Dataset Information

Phylogenetic and Comparative Analyses of Complete Chloroplast Genomes of Chinese Viburnum and Sambucus (Adoxaceae).

ABSTRACT: Phylogenetic analyses of complete chloroplast genome sequences have yielded significant improvements in our understanding of relationships in the woody flowering genus Viburnum (Adoxaceae, Dipsacales); however, these relationships were evaluated focusing only on Viburnum species within Central and South America and Southeast Asia. By contrast, despite being a hotspot of Viburnum diversity, phylogenetic relationships of Viburnum species in China are less well known. Here, we characterized the complete chloroplast (cp) genomes of 21 Viburnum species endemic to China, as well as three Sambucus species. These 24 plastomes were highly conserved in genomic structure, gene order and content, also when compared with other Adoxaceae. The identified repeat sequences, simple sequence repeats (SSRs) and highly variable plastid regions will provide potentially valuable genetic resources for further population genetics and phylogeographic studies on Viburnum and Sambucus. Consistent with previous combined phylogenetic analyses of 113 Viburnum species, our phylogenomic analyses based on the complete cp genome sequence dataset confirmed the sister relationship between Viburnum and the Sambucus-Adoxa-Tetradoxa-Sinadoxa group, the monophyly of four recognized sections in Flora of China (i.e., Viburnum sect. Tinus, Viburnum sect. Solenotinus, Viburnum sect. Viburnum and Viburnum sect. Pseudotinus) and the nonmonophyly of Viburnum sect. Odontotinus and Viburnum sect. Megalotinus. Additionally, our study confirmed the sister relationships between the clade Valvatotinus and Viburnum sect. Pseudotinus, as well as between Viburnum sect. Opulus and the Odontotinus-Megalotinus group. Overall, our results clearly document the power of the complete cp genomes in improving phylogenetic resolution, and will contribute to a better understanding of plastome evolution in Chinese Adoxaceae.

SUBMITTER: Ran H

PROVIDER: S-EPMC7570041 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Phylogenetic and Comparative Analyses of Complete Chloroplast Genomes of Chinese Viburnum and Sambucus (Adoxaceae).

Ran Hang H Liu Yanyan Y Wu Cui C Cao Yanan Y

Plants (Basel, Switzerland) 20200903 9

Phylogenetic analyses of complete chloroplast genome sequences have yielded significant improvements in our understanding of relationships in the woody flowering genus Viburnum (Adoxaceae, Dipsacales); however, these relationships were evaluated focusing only on Viburnum species within Central and South America and Southeast Asia. By contrast, despite being a hotspot of Viburnum diversity, phylogenetic relationships of Viburnum species in China are less well known. He ...[more]

PMID: 32899372

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Project description:BackgroundIn South-east Asia, Dipterocarpoideae is predominant in most mature forest communities, comprising around 20% of all trees. As large quantity and high quality wood are produced in many species, Dipterocarpoideae plants are the most important and valuable source in the timber market. The d-borneol is one of the essential oil components from Dipterocarpoideae (for example, Dryobalanops aromatica or Dipterocarpus turbinatus) and it is also an important traditional Chinese medicine (TCM) formulation known as "Bingpian" in Chinese, with antibacterial, analgesic and anti-inflammatory effects and can enhance anticancer efficiency.MethodsIn this study, we analyzed 20 chloroplast (cp) genomes characteristics of Dipterocarpoideae, including eleven newly reported genomes and nine cp genomes previously published elsewhere, then we explored the chloroplast genomic features, inverted repeats contraction and expansion, codon usage, amino acid frequency, the repeat sequences and selective pressure analyses. At last, we constructed phylogenetic relationships of Dipterocarpoideae and found the potential barcoding loci.ResultsThe cp genome of this subfamily has a typical quadripartite structure and maintains a high degree of consistency among species. There were slightly more tandem repeats in cp genomes of Dipterocarpus and Vatica, and the psbH gene was subjected to positive selection in the common ancestor of all the 20 species of Dipterocarpoideae compared with three outgroups. Phylogenetic tree showed that genus Shorea was not a monophyletic group, some Shorea species and genus Parashorea are placed in one clade. In addition, the rpoC2 gene can be used as a potential marker to achieve accurate and rapid species identification in subfamily Dipterocarpoideae.ConclusionsDipterocarpoideae had similar cp genomic features and psbM, rbcL, psbH may function in the growth of Dipterocarpoideae. Phylogenetic analysis suggested new taxon treatment is needed for this subfamily indentification. In addition, rpoC2 is potential to be a barcoding gene to TCM distinguish.

Project description:BackgroundSorbus sensu stricto (Sorbus s.s.) is a genus with important economical values because of its beautiful leaves, and flowers and especially the colorful fruits. It belongs to the tribe Maleae of the family Rosaceae, and comprises about 90 species mainly distributed in China. There is on-going dispute about its infrageneric classification and species delimitation as the species are morphologically similar. With the aim of shedding light on the circumscription of taxa within the genus, phylogenetic analyses were performed using 29 Sorbus s.s. chloroplast (cp) genomes (16 newly sequenced) representing two subgenera and eight sections.ResultsThe 16 cp genomes newly sequenced range between 159,646 bp and 160,178 bp in length. All the samples examined and 22 taxa re-annotated in Sorbus sensu lato (Sorbus s.l.) contain 113 unique genes with 19 of these duplicated in the inverted repeat (IR). Six hypervariable regions including trnR-atpA, petN-psbM, rpl32-trnL, trnH-psbA, trnT-trnL and ndhC-trnV were screened and 44-53 SSRs and 14-31 dispersed repeats were identified as potential molecular markers. Phylogenetic analyses under ML/BI indicated that Sorbus s.l. is polyphyletic, but Sorbus s.s. and the other five segregate genera, Aria, Chamaemespilus, Cormus, Micromeles and Torminalis are monophyletic. Two major clades and four sub-clades resolved with full-support within Sorbus s.s. are not consistent with the existing infrageneric classification. Two subgenera, subg. Sorbus and subg. Albocarmesinae are supported as monophyletic when S. tianschanica is transferred to subg. Albocarmesinae from subg. Sorbus and S. hupehensis var. paucijuga transferred to subg. Sorbus from subg. Albocarmesinae, respectively. The current classification at sectional level is not supported by analysis of cp genome phylogeny.ConclusionPhylogenomic analyses of the cp genomes are useful for inferring phylogenetic relationships in Sorbus s.s. Though genome structure is highly conserved in the genus, hypervariable regions and repeat sequences used are the most promising molecule makers for population genetics, species delimitation and phylogenetic studies.

Dataset Information

Phylogenetic and Comparative Analyses of Complete Chloroplast Genomes of Chinese Viburnum and Sambucus (Adoxaceae).

Publications

Phylogenetic and Comparative Analyses of Complete Chloroplast Genomes of Chinese <i>Viburnum</i> and <i>Sambucus</i> (Adoxaceae).

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