Guoling Li1, Zonglian Pan1, Shichen Gao1, Yuyang He1, Qiaoyu Xia1, Yan Jin1, Huipeng Yao2. 1. College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China. 2. College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China. yaohuipeng0921@163.com.
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.
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.
Authors: Susan H Brawley; Nicolas A Blouin; Elizabeth Ficko-Blean; Glen L Wheeler; Martin Lohr; Holly V Goodson; Jerry W Jenkins; Crysten E Blaby-Haas; Katherine E Helliwell; Cheong Xin Chan; Tara N Marriage; Debashish Bhattacharya; Anita S Klein; Yacine Badis; Juliet Brodie; Yuanyu Cao; Jonas Collén; Simon M Dittami; Claire M M Gachon; Beverley R Green; Steven J Karpowicz; Jay W Kim; Ulrich Johan Kudahl; Senjie Lin; Gurvan Michel; Maria Mittag; Bradley J S C Olson; Jasmyn L Pangilinan; Yi Peng; Huan Qiu; Shengqiang Shu; John T Singer; Alison G Smith; Brittany N Sprecher; Volker Wagner; Wenfei Wang; Zhi-Yong Wang; Juying Yan; Charles Yarish; Simone Zäuner-Riek; Yunyun Zhuang; Yong Zou; Erika A Lindquist; Jane Grimwood; Kerrie W Barry; Daniel S Rokhsar; Jeremy Schmutz; John W Stiller; Arthur R Grossman; Simon E Prochnik Journal: Proc Natl Acad Sci U S A Date: 2017-07-17 Impact factor: 11.205
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