A Metabolomics and Transcriptomics Resource for Identifying Candidate Genes in the Biosynthesis of Specialised Metabolites in Populus tremula. Rydman, S. M., Lihavainen, J., Robinson, K. M., Jansson, S., Albrectsen, B. R., & Street, N. R. Physiologia Plantarum, 177(5):e70567, 2025. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70567![A Metabolomics and Transcriptomics Resource for Identifying Candidate Genes in the Biosynthesis of Specialised Metabolites in Populus tremula [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex This study aims to identify candidate genes involved in the biosynthesis of salicinoid phenolic glycosides (SPGs), a group of specialised metabolites characteristic of the Salicaceae family. While the integration of multi-omics data represents a powerful approach to link genes encoding enzymes and their regulatory factors to metabolite biosynthesis, suitable multi-omics data resources are scarce. We present a comprehensive dataset comprising untargeted liquid chromatography–mass spectrometry (LC–MS) and mRNA-sequencing data from various organs of European aspen (Populus tremula L.) and from genotypes that produce contrasting sets of SPGs. We present a reproducible pipeline for the analysis of the LC–MS data, including predicted annotation of potential novel SPGs. We demonstrate the utility of the resource by identifying candidate genes involved in the biosynthesis of SPGs with a cinnamoyl moiety. By integrating gene and metabolite differential analyses with a gene co-expression network, we identified two HXXXD-type acyltransferase genes and one UDP-glucosyltransferase gene as candidates for future downstream characterisation. The combined gene expression and metabolomics resource is integrated into PlantGenIE.org to facilitate easy access and data mining. All raw data are available in public databases, and all data and results files are available at an associated Figshare repository.
@article{rydman_metabolomics_2025,
title = {A {Metabolomics} and {Transcriptomics} {Resource} for {Identifying} {Candidate} {Genes} in the {Biosynthesis} of {Specialised} {Metabolites} in {Populus} tremula},
volume = {177},
copyright = {© 2025 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
issn = {1399-3054},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70567},
doi = {10.1111/ppl.70567},
abstract = {This study aims to identify candidate genes involved in the biosynthesis of salicinoid phenolic glycosides (SPGs), a group of specialised metabolites characteristic of the Salicaceae family. While the integration of multi-omics data represents a powerful approach to link genes encoding enzymes and their regulatory factors to metabolite biosynthesis, suitable multi-omics data resources are scarce. We present a comprehensive dataset comprising untargeted liquid chromatography–mass spectrometry (LC–MS) and mRNA-sequencing data from various organs of European aspen (Populus tremula L.) and from genotypes that produce contrasting sets of SPGs. We present a reproducible pipeline for the analysis of the LC–MS data, including predicted annotation of potential novel SPGs. We demonstrate the utility of the resource by identifying candidate genes involved in the biosynthesis of SPGs with a cinnamoyl moiety. By integrating gene and metabolite differential analyses with a gene co-expression network, we identified two HXXXD-type acyltransferase genes and one UDP-glucosyltransferase gene as candidates for future downstream characterisation. The combined gene expression and metabolomics resource is integrated into PlantGenIE.org to facilitate easy access and data mining. All raw data are available in public databases, and all data and results files are available at an associated Figshare repository.},
language = {en},
number = {5},
urldate = {2025-10-13},
journal = {Physiologia Plantarum},
author = {Rydman, Sara M. and Lihavainen, Jenna and Robinson, Kathryn M. and Jansson, Stefan and Albrectsen, Benedicte R. and Street, Nathaniel R.},
year = {2025},
note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70567},
keywords = {Populus tremula, RNA-Seq, aspen, biosynthesis, chemotype, liquid chromatography–mass spectrometry (LC–MS), metabolomics, phenolic glycosides, salicinoid, specialised metabolite},
pages = {e70567},
}
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