title: Insights from the cold transcriptome of Physcomitrella patens: global specialization pattern of conserved transcriptional regulators and identification of orphan genes involved in cold acclimation.
abstract: 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.
authors.affiliation: Plant Biotechnology, Faculty of Biology, University of Freiburg, Schänzlestraße 1, D-79104, Freiburg, Germany.
authors.forename: Anna K
authors.initials: AK
authors.lastname: Beike
authors.forename: Daniel
authors.initials: D
authors.lastname: Lang
authors.forename: Andreas D
authors.initials: AD
authors.lastname: Zimmer
authors.forename: Florian
authors.initials: F
authors.lastname: Wüst
authors.forename: Danika
authors.initials: D
authors.lastname: Trautmann
authors.forename: Gertrud
authors.initials: G
authors.lastname: Wiedemann
authors.forename: Peter
authors.initials: P
authors.lastname: Beyer
authors.forename: Eva L
authors.initials: EL
authors.lastname: Decker
authors.forename: Ralf
authors.initials: R
authors.lastname: Reski
mesh_terms: D000040:Abscisic Acid / Q000378:metabolism; D000064:Acclimatization / Q000235:genetics* / Q000502:physiology; D019068:Bryopsida / Q000235:genetics / Q000254:growth & development / Q000502:physiology*; D003080:Cold Temperature; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D015203:Reproducibility of Results; D015398:Signal Transduction / Q000235:genetics; D059467:Transcriptome
chemical_list: D000040:Abscisic Acid
keywords: Physcomitrella patens; abiotic stress; abscisic acid (ABA); cold acclimation; microarray; moss; orphan genes; transcriptome