Comparative analysis of codon usage bias and phylogenetic relationships in chloroplast genomes across 49 Dendrobium...

Dendrobium is the second-largest genus in the Orchidaceae family. However, research on codon usage bias (CUB) in Dendrobium genus remains relatively limited. This knowledge gap impedes progress in genetic engineering and the breeding of superior varieties, making it challenging to meet the growing demand for higher yield and quality of Dendrobium.

The cp genomes of Dendrobium species exhibited codon composition biased toward A/T bases, with GC content below 50% (GC1 > GC2 > GC3). Eleven to nineteen optimal codons were identified across these species, with the third base of most codons predominantly ending with A/U. Parity rule 2-bias plots, effective number of codons plots, and neutrality plot analysis further revealed that natural selection serves as the primary driver of CUB variation, while mutation pressure played a secondary role. Notably, the positions of some species were different in the phylogenetic topologies from cp genomes and cp CDS.

CUB is an effective tool for investigating the phylogenetic evolution of Dendrobium. The CUB in Dendrobium species is primarily driven by natural selection, while mutation pressure plays a secondary role.