DOI: https://doi.org/10.21203/rs.3.rs-2486972/v1
Viburnum japonicum (Thunb.) Sprengel is a unique and endangered species in the family Adoxaceae and is endemic to the coastal region of Eastern Asia (China, Japan, and South Korea). However, its systematic position remains controversial. Here, we characterized and reported a second complete chloroplast genome of V. japonicum using the Illumina NovaSeq platform. The total length of the chloroplast genome is 158,606 bp with G + C contents of 38.08%, including a large single-copy (LSC) region, a small single-copy (SSC) region, and a pair of inverted repeats (IRs) regions with lengths of 87,060 bp, 18,510 bp, and 26,516 bp, respectively. Phylogenetic analysis revealed that the two accessions of V. japonicum were close related to a clade of V. setigerum, V. erosum, and V. fordiae within the genus Viburnum.
Viburnum japonicum, commonly called Japanese viburnum, is a species in the family Adoxaceae. It can be easily distinguished from other recorded species of Viburnum by having characteristics such as rounded and evergreen shrubs, broad leaves, and glabrous texture. Thus the species has great potential for ornamental and economic use. In the past, the species was thought to be only naturally distributed on the coast of Japan (Mainly Honshu, Kyushu, and Ryukyu Islands). In 1994, V. japonicum was first reported by Chinese plant taxonomists from the east coast of Zhejiang Province. Since then, it was recognized as a plant species with extremely small populations (PSESP) and listed among Zhejiang’s key protected wild plant list. By 2003, V. japonicum occurred in South Korea (Gageo-do Island) (Hong and Im, 2003) subsequently. However, the taxonomic status and phylogenetic position of V. japonicum remains controversial. In recent years, comparative analysis of the complete chloroplast genome sequences has been used as an effective tool for studying plant phylogeny and taxonomy (Ju et al. 2019). Some botanists thought it was close to V. utile (Cho et al. 2018), while others thought it was sister to V. erosum (Park et al. 2019; Choi et al. 2020). In this paper, we report a second complete chloroplast genome of V. japonicum, which provides a useful resource for genetic diversity studies. We also performed a phylogenetic analysis to demonstrate the relationships between V. japonicum and other relative species.
One individual of V. japonicum was collected and deposited at the Zhejiang Academy of Forestry, Zhejiang Province, China (30°12′N, 120°01′E) under the voucher number HZ2022-05 (contact person: Hong Zhu, Email: [email protected]). The total genomic DNA was extracted from fresh leaves of V. japonicum according to the modified CTAB methods. Then, it was sequenced on the Illumina NovaSeq platform at Personalbio Biotech (Shanghai, China). The annotated complete chloroplast genome sequence of V. japonicum was submitted to the GenBank database with the accession number OP644292.
The complete chloroplast genome of V. japonicum was 158,606 bp in length. Consisting of four subregions; a large single-copy (LSC) of 87,060 bp, a small single-copy (SSC) region of 18,510 bp, and a pair of inverted repeat regions (IRs) each of 26,516 bp (Fig. 1). The overall nucleotide composition of the chloroplast genome sequence is: A (30.62%), T (31.29%), C (19.38%), and G (18.71%), and the total G+C contents of the chloroplast genome were 38.08%; LSC (36.42%), SSC (31.97%), and IRs (42.97%). The genome contained a total of 131 genes, including 87 Protein-coding genes (PCGs), eight rRNA genes, and 36 tRNA genes.
To clarify the phylogenetic position of V. japonicum within the genus Viburnum, 17 additional complete chloroplast genome sequences (Dipsacus japonicus MZ934745, Sambucus chinensis MW455170, and S. williamsii KX510276 as outgroups) were aligned using the program MAFFT v7.429 (Katoh et al. 2019). The software RAxML version 8.2.12 (Stamatakis 2014) was used for phylogenetic tree construction based on the maximum likelihood (ML) algorithm under the parameter model of GTRGAMMA and 1 000 bootstrap replicates. The ML tree showed that all the Viburnum species clustered into two clades (Clade A and Clade B) by high bootstrap support. The two accessions of V. japonicum were a sister group to a small clade of three Viburnum species including V. setigerum, V. erosum, and V. fordiae, and were placed in a monophyletic group with other two Viburnum species (V. luzonicum and V. melanocarpum) in Clade A, while the rest of six Viburnum species were placed in a sister Clade B (Fig. 2). The study will provide essential data for future research on the phylogenetic and evolutionary relationship between V. japonicum and the genus Viburnum.
This research was financially supported by the Zhejiang Provincial Scientific Research Institute special project (2022F1068-3 and 2021F1065-6).