Comparative chloroplast genomics and phylogenetic analysis of the Viburnum dilatatum complex (Adoxaceae) in Korea

Korean Journal of Plant Taxonomy
Jongsun Park, Hong Xi, Sang-Hun Oh
Complete chloroplast genome sequences provide detailed information about any structural changes of the genome, instances of phylogenetic reconstruction, and molecular markers for fine-scale analyses. Recent developments of next-generation sequencing (NGS) tools have led to the rapid accumulation of genomic data, especially data pertaining to chloroplasts. Short reads deposited in public databases such as the Sequence Read Archive of the NCBI are open resources, and the corresponding chloroplast genomes are yet to be completed. The V. dilatatum complex in Korea consists of four morphologically similar species: V. dilatatum, V. erosum, V. japonicum, and V. wrightii. Previous molecular phylogenetic analyses based on several DNA regions did not resolve the relationship at the species level. In order to examine the level of variation of the chloroplast genome in the V. dilatatum complex, raw reads of V. dilatatum deposited in the NCBI database were used to reconstruct the whole chloroplast genome, with these results compared to the genomes of V. erosum, V. japonicum, and three other species in Viburnum. These comparative genomics results found no significant structural changes in Vibur-num. The degree of interspecific variation among the species in the V. dilatatum complex is very low, suggesting that the species of the complex may have been differentiated recently. The species of the V. dilatatum complex share large unique deletions, providing evidence of close relationships among the species. A phylo-genetic analysis of the entire genome of the Viburnum showed that V. dilatatum is a sister to one of two accessions of V. erosum, making V. erosum paraphyletic. Given that the overall degree of variation among the species in the V. dilatatum complex is low, the chloroplast genome may not provide a phylogenetic signal pertaining to relationships among the species. Viburnum L. (Adoxaceae) widely distributed in temperate and subtropical regions of the Northern Hemisphere encompassing Europe, North Africa, Asia, and the Americas includes 175-200 species of small trees and shrubs (Rehder, 1908; Donoghue, 1983; Hara, 1983; Donoghue et al., 2004). There are ten species of the genus in Korea (Choi et al., 2018; Choi and Oh, 2019). The V. dilatatum complex in Korea consists of four morphologically similar species, i.e., V. dilatatum Thunb., V. erosum Thunb., V. japonicum (Thunb.) C. K. Spreng., and V. wrightii Miq. It is characterized by free bud scales and serrate leaves with pinnate veins and extrafloral nectaries at base on the abaxial surface (Choi and Oh, 2019). Phylogenetic analysis of Viburnum based on the nuclear internal transcribed spacers (ITS) regions and chloroplast rbcL, matK, and psbA-trnH regions strongly supported the complex as monophyletic but the relationships among the species within the complex remain unclear (Choi et al., 2018). Viburnum japonicum was supported as a monophyletic group in the ITS data but unresolved with V. dilatatum, V. erosum, and some accessions of V. wrightii. The cpDNA data showed one or two substitutions among the individuals of the complex included in the analysis. Recent applications of next-generation sequencing (NGS) tools have generated the rapid accumulation of genomic data
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