Analysis of codon usage patterns in Polyporus umbellatus based on transcriptome data
10.16438/j.0513-4870.2019-0900
- VernacularTitle:基于转录组数据分析药用真菌猪苓密码子使用偏好性
- Author:
Meng-meng LIU
1
,
2
,
3
;
Yong-mei XING
1
;
Shun-xing GUO
1
Author Information
1. Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
2. College of Traditional Chinese Medicine, Hebei University, Baoding 071002, China
3. Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
- Publication Type:Research Article
- Keywords:
italic>Polyporus umbellatus;
transcriptome;
codon usage bias;
preferred codon
- From:
Acta Pharmaceutica Sinica
2020;55(5):1050-1055
- CountryChina
- Language:Chinese
-
Abstract:
We obtained 332 coding sequences from the Polyporus umbellatus transcriptome based on the BLASTx and ESTScan analyses. The codon usage patterns of P. umbellatus were calculated and statistically analyzed using CodonW. The results showed that the average GC content of genes was 53.57% and the average GC3 content was 57.98%, suggesting that genes favored codons ending with G or C. The effective number of codons (ENC) value range from 38.46 to 61, which indicates that these genes have low codon usage bias. The neutrality plot and ENC-plot analysis revealed that many factors such as mutation and selective pressure play an important role in shaping codon usage bias in P. umbellatus genes. Twenty-two optimal codons were identified as being biased toward codons ending with G or C using the high expression superior codon analysis method. This study will lay a foundation for future research on genetic engineering and molecular evolution in P. umbellatus.
