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Evolutionary Dynamics of Chloroplast Genome and Codon Usage in the Genus Diospyros (Ebenaceae)

Jisi Zhang,Zhuo Li

Published 2025 in Biology

ABSTRACT

Simple Summary Diospyros is a large and important genus of trees with ecological and economic value. This study analyzed chloroplast genomes and codon usage in 15 Diospyros species to understand their evolution and genetic diversity. The results showed low genetic variation in the IR regions and high conservation at boundary areas, with three main evolutionary groups identified. Codon usage analysis revealed a preference for A or U at the third position and weak codon bias overall. Natural selection, rather than mutation pressure, was found to be the main factor shaping codon usage patterns. These findings provide a robust foundation for future investigations into molecular evolution and phylogenetic relationships in the genus Diospyros. Abstract Diospyros, the most species-rich woody plant genus in Ebenaceae, has attracted significant academic interest due to its ecological and economic importance. This study presented the first complete assembly and annotation of the chloroplast genome of Diospyros tsangii. The chloroplast genome measured 157,445 bp, with a typical quadripartite circular structure and 132 annotated coding genes. A comprehensive analysis of evolutionary traits and codon usage preferences across chloroplast genomes of 15 Diospyros species were conducted. The main objective was to provide a theoretical basis for understanding phylogenetic relationships and assessing genetic diversity within Diospyros. Our findings showed that genetic diversity in the IR regions of the chloroplast genomes is notably lower than that in the LSC and SSC regions. The boundary regions exhibited high conservation with minimal variation. Selected pressure analysis indicated that most coding genes are under purifying selection. Phylogenetic analysis showed that D. tangii was sister to Diospyros oleifera, and Diospyros kaki was closely related to Diospyros vaccinioides with high supporting values. The examination of codon usage patterns showed that the GC content at the first, second, and third codon positions of 52 protein-coding sequences followed the order GC1 > GC2 > GC3, with a preference for A or U bases at the third position. The effective number of codons ranged from 45.13 to 45.43, which indicated the weak codon bias. The neutral-plot, ENC-plot, and PR2-plot analysis suggested that natural selection predominantly influences the codon usage patterns in Diospyros plants. These results would be vital to understand the evolutionary dynamics of the genus Diospyros.

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