Comparative analyses of Diospyros (Ebenaceae) plastomes: Insights into
genomic features, mutational hotspots, and adaptive evolution
Abstract
Diospyros (Ebenaceae) is a widely distributed genus of trees and shrubs
native to tropical and subtropical regions, with numerous species valued
for their fruits (persimmons), timber, and medicinal values. However,
information regarding their plastomes and chloroplast evolution is
scarce. The present study performed comparative genomic and evolutionary
analyses on plastomes of 18 accepted Diospyros species, including three
newly sequenced ones. Our study showed a highly conserved genomic
structure across the species, with plastome size ranging from 157,321 bp
(D. jinzaoshi) to 157,934 bp (D. deyangensis). These plastomes encoded
134–138 genes, including 89–91 protein-coding genes, 1–2 pseudogenes
(Ψycf1 for all, Ψrps19 for a few), 37 tRNA genes, and 8 rRNA genes.
Comparative analysis of Diospyros identified the intergenic regions
(trnH-psbA, rps16-trnQ, trnT-psbD, petA-psbJ, trnL-trnF-ndhJ) as the
mutational hotspots in these species. Phylogenomic analyses identified
three main groups within the genus designated as the evergreen,
deciduous, and island groups. The codon usage analysis identified 30
codons with relative synonymous codon usage (RSCU) values greater than 1
and 29 codons ending with A and U bases. A total of three codons (UUA,
GCU, and AGA) with highest (RSCU) values were identified as the optimal
codons. ENC-plot indicated the significant role of mutational pressure
in shaping codon usage, while most protein-coding genes in Diospyros
experienced relaxed purifying selection (Ka/Ks < 1).
Additionally, the ndhG, rpoC1, and ycf3 genes showed positive selection
(Ka/Ks > 1) in the island, deciduous, and both deciduous
and evergreen species, respectively. Thus, the results provide a
foundation for elaborating Diospyros’s genetic architecture and
taxonomy, conserving genetic diversity and enriching genetic resources.