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Open AccessArticle
Patterns in Genome-Wide Codon Usage Bias in Representative Species of Lycophytes and Ferns
by
Piaoran Xu
Piaoran Xu 1,2
,
Lijuan Zhang
Lijuan Zhang 2,
Liping Lu
Liping Lu 1,2,
Yanli Zhu
Yanli Zhu 1,2,
Dandan Gao
Dandan Gao 1,* and
Shanshan Liu
Shanshan Liu 1,2,*
1
China-Malaysia National Joint Laboratory, Biomedical Reserch Center, Northwest Minzu University, Lanzhou 730030, China
2
College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China
*
Authors to whom correspondence should be addressed.
Genes 2024, 15(7), 887; https://doi.org/10.3390/genes15070887 (registering DOI)
Submission received: 11 May 2024
/
Revised: 29 June 2024
/
Accepted: 4 July 2024
/
Published: 5 July 2024
Abstract
The latest research shows that ferns and lycophytes have distinct evolutionary lineages. The codon usage patterns of lycophytes and ferns have not yet been documented. To investigate the gene expression profiles across various plant lineages with respect to codon usage, analyze the disparities and determinants of gene evolution in primitive plant species, and identify appropriate exogenous gene expression platforms, the whole-genome sequences of four distinct species were retrieved from the NCBI database. The findings indicated that Ceratopteris richardii, Adiantum capillus-veneris, and Selaginella moellendorffii exhibited an elevated A/U content in their codon base composition and a tendency to end with A/U. Additionally, S. capillus-veneris had more C/G in its codons and a tendency to end with C/G. The ENC values derived from both ENC-plot and ENC-ratio analyses deviated significantly from the standard curves, suggesting that the codon usage preferences of these four species were primarily influenced by genetic mutations and natural selection, with natural selection exerting a more prominent influence. This finding was further supported by PR2-Plot, neutrality plot analysis, and COA. A combination of RSCU and ENC values was used as a reference criterion to rank the codons and further identify the optimal codons. The study identified 24 high-frequency codons in C. richardii, A. capillus-veneris, and Diphasiastrum complanatum, with no shared optimal codons among the four species. Arabidopsis thaliana and Ginkgo biloba exhibited similar codon preferences to the three species, except for S. moellendorffii. This research offers a theoretical framework at the genomic codon level for investigating the phylogenetic relationships between lycophytes and ferns, shedding light on gene codon optimization and its implications for genetic engineering in breeding.
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MDPI and ACS Style
Xu, P.; Zhang, L.; Lu, L.; Zhu, Y.; Gao, D.; Liu, S.
Patterns in Genome-Wide Codon Usage Bias in Representative Species of Lycophytes and Ferns. Genes 2024, 15, 887.
https://doi.org/10.3390/genes15070887
AMA Style
Xu P, Zhang L, Lu L, Zhu Y, Gao D, Liu S.
Patterns in Genome-Wide Codon Usage Bias in Representative Species of Lycophytes and Ferns. Genes. 2024; 15(7):887.
https://doi.org/10.3390/genes15070887
Chicago/Turabian Style
Xu, Piaoran, Lijuan Zhang, Liping Lu, Yanli Zhu, Dandan Gao, and Shanshan Liu.
2024. "Patterns in Genome-Wide Codon Usage Bias in Representative Species of Lycophytes and Ferns" Genes 15, no. 7: 887.
https://doi.org/10.3390/genes15070887
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