Analysis of codon usage patterns in Ginkgo biloba reveals codon usage tendency from A/U-ending to G/C-ending.
As one of the most ancient tree species, the codon usage pattern analysis of Ginkgo biloba is a useful way to understand its evolutionary and genetic mechanisms. Several studies have been conducted on angiosperms, but seldom on gymnosperms. Based on RNA-Seq data of the G. biloba transcriptome, amount to 17,579 unigenes longer than 300 bp were selected and analyzed from 68,547 candidates. The codon usage pattern tended towards more frequently use of A/U-ending codons, which showed an obvious gradient progressing from gymnosperms to dicots to monocots. Meanwhile, analysis of high/low-expression unigenes revealed that high-expression unigenes tended to use G/C-ending codons together with more codon usage bias. Variation of unigenes with different functions suggested that unigenes involving in environment adaptation use G/C-ending codons more frequently with more usage bias, and these results were consistent with the conclusion that the formation of G. biloba codon usage bias was dominated by natural selection.
Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
Bing
B
He
Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
Hui
H
Dong
Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA.|State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shanxi 712100, China.
Cong
C
Jiang
Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
Fuliang
F
Cao
Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
Shentong
S
Tao
Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
Li-An
LA
Xu
D001482:Base Composition; D003062:Codon; D020441:Ginkgo biloba / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics*; D018749:RNA, Plant; D012641:Selection, Genetic; D059467:Transcriptome
D003062:Codon; D010940:Plant Proteins; D018749:RNA, Plant