Abstract
BackgroundRegulation of gene expression plays a pivotal role in controlling the development of multicellular plants. To explore the molecular mechanism of plant developmental-stage transition and cell-fate determination, a genome-wide analysis was undertaken of sequential developmental time-points and individual tissue types in the model moss Physcomitrella patens because of the short life cycle and relative structural simplicity of this plant.ResultsGene expression was analyzed by digital gene expression tag profiling of samples taken from P. patens protonema at 3, 14 and 24 days, and from leafy shoot tissues at 30 days, after protoplast isolation, and from 14-day-old caulonemal and chloronemal tissues. In total, 4333 genes were identified as differentially displayed. Among these genes, 4129 were developmental-stage specific and 423 were preferentially expressed in either chloronemal or caulonemal tissues. Most of the differentially displayed genes were assigned to functions in organic substance and energy metabolism or macromolecule biosynthetic and catabolic processes based on gene ontology descriptions. In addition, some regulatory genes identified as candidates 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, genes related to protein/amino acid methylation, and auxin, ethylene, and cytokinin signaling pathways.ConclusionsThese genes that show highly dynamic changes in expression during development in P. patens are potential targets for further functional characterization and evolutionary developmental biology studies.
Highlights
Regulation of gene expression plays a pivotal role in controlling the development of multicellular plants
Gametophytic morphogenesis during the culture of P. patens protoplasts Morphogenesis of moss gametophytes from protoplasts is similar to morphological development following germination of spores, but the similarity in gene expression level is unknown
We identified 4333 differentially expressed genes during gametophyte development in P. patens with false discovery rate (FDR) corrected P-values of less than 0.01 (Figure 2; Additional files 3 and 4)
Summary
Regulation of gene expression plays a pivotal role in controlling the development of multicellular plants. To explore the molecular mechanism of plant developmental-stage transition and cell-fate determination, a genome-wide analysis was undertaken of sequential developmental time-points and individual tissue types in the model moss Physcomitrella patens because of the short life cycle and relative structural simplicity of this plant. Despite the practical difficulties, understanding the regulation of plant development is reasonably well advanced for some processes, including lateral root formation, seed development, and fruit development, and genes that regulate these processes have been identified [2,3,4,5,6]. We are still far from fully understanding the molecular mechanisms that govern development. The increasing power of genomic tools enables the changes in expression of thousands of genes to be profiled in parallel during sequential developmental stages.
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