Aucuba Thunberg is small genus of ~ 10 evergreen woody species distributed in the Eastern Himalayas, China, Korea, Japan, Myanmar, and Vietnam [1]. Although the genus is currently endemic to East Asia, the earliest Aucuba fossil, which has been dated to the Eocene, was found in Washington State, USA, suggesting that Aucuba had a much broader distribution in the early Cenozoic [2] and its extant, relatively narrow distribution may have resulted from a range contraction triggered by the Neogene global cooling and the Pleistocene glaciations [3]. Aucuba is easy to recognize owing to its morphological distinctiveness, but difficult to place taxonomically. The taxonomic affinities of Aucuba have been in dispute since the establishment of the genus. Historically, this genus was placed into either the family Cornaceae [4–7] or the monotypic family Aucubaceae [8–11]. Recently, phylogenetic analyses based on DNA sequences revealed a sister relationship between Aucuba and Garrya, and the two genera are in turn closely related to Eucommiaceae [12–15]. Since Aucuba and Garrya show high levels of similarity in their morphologies and chemical components, they were grouped together as the family Garryaceae [16, 17]. Together with the monotypic family Eucommiaceae, which includes only one “living fossil” species (Eucommia ulmoides), Garryaceae was placed in the order Garryales within lamiids by the Angiosperm Phylogeny Group [16, 17].
Aucuba possesses remarkable horticultural merits. Because of their evergreen habit, spotted and colorful leaves, and showy fruits, Aucuba species have been widely introduced and cultivated as garden plants for centuries in East Asia, Europe, and North America [18, 19]. Previous research on Aucuba mainly focused on cultivation management, introduction and domestication, phytochemistry, and cytogenetics [18–22]. Genomic resources crucial for plant breeding, however, have received much less attention. In addition, the morphologies of Aucuba species are highly divergent and plastic, making morphology-based taxonomy perplexing and problematic [23], and hindering the effective conservation and exploitation of the germplasm. Development of robust and polymorphic molecular markers as DNA barcodes will contribute to accurate and reliable species identification in Aucuba.
Chloroplasts are organelles in green plants that perform photosynthesis and the biosynthesis of starch, fatty acids, pigments, and amino acids [24]. Typical angiosperm plastid genomes (plastomes), which consist of a large single copy (LSC, 80–90 kbp) region and a small single copy (SSC, 16–27 kbp) region separated by a pair of inverted repeat (IR, 20–30 kbp) regions, are characterized by circular DNA, uniparentally inherited, and highly conserved in structure and gene content [24–27]. Accordingly, gene content, structural arrangement, gene loss or pseudogenization, cytonuclear gene transfer, and sequence variations can provide informative and valuable resources for elucidating evolutionary relationships and species discrimination in plants [28–31]. With the advent of next-generation DNA sequencing technologies, plastome sequencing has been widely used in recent years to investigate evolutionary relationships among closely related species [28, 31–34] and to develop molecular markers for species identification [35–40] and population genetics [41–44]. Plastome sequencing can also offer genetic information related to synthesis of metabolic compounds, biopharmaceuticals, and tolerance to biotic and abiotic stress [45–49]. The availability and use of complete plastome sequences in biotechnology is likely to increase the performance of cultivated plants in the field [24, 50–52].
In the current study, we sequenced and characterized the complete plastomes of three Aucuba species (i.e., Aucuba chlorascens, Aucuba eriobotryifolia, and Aucuba japonica). Under a comparative framework within Garryales, we detected massive genomic arrangements between Aucuba and Eucommia. We used plastome DNA sequences to infer the phylogenetic relationships of Aucuba with other lamiids. The plastid genomic resources presented here will be beneficial for conservation and exploitation of Aucuba species.