Analysis of synonymous codon usage of chloroplast genome in Porphyra umbilicalis

Guoling Li; Zonglian Pan; Shichen Gao; Yuyang He; Qiaoyu Xia; Yan Jin; Huipeng Yao

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자료유형: 학술저널

저자정보: Guoling Li (Sichuan Agricultural University) Zonglian Pan (Sichuan Agricultural University) Shichen Gao (Sichuan Agricultural University) Yuyang He (Sichuan Agricultural University) Qiaoyu Xia (Sichuan Agricultural University) Yan Jin (Sichuan Agricultural University) Huipeng Yao (Sichuan Agricultural University)

저널정보: 한국유전학회 Genes & Genomics Genes & Genomics Vol.41 No.10

발행연도: 2019.1

수록면: 1,173 - 1,181 (9page)

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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.

#Synonymous codon usage · Chloroplast genome · Porphyra umbilicalis · Natural selection

참고문헌 (24)

참고문헌 신청

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Brawley SH / 2017 / Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta) / P Natl Acad Sci USA 114:E6361~E6370

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