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Updated: Jul 17, 2025

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PEATmoss: A Gene Expression Atlas for Bryophytes.

Noe Fernandez-Pozo1,2

  • 1Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany. noe.fernandez.pozo@csic.es.

Methods in Molecular Biology (Clifton, N.J.)
|August 30, 2023
PubMed
Summary

PEATmoss is an interactive gene expression atlas for bryophytes, expanding to include multiple species like Physcomitrium patens. It offers advanced visualization and data tools for enhanced research in plant genomics.

Keywords:
AnnotationsBioinformaticsBryophytesGene expressionMarchantia polymorphaMicroarraysPhyscomitrium patensRNA-seq

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Area of Science:

  • Plant Biology
  • Genomics
  • Bioinformatics

Background:

  • Gene expression atlases are crucial for understanding plant development and responses.
  • Bryophytes, like Physcomitrium patens, are important model organisms in plant science.
  • Existing resources often lack comprehensive, multi-species gene expression data and advanced analytical tools.

Purpose of the Study:

  • To introduce PEATmoss, an enhanced interactive gene expression atlas for bryophytes.
  • To integrate diverse RNA-seq and microarray data for Physcomitrium patens and expand to other species.
  • To provide advanced visualization, data download, and gene lookup functionalities.

Main Methods:

  • Unified RNA-seq and microarray expression data from multiple gene annotation versions.
  • Developed interactive visualization methods and data downloading tools.
  • Integrated the Physcomitrium patens Gene Model Lookup Database (PpGML DB) for comprehensive gene information.

Main Results:

  • PEATmoss hosts over 100 experiments for Physcomitrium patens, with ongoing expansion to Anthoceros agrestis and Marchantia polymorpha.
  • New features include dataset privacy control, multispecies support, interactive color scales, co-expression network visualization, and replicate data downloading.
  • The atlas facilitates gene version lookup, sequence, and annotation extraction through PpGML DB integration.

Conclusions:

  • PEATmoss serves as a valuable, expanding resource for comparative transcriptomics in bryophytes.
  • The platform's features enhance data accessibility, analysis, and discovery in plant gene expression research.
  • It supports future research by providing a robust foundation for multi-species genomic data integration.