Comparative analysis of codon usage patterns in the chloroplast genomes of nine forage legumes.

Leguminosae is one of the three largest families of angiosperms after Compositae and Orchidaceae. It is widely distributed and grows in a variety of environments, including plains, mountains, deserts, forests, grasslands, and even waters where almost all legumes can be found. It is one of the most important sources of starch, protein and oil in the food of mankind and also an important source of high-quality forage material for animals, which has important economic significance. In our study, the codon usage patterns and variation sources of the chloroplast genome of nine important forage legumes were systematically analyzed. Meanwhile, we also constructed a phylogenetic tree based on the whole chloroplast genomes and protein coding sequences of these nine forage legumes. Our results showed that the chloroplast genomes of nine forage legumes end with A/T bases, and seven identical high-frequency (HF) codons were detected among the nine forage legumes. ENC-GC3s mapping, PR2 analysis, and neutral analysis showed that the codon bias of nine forage legumes was influenced by many factors, among which natural selection was the main influencing factor. The codon usage frequency showed that the Nicotiana tabacum and Saccharomyces cerevisiae can be considered as receptors for the exogenous expression of chloroplast genes of these nine forage legumes. The phylogenetic relationships of the chloroplast genomes and protein coding genes were highly similar, and the nine forage legumes were divided into three major clades. Among the clades Melilotus officinalis was more closely related to Medicago sativa, and Galega officinalis was more closely related to Galega orientalis. This study provides a scientific basis for the molecular markers research, species identification and phylogenetic studies of forage legumes. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-024-01421-0.

An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea.

BACKGROUND: The chloroplast genome of plants is known for its small size and low mutation and recombination rates, making it a valuable tool in plant phylogeny, molecular evolution, and population genetics studies. Codon usage bias, an important evolutionary feature, provides insights into species evolution, gene function, and the expression of exogenous genes. Coffee, a key crop in the global tropical agricultural economy, trade, and daily life, warrants investigation into its codon usage bias to guide future research, including the selection of efficient heterologous expression systems for coffee genetic transformation. RESULTS: Analysis of the codon utilization patterns in the chloroplast genomes of three Coffea species revealed a high degree of similarity among them. All three species exhibited similar base compositions, with high A/T content and low G/C content and a preference for A/T-ending codons. Among the 30 high-frequency codons identified, 96.67% had A/T endings. Fourteen codons were identified as ideal. Multiple mechanisms, including natural selection, were found to influence the codon usage patterns in the three coffee species, as indicated by ENc-GC3s mapping, PR2 analysis, and neutral analysis. Nicotiana tabacum and Saccharomyces cerevisiae have potential value as the heterologous expression host for three species of coffee genes. CONCLUSION: This study highlights the remarkable similarity in codon usage patterns among the three coffee genomes, primarily driven by natural selection. Understanding the gene expression characteristics of coffee and elucidating the laws governing its genetic evolution are facilitated by investigating the codon preferences in these species. The findings can enhance the efficacy of exogenous gene expression and serve as a basis for future studies on coffee evolution.

Complete chloroplast genome of Loropetalum chinense var. rubrum and phylogenetic analysis from Baoshan, China.

In this study, the complete chloroplast genome of Loropetalum chinense var. rubrum Yieh was sequenced and characterized. The chloroplast genome is 159,427 bp in length, and contains a large single-copy (LSC) region of 88,185 bp and a small single-copy (SSC) region of 18,772 bp separated by a pair of inverted repeat (IR) regions of 26,235 bp. There are 128 genes in the genome including 83 protein-coding, 37 tRNA, and eight rRNA genes. The overall GC is 38.0% and the LSC, SSC, and IR regions are 36.1, 32.7, and 43.1%, respectively. Phylogenetic analysis of L. chinense var. rubrum fully resolved it in a clade with L. subcordatum. This complete chloroplast genome will provide valuable insight into evolution, molecular breeding, and phylogenetic analysis of Loropetalum species.

The complete chloroplast genome of Pittosporum brevicalyx.

Here, we report the complete chloroplast genome of Pittosporum brevicalyx. The genome is 153,388 bp in size, which is comprised of a large single-copy (LSC) region of 84,724 bp, a small single-copy (SSC) region of 18,716 bp, and two inverted repeat (IR) regions of 24,974 bp. The overall GC content of the plastome was 38.3%. The new sequence comprised 127 unique genes, including 82 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. Phylogenetic analysis showed that P.brevicalyx was close to Pittosporum kerrii and Pittosporum eugenioides. These data may providing useful information for phyletic evolution of P.brevicalyx within the Pittosporaceae family.