Molecular Evolution of Chloroplast Gene ycf94 in Ferns

Abstract:

As a newly discovered chloroplast gene in recent years, ycf94 gene, with length of about 200 bp, is conserved among ferns. However, the origin and function of ycf94 require further investigation. The study was performed on the ycf94 gene sequence of 94 species of ferns, in the phylogenetic background, analyzing codon usage bias, evolution rate and selection pressure. Results showed that the codon bias was weak in ycf94 gene which the 3rd position of codon prefers A/U, variously in closely species. The codon bias was mainly produced by gene mutation. In addition, based on the differences in the structural characteristics of ycf94 between Pteridaceae and other ferns, their evolution rate was compared, suggesting that there were significant difference in transversion rate, nonsynonymous substitution rate and omega. Besides, only one position selection site 74A was detected. The strong negative selection pressure indicated that the function and structure of ycf94 were mostly stabilized. The results provide a new clue of phylogenetic analysis in ferns and functional studies of ycf94 gene.

Key words:Fern;ycf94 gene;Codon usage bias;Evolutionary rate;Adaptive evolution