Comparative chloroplast genomic and phylogenetic analysis of Aralia and related species

The chloroplast genomes of two species of Aralia and Pentapanax were sequenced, assembled, annotated, and structurally analyzed. Furthermore, combined with chloroplast genome sequences of related species downloaded from the NCBI database, phylogenetic analysis was conducted. The chloroplast genomes of the four species all exhibited a quadripartite circular structure with a length of 155 744 – 156 201 bp and GC content of 38.1%. Both genera contained 132 genes, including 87 protein-coding genes, eight ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. Boundary analysis found that neither contraction nor expansion occurred in the inverted repeat regions. The number of simple sequence repeat (SSR) loci ranged from 39 to 43, most of which were mononucleotide and dinucleotide repeats, and mostly located in non-coding regions. Sequence differences mainly occurred in the non-coding regions of the large single copy (LSC) and small single copy (SSC) regions. The maximum-likelihood tree revealed two highly supported monophyletic branches: the first composed of Pentapanax, Aralia atropurpurea Franch., Aralia cordata Thunb., and Aralia continentalis Kitagawa and the second composed of other Aralia species. In general, the chloroplast genome sequences of Aralia and Pentapanax plants were relatively conserved. The phylogenetic results supported the placement of Pentapanax into the genus Aralia, with each Aralia species forming a monophyly.