PEATmoss (Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens

Research output: Contribution to journalArticlepeer-review

Authors

  • Noe Fernandez-Pozo
  • Fabian B Haas
  • Rabea Meyberg
  • Kristian K Ullrich
  • Manuel Hiss
  • Pierre-François Perroud
  • Sebastian Hanke
  • Viktor Kratz
  • Adrian F Powell
  • Eleanor F Vesty
  • Christopher G Daum
  • Matthew Zane
  • Anna Lipzen
  • Avinash Sreedasyam
  • Jane Grimwood
  • Kerrie Barry
  • Jeremy Schmutz
  • Lukas A Mueller
  • Stefan A Rensing

Colleges, School and Institutes

External organisations

  • University Hospital Marburg
  • Max Planck Institute for Evolutionary Biology
  • Boyce Thompson Institute for Plant Research
  • US Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
  • HudsonAlpha Institute for Biotechnology, Huntsville, AL

Abstract

Physcomitrella patens is a bryophyte model plant that is often used to study plant evolution and development. Its resources are of great importance for comparative genomics and evo-devo approaches. However, expression data from Physcomitrella patens were so far generated using different gene annotation versions and three different platforms: CombiMatrix and NimbleGen expression microarrays and RNA sequencing. The currently available P. patens expression data are distributed across three tools with different visualization methods to access the data. Here, we introduce an interactive expression atlas, Physcomitrella Expression Atlas Tool (PEATmoss), that unifies publicly available expression data for P. patens and provides multiple visualization methods to query the data in a single web-based tool. Moreover, PEATmoss includes 35 expression experiments not previously available in any other expression atlas. To facilitate gene expression queries across different gene annotation versions, and to access P. patens annotations and related resources, a lookup database and web tool linked to PEATmoss was implemented. PEATmoss can be accessed at https://peatmoss.online.uni-marburg.de.

Bibliographic note

© 2019 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

Details

Original languageEnglish
Pages (from-to)165-177
Number of pages13
JournalThe Plant journal : for cell and molecular biology
Volume102
Issue number1
Publication statusPublished - Apr 2020