loading page

Comparative analyses of Diospyros (Ebenaceae) plastomes: Insights into genomic features, mutational hotspots, and adaptive evolution
  • +4
  • Jing Sun,
  • Qing Ma,
  • Yue Huang,
  • Chan-Juan Lai,
  • Pan Li,
  • Xin-Jie Jin,
  • Yong-Hua Zhang
Jing Sun
Wenzhou University

Corresponding Author:[email protected]

Author Profile
Qing Ma
Zhejiang Shuren University
Author Profile
Yue Huang
Wenzhou University
Author Profile
Chan-Juan Lai
Wenzhou University
Author Profile
Pan Li
Zhejiang University
Author Profile
Xin-Jie Jin
Wenzhou University
Author Profile
Yong-Hua Zhang
Wenzhou University
Author Profile


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.
25 Oct 2022Submitted to Ecology and Evolution
25 Oct 2022Submission Checks Completed
25 Oct 2022Assigned to Editor
28 Oct 2022Reviewer(s) Assigned
15 Dec 2022Review(s) Completed, Editorial Evaluation Pending
19 Dec 2022Editorial Decision: Revise Minor
27 Feb 20231st Revision Received
27 Feb 2023Assigned to Editor
27 Feb 2023Submission Checks Completed
27 Feb 2023Review(s) Completed, Editorial Evaluation Pending
27 Feb 2023Reviewer(s) Assigned
03 Apr 2023Editorial Decision: Revise Minor
15 Jun 20232nd Revision Received
20 Jun 2023Assigned to Editor
20 Jun 2023Submission Checks Completed
20 Jun 2023Review(s) Completed, Editorial Evaluation Pending
03 Jul 2023Editorial Decision: Accept