Complete Chloroplast Genome Sequence of the Endemic and Endangered Plant Dendropanax oligodontus: Genome Structure, Comparative and Phylogenetic Analysis

Abstract

Dendropanax oligodontus, which belongs to the family Araliaceae, is an endemic and endangered species of Hainan Island, China. It has potential economic and medicinal value owing to the presence of phenylpropanoids, flavonoids, triterpenoids, etc. The analysis of the structure and characteristics of the D. oligodontus chloroplast genome (cpDNA) is crucial for understanding the genetic and phylogenetic evolution of this species. In this study, the cpDNA of D. oligodontus was sequenced for the first time using next-generation sequencing methods, assembled, and annotated. We observed a circular quadripartite structure comprising a large single-copy region (86,440 bp), a small single-copy region (18,075 bp), and a pair of inverted repeat regions (25,944 bp). The total length of the cpDNA was 156,403 bp, and the GC% was 37.99%. We found that the D. oligodontus chloroplast genome comprised 131 genes, with 86 protein-coding genes, 8 rRNA genes, and 37 tRNAs. Furthermore, we identified 26,514 codons, 13 repetitive sequences, and 43 simple sequence repeat sites in the D. oligodontus cpDNA. The most common amino acid encoded was leucine, with a strong A/T preference at the third position of the codon. The prediction of RNA editing sites in the protein-coding genes indicated that RNA editing was observed in 19 genes with a total of 54 editing sites, all of which involved C-to-T transitions. Finally, the cpDNA of 11 species of the family Araliaceae were selected for comparative analysis. The sequences of the untranslated regions and coding regions among 11 species were highly conserved, and minor differences were observed in the length of the inverted repeat regions; therefore, the cpDNAs were relatively stable and consistent among these 11 species. The variable hotspots in the genome included clpP, ycf1, rnK-rps16, rps16-trnQ, atpH-atpI, trnE-trnT, psbM-trnD, ycf3-trnS, and rpl32-trnL, providing valuable molecular markers for species authentication and regions for inferring phylogenetic relationships among them, as well as for evolutionary studies. Evolutionary selection pressure analysis indicated that the atpF gene was strongly subjected to positive environmental selection. Phylogenetic analysis indicated that D. oligodontus and Dendropanax dentiger were the most closely related species within the genus, and D. oligodontus was closely related to the genera Kalopanax and Metapanax in the Araliaceae family. Overall, the cp genomes reported in this study will provide resources for studying the genetic diversity and conservation of the endangered plant D. oligodontus, as well as resolving phylogenetic relationships within the family.

Keywords: Dendropanax; chloroplast genomes; nucleotide diversity; phylogenetic analysis.

Figure 1

Gene map of the D. oligodontus chloroplast genome. Genes shown outside the outer circle are transcribed clockwise, and genes shown inside the circle are transcribed counter-clockwise. Genes belonging to different functional groups are colour-coded. The dashed area in the inner circle indicates the GC content of the chloroplast, and the light grey area corresponds to the AT content of the chloroplast.

Figure 2

Distribution, type, and presence of simple sequence repeats (SSRs) in the chloroplast genome of D. oligodontus. (A) Presence of SSRs in the large single-copy (LSC), small single-copy (SSC), and inverted repeat (IR) regions. (B) Presence of SSRs in the protein-coding regions, introns, and intergenic spacers of LSC, SSC, and IR regions. (C) Presence of polymers in the chloroplast genome.

Figure 3

Visualisation alignment of the chloroplast genome sequence of 11 species. The identity percentages are shown on the y-axis and range from 50% to 100%, while the horizontal axis shows the position within the chloroplast genome. Each arrow indicates the annotated genes and the direction of their transcription in the reference genome. Genome regions, i.e., exons, untranslated regions (UTRs), conserved noncoding sequences (CNS), and mRNA, are colour-coded.

Figure 4

Nucleotide diversity (Pi) analysis of 11 species’ chloroplast genes.

Figure 5

Comparison of the boundaries of the LSC, SSC, and IR regions of the 11 chloroplast genomes. JLB: junction between LSC and IRb; JSB: junction between SSC and IRb; JSA: junction between SSC and IRa; JLA: junction between LSC and IRa.

Figure 6

Phylogenetic trees of the Araliaceae species inferred from maximum likelihood (ML) analyses based on the chloroplast genome constructed using coding region data. Support for branches is given by bootstrap values.