Related Experiment Video
Updated: Dec 27, 2025
13:03
Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens
Published on: March 8, 2018
11.0K
Codon usage by chloroplast gene is bias in Hemiptelea davidii
Huabo Liu1, Yizeng Lu, Baoliang Lan
1National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, People's Republic of China. jcxu282@sina.com.
Journal of Genetics
|February 25, 2020
Summary
This study analyzed chloroplast genes in Hemiptelea davidii, revealing codon usage patterns influenced by natural selection. Findings offer insights into plant evolution and potential applications in molecular breeding programs.
Area of Science:
- Plant molecular biology
- Evolutionary genetics
- Bioinformatics
Background:
- Chloroplast genes are crucial for plant evolution.
- Understanding base composition and codon usage provides evolutionary insights.
- Hemiptelea davidii chloroplast genes' patterns are not well-documented.
Purpose of the Study:
- To investigate the base composition and codon usage patterns of chloroplast protein-coding genes in Hemiptelea davidii.
- To explore the factors influencing codon bias in these genes.
- To provide a foundation for future molecular breeding strategies.
Main Methods:
- Analysis of 48 chloroplast protein-coding genes from Hemiptelea davidii.
- Calculation of GC content at different codon positions.
- Relative Synonymous Codon Usage (RSCU) analysis.
- Neutrality plot, ENC-plot, and PR2-plot analyses.
Main Results:
- Average GC content was 37.32%, with 27.80% at the third codon position.
- 30 high-frequency and 11 optimal codons were identified, predominantly ending in A or T.
- Codon usage bias is significantly influenced by natural selection pressures.
- Similarities in codon usage frequency were observed across different plant species.
Conclusions:
- The codon usage pattern of Hemiptelea davidii chloroplast genes is shaped by natural selection.
- Specific synonymous codons are preferred in H. davidii.
- This research enhances understanding of chloroplast gene expression and aids molecular breeding.
Related Concept Videos
02:16Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
14.9K
The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
14.9K
02:19Export of Mitochondrial and Chloroplast Genes
4.0K
A eukaryotic cell can have up to three different types of genetic systems: nuclear, mitochondrial, and chloroplast. During evolution, organelles have exported many genes to the nucleus; this transfer is still ongoing in some plant species. Approximately 18% of the Arabidopsis thaliana nuclear genome is thought to be derived from the chloroplast’s cyanobacterial ancestor, and around 75% of the yeast genome derived from the mitochondria’s bacterial ancestor. This export has occurred...
4.0K
03:06From DNA to Protein
21.7K
The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...
21.7K
01:18Protein Transport to the Inner Chloroplast Membrane
2.3K
Proteins targeted to the inner chloroplast membrane, or plastid proteins, are transported by two general pathways: the stop-transfer and the re-insertion or post-import pathways. Most plastid proteins carry N-terminal transit sequences and internal import sequences targeting it to the specific chloroplast subcompartment. Proteins targeted by the stop-transfer pathway have internal hydrophobic sequences that inhibit their translocation into the stroma. As a result, these precursors are arrested...
2.3K
02:32Position-effect Variegation
6.9K
In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.
6.9K
01:11Protein Transport to the Outer Chloroplast Membrane
2.3K
Chloroplast outer membrane proteins encoded by the nucleus are synthesized in the cytosol. Soon after synthesis, they bind cytosolic factors such as 14-3-3 protein and the Hsp70 chaperones that keep these precursors in an unfolded state until their translocation.
Two models describe the mechanism of precursor recognition and entry across the outer membrane through the TOC complex. Model 1 suggests the newly synthesized precursor binds to the TOC receptor 159 and forms a complex.
Two models describe the mechanism of precursor recognition and entry across the outer membrane through the TOC complex. Model 1 suggests the newly synthesized precursor binds to the TOC receptor 159 and forms a complex.
2.3K