Characterization, comparison, and phylogenetic analyses of chloroplast genomes of Euphorbia species

Abstract

The genus Euphorbia (Euphorbiaceae) has near-cosmopolitan distribution and serves as a significant resource for both ornamental and medicinal purposes. Despite its economic importance, Euphorbia's taxonomy has long been challenged by the intricate nature of morphological traits exhibiting high levels of convergence. While molecular markers are essential for phylogenetic studies, their availability for Euphorbia has been limited. To address this gap, we conducted comparative analyses focusing on the chloroplast (CP) genomes of nine Euphorbia species, incorporating three newly sequenced and annotated accessions. In addition, phylogenetic informativeness and nucleotide diversity were computed to identify candidate markers for phylogenetic analyses among closely related taxa in the genus. Our investigation revealed relatively conserved sizes and structures of CP genomes across the studied species, with notable interspecific variations observed primarily in non-coding regions and IR/SC borders. By leveraging phylogenetic informativeness and nucleotide diversity, we identified rpoB gene as the optimal candidate for species delimitation and shallow-level phylogenetic inference within the genus. Through this comprehensive analysis of CP genomes across multiple taxa, our study sheds light on the evolutionary dynamics and taxonomic intricacies of Euphorbia, offering valuable insights into its CP genome evolution and taxonomy.

Keywords: Euphorbia; Chloroplast genome; Comparative analysis; Intraspecific variation; Phylogenetic analysis.

Figure 1

Plot of sequence divergence in chloroplast genomes among nine species of Euphorbia estimated from mVISTA. Euphorbia hirta was used as a reference to estimate the percent sequence identities. Pink and purple areas indicate non-coding regions and coding regions, respectively.

Figure 2

Comparison of the borders between the Large Single Copy (LSC), Inverted Repeat (IR), and Small Single Copy (SSC) regions among chloroplast genomes of nine Euphorbia species.

Figure 3

Nucleotide diversity plot estimated among the chloroplast genomes of nine Euphorbia species.

Figure 4

Bar plots illustrating inter- and intra-specific variations in genome size. (A) Variation in complete CP genome length; (B) Variation in Large Single Copy (LSC) region length; (C) Variation in Small Single Copy (SSC) region length; and (D) Variation in Inverted Repeat (IR) region length. The lines within the boxes represent the mean values. Error bars, denoted by vertical dotted lines, indicate standard deviation.

Figure 5

Phylogenetic relationships among 42 Euphorbia species inferred from complete CP genomes using the Maximum Likelihood (ML) method. Bootstrap values are indicated at branch nodes. The four colors represent each of the four subgenera in Euphorbia.

Figure 6

Phylogenetic relationships among Euphorbia species based on the rpoB gene (right) and complete CP genomes (left), inferred using the Maximum Likelihood (ML) method. Dashed lines connect identical samples in both trees. The four colors represent each of the four subgenera in Euphorbia: Red for subg. Chamaesyce, Green for subg. Euphorbia, Orange for subg. Athymalus, and Blue for subg. Esula.