Untargeted Metabolomics for Integrative Taxonomy: Metabolomics, DNA Marker-Based Sequencing, and Phenotype Bioimaging

Abstract

Integrative taxonomy is a fundamental part of biodiversity and combines traditional morphology with additional methods such as DNA sequencing or biochemistry. Here, we aim to establish untargeted metabolomics for use in chemotaxonomy. We used three thallose liverwort species Riccia glauca, R. sorocarpa, and R. warnstorfii (order Marchantiales, Ricciaceae) with Lunularia cruciata (order Marchantiales, Lunulariacea) as an outgroup. Liquid chromatography high-resolution mass-spectrometry (UPLC/ESI-QTOF-MS) with data-dependent acquisition (DDA-MS) were integrated with DNA marker-based sequencing of the trnL-trnF region and high-resolution bioimaging. Our untargeted chemotaxonomy methodology enables us to distinguish taxa based on chemophenetic markers at different levels of complexity: (1) molecules, (2) compound classes, (3) compound superclasses, and (4) molecular descriptors. For the investigated Riccia species, we identified 71 chemophenetic markers at the molecular level, a characteristic composition in 21 compound classes, and 21 molecular descriptors largely indicating electron state, presence of chemical motifs, and hydrogen bonds. Our untargeted approach revealed many chemophenetic markers at different complexity levels that can provide more mechanistic insight into phylogenetic delimitation of species within a clade than genetic-based methods coupled with traditional morphology-based information. However, analytical and bioinformatics analysis methods still need to be better integrated to link the chemophenetic information at multiple scales.

Production of Polyphenolic Natural Products by Bract-Derived Tissue Cultures of Three Medicinal Tilia spp.: A Comparative Untargeted Metabolomics Study

“…Another study successfully utilized untargeted metabolomics to obtain chemotaxonomic information on three Riccia spp. [68]. The latter study was able to present a clear separation of the three species since chemical differences between species were greater than observed in our study.…”

Estimating essential phenotypic and molecular traits from integrative biodiversity data

“…We followed extraction procedures for LC-MS originally developed for vascular plants by 56 and adapted for the use with bryophytes and the different analytical setup used herein by 57 . This data-dependent acquisition method has been shown to provide robust results and high-quality spectra for thallose liverworts 58 . In detail, frozen plants were homogenized for 5 minutes at 30 Hz in Teflon chambers equipped with two stainless steel balls.…”

“…Annotation of MS-MS spectra Annotation of MS-MS fragment spectra was carried out using the software SIRIUS version 5.7 14 . The settings described in 58 were used for both ionizations. Annotation was accomplished automatically by selecting the highest-ranking candidate for each spectrum.…”

Unlocking Potentially Therapeutic Phytochemicals in Capadulla (Doliocarpus dentatus) from Guyana Using Untargeted Mass Spectrometry-Based Metabolomics

“…If the SIRIUS score was < 50% with no accompanying ZODIAC score, no identification was made. A combination of scores of >90% for SIRIUS and >70% for ZODIAC was used for screening [75][76][77].…”