Comparative analysis 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 from pantropical to temperate regions, with numerous species valued for their fruits (persimmons), timber, and medicinal values. However, information regarding their plastomes and chloroplast evolution is scarce. The pr...
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Wiley
2023-07-01
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| Series: | Ecology and Evolution |
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| Online Access: | https://doi.org/10.1002/ece3.10301 |
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| author | Yue Huang Qing Ma Jing Sun Li‐Na Zhou Chan‐Juan Lai Pan Li Xin‐Jie Jin Yong‐Hua Zhang |
| author_facet | Yue Huang Qing Ma Jing Sun Li‐Na Zhou Chan‐Juan Lai Pan Li Xin‐Jie Jin Yong‐Hua Zhang |
| author_sort | Yue Huang |
| collection | DOAJ |
| description | Abstract Diospyros (Ebenaceae) is a widely distributed genus of trees and shrubs from pantropical to temperate 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 45 accepted Diospyros species, including three newly sequenced ones. Our study showed a highly conserved genomic structure across the Diospyros species, with 135–136 encoding genes, including 89 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 three intergenic regions (ccsA‐ndhD, rps16‐psbK and petA‐psbJ) and five genes (rpl33, rpl22, petL, psaC and rps15) as the mutational hotspots in these species. Phylogenomic analysis identified the phylogenetic position of three newly sequenced ones and well supported a monophylogenetic (sub)temperate taxa and four clades in the pantropical taxa. The analysis codon usage identified 30 codons with relative synonymous codon usage (RSCU) values >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. Effective number of 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 (dN/dS < 1). Additionally, the psbH gene showed positive selection (dN/dS > 1) in the (sub)temperate species. Thus, the results provide a meaningful foundation for further elaborating Diospyros's genetic architecture and taxonomy, enriching genetic diversity and conserving genetic resources. |
| format | Article |
| id | doaj-art-ebe430f95633466b9786f5d0d07a644a |
| institution | DOAJ |
| issn | 2045-7758 |
| language | English |
| publishDate | 2023-07-01 |
| publisher | Wiley |
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| series | Ecology and Evolution |
| spelling | doaj-art-ebe430f95633466b9786f5d0d07a644a2025-08-20T03:01:35ZengWileyEcology and Evolution2045-77582023-07-01137n/an/a10.1002/ece3.10301Comparative analysis of Diospyros (Ebenaceae) plastomes: Insights into genomic features, mutational hotspots, and adaptive evolutionYue Huang0Qing Ma1Jing Sun2Li‐Na Zhou3Chan‐Juan Lai4Pan Li5Xin‐Jie Jin6Yong‐Hua Zhang7College of Life and Environmental Science Wenzhou University Wenzhou ChinaCollege of Biology and Environmental Engineering Zhejiang Shuren University Hangzhou ChinaCollege of Life and Environmental Science Wenzhou University Wenzhou ChinaCollege of Life and Environmental Science Wenzhou University Wenzhou ChinaCollege of Life and Environmental Science Wenzhou University Wenzhou ChinaLaboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences Zhejiang University Hangzhou ChinaCollege of Life and Environmental Science Wenzhou University Wenzhou ChinaCollege of Life and Environmental Science Wenzhou University Wenzhou ChinaAbstract Diospyros (Ebenaceae) is a widely distributed genus of trees and shrubs from pantropical to temperate 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 45 accepted Diospyros species, including three newly sequenced ones. Our study showed a highly conserved genomic structure across the Diospyros species, with 135–136 encoding genes, including 89 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 three intergenic regions (ccsA‐ndhD, rps16‐psbK and petA‐psbJ) and five genes (rpl33, rpl22, petL, psaC and rps15) as the mutational hotspots in these species. Phylogenomic analysis identified the phylogenetic position of three newly sequenced ones and well supported a monophylogenetic (sub)temperate taxa and four clades in the pantropical taxa. The analysis codon usage identified 30 codons with relative synonymous codon usage (RSCU) values >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. Effective number of 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 (dN/dS < 1). Additionally, the psbH gene showed positive selection (dN/dS > 1) in the (sub)temperate species. Thus, the results provide a meaningful foundation for further elaborating Diospyros's genetic architecture and taxonomy, enriching genetic diversity and conserving genetic resources.https://doi.org/10.1002/ece3.10301Diospyrosgenetic diversityhyper‐variable regionplastome |
| spellingShingle | Yue Huang Qing Ma Jing Sun Li‐Na Zhou Chan‐Juan Lai Pan Li Xin‐Jie Jin Yong‐Hua Zhang Comparative analysis of Diospyros (Ebenaceae) plastomes: Insights into genomic features, mutational hotspots, and adaptive evolution Ecology and Evolution Diospyros genetic diversity hyper‐variable region plastome |
| title | Comparative analysis of Diospyros (Ebenaceae) plastomes: Insights into genomic features, mutational hotspots, and adaptive evolution |
| title_full | Comparative analysis of Diospyros (Ebenaceae) plastomes: Insights into genomic features, mutational hotspots, and adaptive evolution |
| title_fullStr | Comparative analysis of Diospyros (Ebenaceae) plastomes: Insights into genomic features, mutational hotspots, and adaptive evolution |
| title_full_unstemmed | Comparative analysis of Diospyros (Ebenaceae) plastomes: Insights into genomic features, mutational hotspots, and adaptive evolution |
| title_short | Comparative analysis of Diospyros (Ebenaceae) plastomes: Insights into genomic features, mutational hotspots, and adaptive evolution |
| title_sort | comparative analysis of diospyros ebenaceae plastomes insights into genomic features mutational hotspots and adaptive evolution |
| topic | Diospyros genetic diversity hyper‐variable region plastome |
| url | https://doi.org/10.1002/ece3.10301 |
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