Dataset Information

A biosynthetically informed distance measure to compare secondary metabolite profiles.

ABSTRACT: Secondary metabolite profiles are one of the most diverse phenotypes of organisms and can consist of a large number of compounds originating from a limited number of biosynthetic pathways. The statistical treatment of such profiles often is complicated due to their diversity as well as the intra- and interspecific variability in the quantitative and qualitative composition of secondary metabolites. Most importantly, the assumption of independence of the presence/absence and the quantity of compounds is violated due to the shared biosynthetic origin of many compounds. Therefore, I propose a biosynthetically informed pairwise distance measure that fully considers the biosynthesis of the compounds and thus quantifies the similarity in the enzymatic equipment of two samples. The biosynthetic similarity of compounds is calculated based on the proportion of shared enzymes that are required for their biosynthesis. Using this information (provided as dendrogram structure) and the quantitative composition of the samples, generalized UniFrac distances are calculated measuring that fraction of the dendrogram (i.e., the branch lengths) that is unique to either of the samples but not shared by both samples. To allow a straightforward cross-platform application of the approach, I provide functions for the statistical software R and sample data sets. A hypothetical and a real world example show the feasibility of the biosynthetically informed distances dA,B and highlight the differences to conventional distance measures. The advantages of this approach and potential fields of application are discussed.

SUBMITTER: Junker RR

PROVIDER: S-EPMC5840250 | biostudies-other | 2018

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

A biosynthetically informed distance measure to compare secondary metabolite profiles.

Junker Robert R RR

Chemoecology 20171127 1

Secondary metabolite profiles are one of the most diverse phenotypes of organisms and can consist of a large number of compounds originating from a limited number of biosynthetic pathways. The statistical treatment of such profiles often is complicated due to their diversity as well as the intra- and interspecific variability in the quantitative and qualitative composition of secondary metabolites. Most importantly, the assumption of independence of the presence/absence and the quantity of compo ...[more]

PMID: 29540963

Similar Datasets

Project description:Insect herbivores have dramatic effects on the chemical composition of plants. Many of these induced metabolites contribute to the quality (e.g., flavor, human health benefits) of specialty crops such as the tea plant (Camellia sinensis). Induced chemical changes are often studied by comparing plants damaged and undamaged by herbivores. However, when herbivory is quantitative, the relationship between herbivore pressure and induction can be linearly or non-linearly density dependent or density independent, and induction may only occur after some threshold of herbivory. The shape of this relationship can vary among metabolites within plants. The tea green leafhopper (Empoasca onukii) can be a widespread pest on tea, but some tea farmers take advantage of leafhopper-induced metabolites in order to produce high-quality "bug-bitten" teas such as Eastern Beauty oolong. To understand the effects of increasing leafhopper density on tea metabolites important for quality, we conducted a manipulative experiment exposing tea plants to feeding by a range of E. onukii densities. After E. onukii feeding, we measured volatile and non-volatile metabolites, and quantified percent damaged leaf area from scanned leaf images. E. onukii density had a highly significant effect on volatile production, while the effect of leaf damage was only marginally significant. The volatiles most responsive to leafhopper density were mainly terpenes that increased in concentration monotonically with density, while the volatiles most responsive to leaf damage were primarily fatty acid derivatives and volatile phenylpropanoids/benzenoids. In contrast, damage (percent leaf area damaged), but not leafhopper density, significantly reduced total polyphenols, epigallocatechin gallate (EGCG), and theobromine concentrations in a dose-dependent manner. The shape of induced responses varied among metabolites with some changing linearly with herbivore pressure and some responding only after a threshold in herbivore pressure with a threshold around 0.6 insects/leaf being common. This study illustrates the importance of measuring a diversity of metabolites over a range of herbivory to fully understand the effects of herbivores on induced metabolites. Our study also shows that any increases in leafhopper density associated with climate warming, could have dramatic effects on secondary metabolites and tea quality.

Dataset Information

A biosynthetically informed distance measure to compare secondary metabolite profiles.

Publications

A biosynthetically informed distance measure to compare secondary metabolite profiles.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure