project
ID : (Grant No. Telinyan 2020-18 )
Informations de copyright
© 2024. The Author(s).
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