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Genome-wide codon usage pattern analysis reveals the correlation between codon usage bias and gene expression in Cuscuta australis
- Source :
- Genomics. 112:2695-2702
- Publication Year :
- 2020
- Publisher :
- Elsevier BV, 2020.
-
Abstract
- The protein-coding genes and pseudogenes of Cuscuta australis had the diverse contribution to the formation and evolution of parasitism. The codon usage pattern analysis of these two type genes could be used to understand the gene transcription and translation. In this study, we systematically analyzed the codon usage patterns of protein-coding sequences and pseudogenes sequences in C. australis. The results showed that the high frequency codons of protein coding sequences and pseudogenes had the same A/U bias in the third position. However, these two sequences had converse bias at the third base in optimal codons: the protein coding sequences preferred G/C-ending codons while pseudogene sequences preferred A/U-ending codons. Neutrality plot and effective number of codons plot revealed that natural selection played a more important role than mutation pressure in two sequences codon usage bias. Furthermore, the gene expression level had a significant positive correlation with codon usage bias in C. australis. Highly-expressed protein coding genes exhibited a higher codon bias than lowly-expressed genes. Meanwhile, the high-expression genes tended to use G/C-ending synonymous codons. This result further verified the optimal codons usage bias and its correlation with the gene expression in C. australis.
- Subjects :
- 0106 biological sciences
Pseudogene
Gene Expression
Biology
medicine.disease_cause
01 natural sciences
Genome
03 medical and health sciences
Gene expression
Genetics
medicine
Codon
Codon Usage
Gene
Plant Proteins
030304 developmental biology
0303 health sciences
Mutation
Natural selection
Translation (biology)
Cuscuta
Codon usage bias
Genome, Plant
Pseudogenes
010606 plant biology & botany
Subjects
Details
- ISSN :
- 08887543
- Volume :
- 112
- Database :
- OpenAIRE
- Journal :
- Genomics
- Accession number :
- edsair.doi.dedup.....02e3269448c5745b0bd7f65a49eb1db8