Comparative and evolutionary analysis of chloroplast genomes from five rare Styrax species

Abstract

Background: Styrax, a vital raw material for shipbuilding, construction, perfumes, and drugs, represents the largest and most diverse genus in the Styracaceae. However, there is a relative scarcity of research on Styrax, particularly in evolution and genetics. Therefore, this study conducted comparative and evolutionary analyses of the chloroplast genomes of five rare Styrax species (S. argentifolius, S. buchananii, S. chrysocarpus, S. finlaysonianus, and S. rhytidocarpus).

Results: The results indicated that, despite high levels of conservation in chloroplast genome structure among these species, specific mutation hotspot regions exist, particularly involving the expansion and contraction of the IR region. Additionally, evidence of positive selection was detected in eight genes (atpB, ccsA, ndhD, petA, rbcL, rpoC1, ycf1, and ycf2), which may be associated with adaptive evolution in response to environmental changes. Phylogenetic analysis revealed conflicts between trees constructed based on coding sequences and complete chloroplast genomes for several species, which were similar to previous phylogenetic studies.

Conclusion: This study underscores the importance of increasing sample sizes to enhance the accuracy of phylogenetic analyses and provides a new perspective on understanding the adaptive evolution of Styrax species. These findings are not only important for the conservation and sustainable use of Styrax, but also provide valuable insights for research in plant evolution and ecology within the genus.

Keywords: Styrax; Chloroplast genome diversity; Adaptive evolution; IR region expansion and contraction; Phylogenetic conflict; Selection pressure.

Fig. 1

Analysis of SSR sites and repetitive sequences in five chloroplast genomes. (A). Distribution of SSRs in the five samples; (B). Number of different SSRs loci types; (C). Number of different repeat types. Note: In (A), symbol (+) represented the position of SSRs, and the proportion of text displayed; In (C), C: complementary repeats, F: forward repeats, P: palindromic repeats, R: reverse repeats

Fig. 2

Comparison of chloroplast genome structure in five species and five closely related species. IR (Inverted repeat), LSC (Large single copy) and SSC (Small single copy) regions and border genes are indicated. Note: JLA: junction between LSC and IRa; JLB: junction between LSC and IRb; JSA: junction between SSC and IRa; JSB: junction between SSC and IRb

Fig. 3

Relative synonymous codon usage and selective pressures in the evolution. (A). Codon content of 20 amino acids and stop codons in all protein-coding genes of five chloroplast genome; (B). Distribution of codon preference in five species; (C). Ka/Ks values of protein-coding genes of the five comparative combinations. Note: in (A), the top panels show the RSCU for the corresponding amino acids, and the colored blocks shown below represent different codons; In (C). Ka: nonsynonymous; Ks: synonymous

Fig. 4

Nucleotide diversity of chloroplast genomes in five Styrax species. (A). Pi in CDS; (B). chloroplast genome Pi value. Note: window length: 600 bp, step length: 50 bp; X axis: position of the midpoint of each window; Y axis: Pi of each window. The blue line represents the trajectory of the value of Pi

Fig. 5

Phylogenetic tree analysis using Maximum Likelihood (ML) and Bayesian inference (BI) based on complete chloroplast genomes and CDS sequences. (A) Complete chloroplast genomes with ML method analysis. (B) CDS sequences with BI method analysis. Note: the blue circle at the branch node signifies the support rate of employing the bootstrap method, with its area directly proportional to the degree of support