Insights from the cold transcriptome of Physcomitrella patens: global specialization pattern of conserved transcriptional regulators and identification of orphan genes involved in cold acclimation

New Phytol. 2015 Jan;205(2):869-81. doi: 10.1111/nph.13004. Epub 2014 Sep 10.


The whole-genome transcriptomic cold stress response of the moss Physcomitrella patens was analyzed and correlated with phenotypic and metabolic changes. Based on time-series microarray experiments and quantitative real-time polymerase chain reaction, we characterized the transcriptomic changes related to early stress signaling and the initiation of cold acclimation. Transcription-associated protein (TAP)-encoding genes of P. patens and Arabidopsis thaliana were classified using generalized linear models. Physiological responses were monitored with pulse-amplitude-modulated fluorometry, high-performance liquid chromatography and targeted high-performance mass spectrometry. The transcript levels of 3220 genes were significantly affected by cold. Comparative classification revealed a global specialization of TAP families, a transcript accumulation of transcriptional regulators of the stimulus/stress response and a transcript decline of developmental regulators. Although transcripts of the intermediate to later response are from evolutionarily conserved genes, the early response is dominated by species-specific genes. These orphan genes may encode as yet unknown acclimation processes.

Keywords: Physcomitrella patens; abiotic stress; abscisic acid (ABA); cold acclimation; microarray; moss; orphan genes; transcriptome.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Abscisic Acid / metabolism
  • Acclimatization / genetics*
  • Acclimatization / physiology
  • Bryopsida / genetics
  • Bryopsida / growth & development
  • Bryopsida / physiology*
  • Cold Temperature
  • Gene Expression Regulation, Plant*
  • Gene Ontology
  • Reproducibility of Results
  • Signal Transduction / genetics
  • Transcriptome


  • Abscisic Acid