Abstract
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.
Highlights
Triplet codons play vital roles in all biological organisms as the basic units for the encoding of mRNA
The mean GC content of G. biloba untranslated region (UTR) was 37.89% which was slightly lower than mean GC3 content
To minimize the potential error, only coding sequences ≥300 bp annotated as unigene with ≥more than 90% identity compared to the non-redundant protein sequence (Nr) database using blastx were selected- one unigene corresponded to only one Coding sequences (CDSs) and all unsuitable unigenes or CDSs were discarded
Summary
Triplet codons play vital roles in all biological organisms as the basic units for the encoding of mRNA. Since the genetic code is degenerate, most amino acids except methionine and tryptophan, are encoded by 2–6 different codons[1]. Analysis of codon usage bias provides a clue to reveal laws of genetics and evolution[2], design degenerate primers and study appropriate external expression systems[3]. A recent study reported that codon usage bias was able to affect the expression, structure and function of protein[4] and the local rate of translation elongation as well[5]. Codon usage bias was shown to be closely associated with the molecular mechanism of translation[6], new genes discovery[7], sex determination[8] and other biological functions[9]. Analysis of the codon usage patterns in G. biloba www.nature.com/scientificreports/. We systematically studied the codon usage pattern in G. biloba and evaluated the effects of various factors. The results might provide an explanation or a reference for studies on the genetic evolution mechanism of G. biloba
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