Plastome structure and phylogenetic relationships of Styracaceae (Ericales)

Abstract

Background: The Styracaceae are a woody, dicotyledonous family containing 12 genera and an estimated 160 species. Recent studies have shown that Styrax and Sinojackia are monophyletic, Alniphyllum and Bruinsmia cluster into a clade with an approximately 20-kb inversion in the Large Single-Copy (LSC) region. Halesia and Pterostyrax are not supported as monophyletic, while Melliodendron and Changiostyrax always form sister clades. Perkinsiodendron and Changiostyrax are newly established genera of Styracaceae. However, the phylogenetic relationship of Styracaceae at the generic level needs further research.

Results: We collected 28 complete plastomes of Styracaceae, including 12 sequences newly reported here and 16 publicly available sequences, comprising 11 of the 12 genera of Styracaceae. All species possessed the typical quadripartite structure of angiosperm plastomes, with sequence differences being minor, except for a large 20-kb (14 genes) inversion found in Alniphyllum and Bruinsmia. Seven coding sequences (rps4, rpl23, accD, rpoC1, psaA, rpoA and ndhH) were identified to possess positively selected sites. Phylogenetic reconstructions based on seven data sets (i.e., LSC, SSC, IR, Coding, Non-coding, combination of LSC + SSC and concatenation of LSC + SSC + one IR) produced similar topologies. In our analyses, all genera were strongly supported as monophyletic. Styrax was sister to the remaining genera. Alniphyllum and Bruinsmia form a clade. Halesia diptera does not cluster with Perkinsiodendron, while Perkinsiodendron and Rehderodendron form a clade. Changiostyrax is sister to a clade of Pterostyrax and Sinojackia.

Conclusion: Overall, our results demonstrate the power of plastid phylogenomics in improving estimates of phylogenetic relationships among genera. This study also provides insight into plastome evolution across Styracaceae.

Keywords: Genome structure; Phylogeny; Plastome; Positive selection; Styracaceae.

Fig. 1

Gene map of the Styrax faberi. A The inverted order of genes in Alniphyllum fortunei; B The corresponding region of Styrax faberi

Fig. 2

Visualization of the alignment of 26 Styracaceae plastome sequences. The plastome of Pterostyrax hispidus was used as the reference. The Y-axis depicts percent identity to the reference genome (50–100%) and the X-axis depicts sequence coordinates within the plastome. Genome regions were color-coded according to coding and noncoding regions

Fig. 3

Comparison of the nucleotide diversity (Pi) values across 28 Styracaceae plastomes. A Protein-coding regions. B Noncoding regions

Fig. 4

Synonymous (dS) and nonsynonymous (dN) substitution rates of the protein coding genes

Fig. 5

ω (dN/dS) values of genes in plastomes of the Styracaceae. The red line represents neutral selection, while values above one represents positive/adaptative selection, and values below one represents negative/purifying selection

Fig. 6

Optimal phylogenetic tree resulting from analyses of 79 protein-coding genes using Maximum Likelihood (ML). Bayesian inference (BI) topology is the same as ML. Support values next to the nodes are maximum likelihood bootstrap support/Bayesian posterior probability; asterisks indicate 100%/1.0 support values. The genera of Styracaceae are indicated by different branch colors. The inset shows the same tree as a phylogram