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Oplopanax elatus Nakai is a deciduous shrub within the Araliaceae family and is classified as a first-class protected plant in Jilin Province. To elucidate the structural characteristics of its chloroplast genome and phylogenetic relationships, this study conducted chloroplast genome sequencing of one cultivated individual and five wild populations of O. elatus, followed by comparative chloroplast genomic and phylogenetic analyses with published congeneric species of Oplopanax and allied genera of Araliaceae deposited in GenBank. The results revealed that the chloroplast genomes of the six O. elatus accessions ranged from 156 108-156 193 bp in length, with a uniform GC content of 38.03%. A total of 129-133 genes were annotated, comprising 87-88 protein-coding genes, 6-8 rRNA genes, and 36-37 tRNA genes. The chloroplast genome of cultivated O. elatus contained one additional protein-coding gene compared to those of wild accessions. Using the chloroplast genome sequence of cultivated O. elatus as reference, sequence alignment against wild populations identified 36 single nucleotide polymorphism (SNP) loci and 10 insertion-deletion (InDel) loci. SNPs were distributed in both intergenic spacers and coding sequences (CDS), whereas all InDels were restricted to the large single-copy (LSC) region. Nucleotide diversity (Pi) analysis of the 13 chloroplast genomes detected two hypervariable regions, clpP1-exon3_clpP1-exon2 and ycf1, which are proposed as candidate DNA barcodes and molecular markers for O. elatus. Analysis of codon preference indicated that all 13 samples exhibited a preference for codons terminating in A or T. Discrepancies in codon numbers were observed between cultivated and wild O. elatus chloroplast genomes. A total of 545 simple sequence repeat (SSR) loci and 498 dispersed repeat sequences were identified within the 13 chloroplast genomes. Phylogenetic reconstruction based on branch support values and clustering patterns partitioned the eight Araliaceae genera into four clades. The genus Oplopanax formed a highly supported monophyletic lineage positioned centrally within the tree, diverging subsequently to Panax and constituting a sister group to the fourth major clade, with its closest affinity to Schefflera. This investigation advances the understanding of evolutionary dynamics within Oplopanax and allied genera, with the acquired genomic resources providing a foundation for DNA barcode screening and germplasm conservation of the genus.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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