Abstract
Wikstroemia (Thymelaeaceae) is a diverse genus that extends from Asia to Australia and has been recorded on the Hawaiian Islands. Despite its medicinal properties and resource utilization in pulp production, genetic studies of the species in this important genus have been neglected. In this study, the plastome sequences of six species of Wikstroemia were sequenced and analysed. The plastomes ranged in size between 172,610 bp (W. micrantha) and 173,697 bp (W. alternifolia) and exhibited a typical genome structure consisting of a pair of inverted repeat (IR) regions separated by a large single-copy (LSC) region and a small single-copy (SSC) region. The six plastomes were similar in the 138 or 139 genes predicted, which consisted of 92 or 93 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The overall GC contents were identical (36.7%). Comparative genomic analyses were conducted with the inclusion of two additional published species of Wikstroemia in which the sequence divergence and expansion of IRs in the plastomes were determined. When compared to the coding sequences (CDSs) of Aquilaria sinensis, five genes, namely, rpl2, rps7, rps18, ycf1 and ycf2, indicated positive selection in W. capitata. The plastome-based phylogenetic analysis inferred that Wikstroemia in its current state is paraphyletic to Stellera chamaejasme, while the ITS-based tree analyses could not properly resolve the phylogenetic relationship between Stellera and Wikstroemia. This finding rekindled interest in the proposal to synonymize Stellera with Wikstroemia, which was previously proposed but rejected due to taxonomic conflicts. Nevertheless, this study provides valuable genomic information to aid in the taxonomic implications and phylogenomic reconstruction of Thymelaeaceae.
Highlights
Wikstroemia Engl. (Thymelaeaceae) is a diverse genus of approximately 70 species
The total length of the plastomes of the six species of Wikstroemia analysed in this study ranged from 172,610 bp (W. micrantha) to 173,697 bp (W. alternifolia)
The maximum-likelihood (ML) and Bayesian inference (BI) trees based on the complete plastome sequences excluding the IRa sequences and the dataset of the intergenic spacer (IGS) sequences revealed that all the branch nodes for eight species of Wikstroemia included in the phylogenetic tree were supported with high bootstrap values and Bayesian posterior probabilities (ML: ≥ 90%; BI: ≥ 95%) (Fig. 7)
Summary
Wikstroemia Engl. (Thymelaeaceae) is a diverse genus of approximately 70 species. Members of Wikstroemia are widely distributed in the Asian and Oceanian regions and scattered around the Hawaiian I slands[1]. The taxonomic placement of Wikstroemia has been controversial This genus has experienced a complicated classification history in reviews of members of the Thymelaeaceae. Constituent genera in Thymelaeaceae have experienced similar molecular challenges, in which poor phylogenetic resolution is likely due to low genetic variation in the selected molecular markers[23]. Such conflicts can be overcome by utilizing genome-scale d atasets[24]. We sequenced the complete plastomes of six species of Wikstroemia, W. alternifolia, W. canescens, W. capitata, W. dolicantha, W. micrantha, and W. scytophylla, to analyse and compare genomes using bioinformatic tools. Our aims were to (1) characterize the plastomes of the six species of Wikstroemia; (2) examine the variation in sequence repeats and codon usage in the six plastome sequences; (3) identify highly divergent regions in the plastome sequences; and (4) improve the understanding of the intrageneric/intergeneric phylogeny of Wikstroemia within Thymelaeaceae based on plastome sequences and the nuclear ribosomal DNA internal transcribed spacer (ITS) region
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