gcProfileMakeR: An R Package for Automatic Classification of Constitutive and Non-Constitutive Metabolites

Pérez-Sánz, Fernando; Ruiz-Hernández, Victoria; Terry, Marta I.; Arce-Gallego, Sara; Weiß, Julia; Navarro, Pedro J.; Egea‐Cortines, Marcos

doi:10.3390/metabo11040211

Cited by 3 publications

(1 citation statement)

References 59 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This package enables users to start with a dataset of integrated and identified peaks, and associated sample metadata, and perform filtering steps of their choosing (described above). As such, this package differs from the recently developed gcProfileMakeR (Perez-Sanz et al, 2021), which enables users to identify metabolites that are produced constitutively or non-constitutively. Supplementary material 4 provides an introductory vignette with an example dataset, and complete documentation of each function is included in the package.…”

Section: Compound Filteringmentioning

confidence: 99%

An analytical pipeline to support robust research on the ecology, evolution, and function of floral volatiles

Eisen

Powers²,

Raguso³

et al. 2022

Front. Ecol. Evol.

View full text Add to dashboard Cite

Research on floral volatiles has grown substantially in the last 20 years, which has generated insights into their diversity and prevalence. These studies have paved the way for new research that explores the evolutionary origins and ecological consequences of different types of variation in floral scent, including community-level, functional, and environmentally induced variation. However, to address these types of questions, novel approaches are needed that can handle large sample sizes, provide quality control measures, and make volatile research more transparent and accessible, particularly for scientists without prior experience in this field. Drawing upon a literature review and our own experiences, we present a set of best practices for next-generation research in floral scent. We outline methods for data collection (experimental designs, methods for conducting field collections, analytical chemistry, compound identification) and data analysis (statistical analysis, database integration) that will facilitate the generation and interpretation of quality data. For the intermediate step of data processing, we created the R package bouquet, which provides a data analysis pipeline. The package contains functions that enable users to convert chromatographic peak integrations to a filtered data table that can be used in subsequent statistical analyses. This package includes default settings for filtering out non-floral compounds, including background contamination, based on our best-practice guidelines, but functions and workflows can be easily customized as necessary. Next-generation research into the ecology and evolution of floral scent has the potential to generate broadly relevant insights into how complex traits evolve, their genomic architecture, and their consequences for ecological interactions. In order to fulfill this potential, the methodology of floral scent studies needs to become more transparent and reproducible. By outlining best practices throughout the lifecycle of a project, from experimental design to statistical analysis, and providing an R package that standardizes the data processing pipeline, we provide a resource for new and seasoned researchers in this field and in adjacent fields, where high-throughput and multi-dimensional datasets are common.

show abstract

Section: Compound Filteringmentioning

confidence: 99%

An analytical pipeline to support robust research on the ecology, evolution, and function of floral volatiles

Eisen

Powers²,

Raguso³

et al. 2022

Front. Ecol. Evol.

View full text Add to dashboard Cite

show abstract

Volatile organic compounds in aquatic ecosystems – Detection, origin, significance and applications

Pozzer

Gómez

Weiß

2022

Science of The Total Environment

View full text Add to dashboard Cite

Flower transcriptional response to long term hot and cold environments in Antirrhinum majus

et al. 2023

Self Cite

View full text Add to dashboard Cite

Short term experiments have identified heat shock and cold response elements in many biological systems. However, the effect of long-term low or high temperatures is not well documented. To address this gap, we grew Antirrhinum majus plants from two-weeks old until maturity under control (normal) (22/16°C), cold (15/5°C), and hot (30/23°C) conditions for a period of two years. Flower size, petal anthocyanin content and pollen viability obtained higher values in cold conditions, decreasing in middle and high temperatures. Leaf chlorophyll content was higher in cold conditions and stable in control and hot temperatures, while pedicel length increased under hot conditions. The control conditions were optimal for scent emission and seed production. Scent complexity was low in cold temperatures. The transcriptomic analysis of mature flowers, followed by gene enrichment analysis and CNET plot visualization, showed two groups of genes. One group comprised genes controlling the affected traits, and a second group appeared as long-term adaptation to non-optimal temperatures. These included hypoxia, unsaturated fatty acid metabolism, ribosomal proteins, carboxylic acid, sugar and organic ion transport, or protein folding. We found a differential expression of floral organ identity functions, supporting the flower size data. Pollinator-related traits such as scent and color followed opposite trends, indicating an equilibrium for rendering the organs for pollination attractive under changing climate conditions. Prolonged heat or cold cause structural adaptations in protein synthesis and folding, membrane composition, and transport. Thus, adaptations to cope with non-optimal temperatures occur in basic cellular processes.

show abstract

gcProfileMakeR: An R Package for Automatic Classification of Constitutive and Non-Constitutive Metabolites

Cited by 3 publications

References 59 publications

An analytical pipeline to support robust research on the ecology, evolution, and function of floral volatiles

An analytical pipeline to support robust research on the ecology, evolution, and function of floral volatiles

Volatile organic compounds in aquatic ecosystems – Detection, origin, significance and applications

Flower transcriptional response to long term hot and cold environments in Antirrhinum majus

Contact Info

Product

Resources

About