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Analysis of synonymous codon usage of chloroplast genome in Porphyra umbilicalis

Genes & Genomics 2019년 41권 10호 p.1173 ~ 1181
 ( Li Guoling ) - Sichuan Agricultural University College of Life Science

 ( Pan Zonglian ) - Sichuan Agricultural University College of Life Science
 ( Gao Shichen ) - Sichuan Agricultural University College of Life Science
 ( He Yuyang ) - Sichuan Agricultural University College of Life Science
 ( Xia Qiaoyu ) - Sichuan Agricultural University College of Life Science
 ( Jin Yan ) - Sichuan Agricultural University College of Life Science
 ( Yao Huipeng ) - Sichuan Agricultural University College of Life Science

Abstract


Background: Synonymous codon usage bias is noticed in the genome of every organism, influenced by mutation pressure and natural selection. The analysis of codon usage pattern in Porphyra umbilicalis chloroplast genome are inferred while previous study focused on codon bias in nuclear genome.

Objective: To develop a better understanding of the factors affecting synonymous codon usage, codon usage patterns and nucleotide composition of 150 genes in P. umbilicalis cp genome, and provide a theoretical basis for genetic modification of chloroplast genome.

Methods: In this study, all codon usage bias parameters and nucleotide compositions were calculated by Python script, Codon W, DNA Star, CUSP of EMBOSS and Microsoft Excel.

Results: It shows that codon usage models are mainly influenced by compositional constraints under mutational pressure and synonymous codon prefers to use codons ending with A/T, comparing to C/G. The ENC value is slight low which shows the weak codon bias. For all coding genes of P. umbilicalis chloroplast genome except Photosystem I genes, a weak correlation between GC3 and GC12 suggests natural selection might play a significant role in synonymous codon usage bias.

Conclusion: The codon usage bias in P. umbilicalis cp genome is low and in some way or other, influenced by natural selection, mutation pressure, nucleotide composition. Our results can provide a theoretical basis for codon modification of exogenous genes, accuracy of prediction about new members of chloroplast gene family and identification of unknown genome.

키워드

Synonymous codon usage; Chloroplast genome; Porphyra umbilicalis; Natural selection
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