Comparative Analysis of Codon Usage Patterns in Nuclear and Chloroplast Genome of Dalbergia (Fabaceae)

Abstract

The Dalbergia plants are widely distributed across more than 130 tropical and subtropical countries and have significant economic and medicinal value. Codon usage bias (CUB) is a critical feature for studying gene function and evolution, which can provide a better understanding of biological gene regulation. In this study, we comprehensively analyzed the CUB patterns of the nuclear genome, chloroplast genome, and gene expression, as well as systematic evolution of Dalbergia species. Our results showed that the synonymous and optimal codons in the coding regions of both nuclear and chloroplast genome of Dalbergia preferred ending with A/U at the third codon base. Natural selection was the primary factor affecting the CUB features. Furthermore, in highly expressed genes of Dalbergia odorifera, we found that genes with stronger CUB exhibited higher expression levels, and these highly expressed genes tended to favor the use of G/C-ending codons. In addition, the branching patterns of the protein-coding sequences and the chloroplast genome sequences were very similar in the systematic tree, and different with the cluster from the CUB of the chloroplast genome. This study highlights the CUB patterns and features of Dalbergia species in different genomes, explores the correlation between CUB preferences and gene expression, and further investigates the systematic evolution of Dalbergia, providing new insights into codon biology and the evolution of Dalbergia plants.

The first complete chloroplast genome of Thalictrum fargesii: insights into phylogeny and species identification

“…One of the molecular features known as “codon use bias” also helps unveil chloroplast and nuclear genome relationships and has been influenced by the GC content at codon locations in various organisms ( Yang et al., 2018 ). Moreover, it is a critical feature for studying the functions of genes and contributes to its evolutionary relationship ( Wang et al., 2023 ; Yang et al., 2023 ). We disclosed the presence of AT-rich intergenic regions in our present analysis, which is harmonized with the phenomenon that the overall GC content in the cp genomes of terrestrial plants is often low ( Yang et al., 2017 ).…”

Decoding Evolution of Rubioideae: Plastomes Reveal Sweet Secrets of Codon Usage, Diagnostides, and Superbarcoding

“…Evolution might affect chloroplast genomes by changing their structure, content, and creation of nucleotide differences. Most plastome codons end with A or T (we are using a thymine instead of uracil for a convenience because our analysis is based on DNA material), which might be an effect of many million years of development of chloroplast genomes [43,[54][55][56][57][58]. However, the RSCU is sometimes very similar in the case of specific codons.…”