Antimicrobial Activity of Necklace Orchids is Phylogenetically Clustered and can be Predicted With a Biological Response Method

Comparative chloroplast genomics of 24 species shed light on the genome evolution and phylogeny of subtribe Coelogyninae (Orchidaceae)

BACKGROUND

The orchids of the subtribe Coelogyninae are among the most morphologically diverse and economically important groups within the subfamily Epidendroideae. Previous molecular studies have revealed that Coelogyninae is an unambiguously monophyletic group. However, intergeneric and infrageneric relationships within Coelogyninae are largely unresolved. There has been long controversy over the classification among the genera within the subtribe.

RESULTS

The complete chloroplast (cp.) genomes of 15 species in the subtribe Coelogyninae were newly sequenced and assembled. Together with nine available cp. genomes in GenBank from representative clades of the subtribe, we compared and elucidated the characteristics of 24 Coelogyninae cp. genomes. The results showed that all cp. genomes shared highly conserved structure and contained 135 genes arranged in the same order, including 89 protein-coding genes, 38 tRNAs, and eight rRNAs. Nevertheless, structural variations in relation to particular genes at the IR/SC boundary regions were identified. The diversification pattern of the cp. genomes showed high consistency with the phylogenetic placement of Coelogyninae. The number of different types of SSRs and long repeats exhibited significant differences in the 24 Coelogyninae cp. genomes, wherein mononucleotide repeats (A/T), and palindromic repeats were the most abundant. Four mutation hotspot regions (ycf1a, ndhF-rp132, psaC-ndhE, and rp132-trnL) were determined, which could serve as effective molecular markers. Selection pressure analysis revealed that three genes (ycf1a, rpoC2 and ycf2 genes) might have experienced apparent positive selection during the evolution. Using the alignments of whole cp. genomes and protein-coding sequences, this study presents a well-resolved phylogenetic framework of Coelogyninae.

CONCLUSION

The inclusion of 55 plastid genome data from a nearly complete generic-level sampling provide a comprehensive view of the phylogenetic relationships among genera and species in subtribe Coelogyninae and illustrate the diverse genetic variation patterns of plastid genomes in this species-rich plant group. The inferred relationships and informally recognized major clades within the subtribe are presented. The genetic markers identified here will facilitate future studies on the genetics and phylogeny of subtribe Coelogyninae.

Evaluating Potentials of Species Rich Taxonomic Groups in Cosmetics and Dermatology: Clustering and Dispersion of Skin Efficacy of Asteraceae and Ranunculales Plants on the Species Phylogenetic Tree

BACKGROUND

The medicinal properties of plants can be predicted by virtue of phylogenetic methods, which nevertheless have not been utilized to explore the regularity of skin-related bioactivities of ethnomedicinal plants. We aim to investigate the distribution of skin efficacy of Asteraceae and Ranunculales plants on the species-level Tree of Life.

METHODS

The clinical efficacy data of 551 ethnomedicinal species belonging to Ranunculales, as well as 579 ethnomedicinal species of Asteraceae, were systematically collected and collated; these therapeutic data fell into 15 categories, including skin disease/cosmeceutical. The large phylogenetic tree of all China angiosperm species was used to detect the phylogenetic signals of ethnomedicinal plants by calculating the D statistic, phylogenetic diversity (PD), net relatedness index (NRI), and nearest taxon index (NTI). Of all Chinese ethnomedicinal plants of Ranunculales and Asteraceae, 339 (61.5% of all ethnomedicinal species) and 382 (66.0% of all) are used for skin problems. In Ranunculales, a clustered structure was suggested by the NRI value for skin uses. In Asteraceae, the skin utility was not clustered; Artemisia, Aster, Cremanthodium, Ligularia, and Saussurea are the most used Asteraceae genera for skin issues.

RESULTS

The clustering structure was identified in Artemisia, and the skin efficacy in other genera was of overdispersion (NRI < 0). NTI values and D statistics largely agree with NRI. When compared with PD values of different therapeutic categories, the PD value of the skin category was relatively high in Cremanthodium, Ranunculales, Asteraceae, and Artemisia, suggesting the enormous efficacy space in the new taxa of these taxonomic groups.

CONCLUSION

By resolving the distribution of therapeutic effects of Ranunculales/Asteraceae taxa, the importance of phylogenetic methods in mining botanical resources with skin utilities is validated.

Distribution of Therapeutic Efficacy of Ranunculales Plants Used by Ethnic Minorities on the Phylogenetic Tree of Chinese Species

The medicinal properties of plants can be evolutionarily predicted by phylogeny-based methods, which, however, have not been used to explore the regularity of therapeutic effects of Chinese plants utilized by ethnic minorities. This study aims at exploring the distribution law of therapeutic efficacy of Ranunculales plants on the phylogenetic tree of Chinese species. We collected therapeutic efficacy data of 551 ethnomedicinal species belonging to five species-rich families of Ranunculales; these therapeutic data were divided into 15 categories according to the impacted tissues and organs. The phylogenetic tree of angiosperm species was used to analyze the phylogenetic signals of ethnomedicinal plants by calculating the net relatedness index (NRI) and nearest taxon index (NTI) in R language. The NRI results revealed a clustered structure for eight medicinal categories (poisoning/intoxication, circulatory, gastrointestinal, eyesight, oral, pediatric, skin, and urinary disorders) and overdispersion for the remaining seven (neurological, general, hepatobiliary, musculoskeletal, otolaryngologic, reproductive, and respiratory disorders), while the NTI metric identified the clustered structure for all. Statistically, NRI and NTI values were significant in 5 and 11 categories, respectively. It was found that Mahonia eurybracteata has therapeutic effects on all categories. iTOL was used to visualize the distribution of treatment efficacy on species phylogenetic trees. By figuring out the distribution of therapeutic effects of Ranunculales medicinal plants, the importance of phylogenetic methods in finding potential medicinal resources is highlighted; NRI, NTI, and similar indices can be calculated to help find taxonomic groups with medicinal efficacy based on the phylogenetic tree of flora in different geographic regions.