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Comparison of codon preference patterns in the chloroplast genome of Pinus densata
LI Jiangfei, LI Yaqi, TANG Junrong, CHEN Shi, CHEN Lin, CAI Nianhui, XU Yulan, TANG Hongyan
2023, 40 (1):
52.
doi: 10.3969/j.issn.2095-1736.2023.01.052
To understand the
pattern of codon preference used in the chloroplast genome of Pinus
densata, the factors that influence the formation of codon preference
were explored. Methods such as neutral mapping analysis, ENC-plot,
PR2-plot analysis, and correspondence analysis were performed using
CodonW and CUSP online software. The results showed that the average GC
content of chloroplast codons in P. densata was 39.84%, and the contents
of GC1and GC2were 48.81% and 40.70%, respectively, which were higher than GC3(30.52%), indicating that their chloroplast genome codon endings
preferred to end with A and U. The mean value of effective codon number
ENC was 48.77, indicating a weak codon preference. Results of the
neutral plot analysis, ENC-plot analysis, and PR2-plot bias analysis
showed that selection pressure was the main factor influencing the codon
preference of P. densata, followed by a combination of factors such as
mutations. Further correspondence analysis revealed that axis 1
accounted for 21.18% of the overall variation and was the main
influencing factor, which was not correlated with ENC and GC3,
but was significantly correlated with CAI. The results of these
analyses indicated that natural selection was the main influencing
factor on chloroplast codon preference in P. densata, and was also
influenced by other factors; 15 codons were identified as optimal
codons, showing a strong preference for NNA and NNU codons with high
representation. This study provided basic information for future genetic
engineering of P. densata chloroplasts, codon optimization, improving
the expression level of exogenous genes and the yield and quality of
alpine pine seeds.
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