Correlation in plant volatile metabolites: physiochemical properties as a proxy for enzymatic pathways and an alternative metric of biosynthetic constraint

Dowell, Jordan A.; Mason, Chase M.

doi:10.1007/s00049-020-00322-4

Cited by 6 publications

(6 citation statements)

References 59 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Dissimilarities between chemical compounds may be calculated in a number of different ways, based on e.g. their molecular substructures (Cao et al 2008), physicochemical properties (Dowell and Mason 2020), molecular fingerprints (Cereto-Massagué et al 2015) or what biosynthetic pathways or enzymes produce them (Junker 2018, Petrén et al 2023). Additionally, recently developed methods in the GNPS ecosystem (Wang et al 2016) enable calculations of compound dissimilarities for unidentified compounds.…”

Section: Introductionmentioning

confidence: 99%

Understanding the phytochemical diversity of plants: Quantification, variation and ecological function

Petrén

Anaia

Aragam

et al. 2023

Preprint

View full text Add to dashboard Cite

Plants produce a great number of phytochemical compounds mediating a variety of different functions. Recently, phytochemical diversity (chemodiversity), a way which to quantify the complex phenotype formed by sets of phytochemicals, has been suggested to be important for function. However, no study has systematically examined the potential (in)direct functional importance of chemodiversity on a general level, partly due to a lack of an agreement on how to quantify this aspect of the plant phenotype. This paper has four aims: 1) We discuss how chemodiversity (deconstructed into components of richness, evenness and disparity) may quantify different aspects of the phenotype that are ecologically relevant. 2) We systematically review the literature on chemodiversity to examine methodological practices, explore ecological patterns of variability in diversity across different levels of biological organization, and investigate the functional role of this diversity in interactions between plants and other organisms. 3) We provide a framework facilitating decisions on which measure of chemodiversity is best used in different contexts. 4) We outline open questions and avenues for future research in this area. A more thorough understanding of phytochemical diversity will increase our knowledge on the functional role phytochemical compounds, and how they shape ecological interactions between plants and their environment.

show abstract

Section: Introductionmentioning

confidence: 99%

Understanding the phytochemical diversity of plants: Quantification, variation and ecological function

Petrén

Anaia

Aragam

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…While efficient, the NPClassifier method has a lower resolution compared to using manually collected data on enzymes (Junker, 2018), because the classification is limited to three hierarchical levels. It should also be noted that structural dissimilarity has been used as a proxy for biosynthetic similarity in other studies (Dowell & Mason, 2020; Cna'ani et al ., 2021), and in our simulations dissimilarities calculated with all three methods were correlated (Fig. S4), indicative of an overall consistency between methods.…”

Section: Resultsmentioning

confidence: 99%

Quantifying chemodiversity considering biochemical and structural properties of compounds with the R package chemodiv

2023

View full text Add to dashboard Cite

Summary Plants produce large numbers of phytochemical compounds affecting plant physiology and interactions with their biotic and abiotic environment. Recently, chemodiversity has attracted considerable attention as an ecologically and evolutionary meaningful way to characterize the phenotype of a mixture of phytochemical compounds. Currently used measures of phytochemical diversity, and related measures of phytochemical dissimilarity, generally do not take structural or biosynthetic properties of compounds into account. Such properties can be indicative of the compounds' function and inform about their biosynthetic (in)dependence, and should therefore be included in calculations of these measures. We introduce the R package chemodiv, which retrieves biochemical and structural properties of compounds from databases and provides functions for calculating and visualizing chemical diversity and dissimilarity for phytochemicals and other types of compounds. Our package enables calculations of diversity that takes the richness, relative abundance and – most importantly – structural and/or biosynthetic dissimilarity of compounds into account. We illustrate the use of the package with examples on simulated and real datasets. By providing the R package chemodiv for quantifying multiple aspects of chemodiversity, we hope to facilitate investigations of how chemodiversity varies across levels of biological organization, and its importance for the ecology and evolution of plants and other organisms.

show abstract

“…While efficient, this method has a lower resolution compared to using manually collected data on enzymes (Junker, 2018), because the classification is limited to three hierarchical levels. It should also be noted that structural dissimilarity has been used as a proxy for biosynthetic similarity in other studies (Dowell & Mason, 2020; Cna’ani et al ., 2021), and in our simulations dissimilarities calculated with all three methods were correlated (Fig. S3), indicative of an overall consistency between methods.…”

Section: Resultsmentioning

confidence: 99%

Quantifying chemodiversity considering biochemical and structural properties of compounds with the R packagechemodiv

Petrén

Köllner

Junker

2022

Preprint

View full text Add to dashboard Cite

SummaryPlants produce large numbers of phytochemical compounds affecting plant physiology and interactions with their biotic and abiotic environment. Recently, chemodiversity has attracted considerable attention as an ecologically and evolutionary meaningful way to characterize the phenotype of a mixture of phytochemical compounds.Currently used measures of phytochemical diversity, and related measures of phytochemical dissimilarity, generally do not take structural or biosynthetic properties of compounds into account. Such properties can be indicative of the compounds’ function and inform about their biosynthetic (in)dependence, and should therefore be included in calculations of these measures.We introduce the R package chemodiv, which retrieves biochemical and structural properties of compounds from databases and provides functions for calculating and visualizing chemical diversity and dissimilarity for phytochemicals and other types of compounds. Our package enables calculations of diversity that takes the richness, relative abundance and – most importantly – structural and/or biosynthetic dissimilarity of compounds into account. We illustrate the use of the package with examples on simulated and real datasets.By providing the R package chemodiv for quantifying multiple aspects of chemodiversity, we hope to facilitate investigations of how chemodiversity varies across levels of biological organization, and its importance for the ecology and evolution of plants and other organisms.

show abstract

Correlation in plant volatile metabolites: physiochemical properties as a proxy for enzymatic pathways and an alternative metric of biosynthetic constraint

Cited by 6 publications

References 59 publications

Understanding the phytochemical diversity of plants: Quantification, variation and ecological function

Understanding the phytochemical diversity of plants: Quantification, variation and ecological function

Quantifying chemodiversity considering biochemical and structural properties of compounds with the R package chemodiv

Quantifying chemodiversity considering biochemical and structural properties of compounds with the R packagechemodiv

Contact Info

Product

Resources

About