Analysis of codon usage bias based on Fritillaria cirrhosa transcriptome.

Ying LI; Xue-jun Kuang; Chao Sun; Shi-lin Chen

Return

Analysis of codon usage bias based on Fritillaria cirrhosa transcriptome.

Author: Ying LI ¹ ; Xue-Jun KUANG ¹ ; Chao SUN ¹ ; Shi-Lin CHEN ²
Author Information

1. Institute of Medicinal Plant Development, China Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China.
2. Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
Publication Type:Journal Article
Keywords: Fritillaria cirrhosa; codon usage bias; transcriptome
From: China Journal of Chinese Materia Medica 2016;41(11):2055-2060
CountryChina
Language:Chinese
Abstract: Understanding of codon usage bias of Fritillaria cirrhosa can provide theoretical basis for heterologous biosynthesis of F. cirrhosa alkaloids by genetic engineering technology. A total of 9 843 full length coding sequences (CDS) from the F. cirrhosa transcriptome data were used for the analysis of codon usage bias. The GC and GC3s contents, effective number of codons(ENC) and relative synonymous codon usage (RSCU) were calculated using the CodonW software. The results show that the codon usage bias value is low in the CDS of F. cirrhosa. A total of 15 codons, including UUG, CUU, AUU, GUU, UCA, CCU, CCA, ACU, ACA, GCA, UAU, CAU, AAU, AGA and GGA, were identified as optimal codons in F. cirrhosa. The optimal codons generally end with A/T at the third codon position. By the transcriptome annotation, we found 26 CDSs possibly involved in the biosynthesis of alkaloids in the F. cirrhosa. The proportion of rare codons of Escherichia coli and Saccharomyces cerevisiae are low in these CDSs. We also proposed a method for the codonoptimization in these target genes. Our work lays the foundation for further study on the biosynthesis of alkaloids of the F. cirrhosa in heterologous species.