PFGD: A systematic functional genomics resource for Poplar

As the model species for woody plants, the poplar has excellent experimental properties. The studies of functional genes make up the foundation of improving genetic traits and cultivating elite lines at the molecular level. Although studies of functional genes have been carried out for many years, plenty of experimental data are still scattered across documents and are not unified by a comprehensive statistical analysis, Consequentially, the disjoint in information severely hinders systematic utilization of the accumulated data. This problem can be solved through the use of bioinformatic methodology and technology to gather and organize data to construct this Poplar Functional Gene Database (PFGD). By complining information from an array of studies, this study collected 207 poplar functional genes. 164 of the collected genes, selected for their detailed annotations, were input into Populus Database (http://ccb.bjfu.edu.cn/app/pfgd/). Many important stress genes were located in the database. As an example, we investigate the target genes function of Populus euphratica in response to salt stress. Two small cDNA libraries from P. euphratica plantlets treated with or without salt (300 mM NaCl, 3 days) in the root. Using high-throughput sequencing to identify miRNAs, we found 179 conserved miRNAs and 62 novel miRNAs which have differential expression. After the detailed analysis of these miRNAs, 1254 target genes from conserved miRNAs and 479 target genes from novel miRNAs were predicted, and functional information was annotated using the Gene Ontology databases. These information provides a primary visual field for understanding the gene regulatory network in response to salt stress in Populus.