Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens

Gene expression was analyzed with digital gene expression tag profiling (DGEP) with samples taken from P. patens protonema at 3, 14 and 24 days, and also from or leafy shoot tissues l at 30 days after protoplastes isolated, and from 14-day-old caulonemal and chloronemal tissues. Totally, 4333 genes were identified as differentially displayed. Among them, 4129 were developmental-stage specific and 423 were preferentially expressed in either chloronemal or caulonemal tissues. Most of the differentially displayed genes could be assigned to functions in organic substance and energy metabolism or macromolecule biosynthetic and catabolic process based on gene ontology (GO) description. In addition, some regulatory genes were identified as candidates that might be involved in controlling the developmental stage transition and cell differentiation, namely: MYB-like, HB-8, AL3, zinc finger family proteins, bHLH superfamily, GATA superfamily, GATA and bZIP transcription factors, protein kinases, the genes related to protein/amino acid methylation, and auxin, ethylene, and cytokinin signaling pathways. Overall design: Examination of 4 different sampling times and 2 different organelles.