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

Abstract

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 Viburnum. 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 phylogenetic 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.

The Complete Chloroplast Genome of Arabidopsis thaliana Isolated in Korea (Brassicaceae): An Investigation of Intraspecific Variations of the Chloroplast Genome of Korean A. thaliana

“…There are two significant peaks identified in the sliding window analysis of nucleotide diversity: one is trn L/ trn F (pi value is 0.0147) and the other is trn P/ psa J (pi value is 0.00441). There are fewer peaks than in other studies, including those focusing on Dysphania [ 27 ] and Viburnum [ 32 ], stemming from the low level of nucleotide diversity throughout the chloroplast genome. The first peak, trn L/ trn F, appeared due to one large insertion of the Tsu0 chloroplast genome ( Figure 5(b) ).…”

“…It is caused by 6 bp deletion on ycf2 located in the IR region compared to the rest five A. thaliana chloroplast genomes. Interestingly, Tsu0 shows the longest length of chloroplast genome, caused by an insertion of approximately 500 bp between trnL and trnF , which is similar to the cases of Coffea arabica with one continuous insertion region [ 50 ], Duchesnea chrysantha showing three continuous insertion regions [ 21 ], Viburnum amplificatum showing two continuous insertion regions [ 32 ], and mitochondrial genomes of Populus tremula x Populus glandulosa and Liriodendron tulipifera with four and thirty-three continuous insertion regions, respectively [ 51 , 52 ].…”

“…Nucleotide diversity among six Arabidopsis thaliana chloroplast genomes was calculated, indicating that the average nucleotide diversity is 0.00017 ( Figure 5(a) ), which is at least ten times lower than those of Dysphania (0.0068; Chenopodiaceae) [ 27 ] and Viburnum (0.00176; Adoxaceae) [ 32 ]. This is a justifiable result because sequence diversity within species is usually lower than interspecific nucleotide diversity.…”

“…However, chloroplast genomes are occasionally useful for unravelling corresponding phylogenetic relationships based on the maternal lineage: e.g., Lindera genus [ 13 ], Fagopyrum genus [ 14 ], Potentilla genus [ 15 – 21 ], Pseudostellaria genus [ 22 – 26 ], and Dysphania genus [ 27 – 30 ]. Moreover, several studies that described assembled organelle genomes from NGS raw sequences generated with different purposes have been conducted [ 31 , 32 ].…”

The complete mitochondrial genome of Douinia plicata (Lindb.) Konstant. et. Vilnet (Scapaniaceae, Jungermanniales)

“…Recent molecular phylogenetic studies of family Scapaniaceae show that this species is of the genus Douinia (Vilnet et al 2010;Heinrichs et al 2012;S€ oderstr€ om et al 2016;Bakalin et al 2019). Whole organelle genome sequences will provide better resolution for uncovering phylogenetic relationship by providing more informative sequence variations (Kim et al 2019;Choi, Min, et al 2020;Park et al 2020). We completed mitochondrial genome sequence of D. plicata for understanding its phylogenetic position.…”