Related Experiment Videos
Analysis of codon usage patterns in "Lonicerae Flos" (Lonicera macranthoides Hand. -Mazz.) based on transcriptome
Sisi Liu1, Zhongquan Qiao2, Xiaoming Wang2
1Hunan Academy of Forestry, Changsha 410004, China; Hunan University of Traditional Chinese Medicine, Changsha 410208, China.
Gene
|April 28, 2019
Summary
This study reveals codon usage patterns in Lonicera macranthoides, finding mutation is the primary driver of codon bias. This research aids future genetic engineering and molecular evolution studies in this medicinal plant.
Area of Science:
- Plant genomics
- Molecular evolution
- Medicinal plant research
Background:
- Lonicera macranthoides is a valuable medicinal plant in China.
- Codon usage bias (CUB) in L. macranthoides remains uncharacterized.
Purpose of the Study:
- To investigate codon usage patterns in L. macranthoides genes.
- To identify factors influencing CUB and determine optimal codons.
Main Methods:
- Transcriptome sequencing of L. macranthoides.
- Analysis of 36,090 reconstructed genes.
- Application of neutrality plots, ENC plots, PR2-Bias plots, and correspondence analysis.
Main Results:
- L. macranthoides exhibits an AT-rich genome with a tendency towards A/T-ending codons.
- Both mutation and compositional constraints influence CUB, with mutation being the dominant factor.
- Gene expression levels impact codon usage.
- 29 optimal codons were identified, predominantly ending in A/U.
Conclusions:
- Mutation pressure is the main determinant of CUB in L. macranthoides.
- Identified optimal codons can inform gene expression strategies.
- This foundational research supports future gene prediction and genetic engineering efforts in L. macranthoides.