title: Systematic functional genomics resource and annotation for poplar.
abstract: Poplar, as a model species for forestry research, has many excellent characteristics. Studies on functional genes have provided the foundation, at the molecular level, for improving genetic traits and cultivating elite lines. Although studies on functional genes have been performed for many years, large amounts of experimental data remain scattered across various reports and have not been unified via comprehensive statistical analysis. This problem can be addressed by employing bioinformatic methodology and technology to gather and organise data to construct a Poplar Functional Gene Database, containing data on 207 poplar functional genes. As an example, the authors investigated genes of Populus euphratica involved in the response to salt stress. Four small cDNA libraries were constructed and treated with 300 mM NaCl or pure water for 6 and 24 h. Using high-throughput sequencing, they identified conserved and novel miRNAs that were differentially expressed. Target genes were next predicted and detailed functional information derived using the Gene Ontology database and Kyoto Encyclopedia of Genes and Genomes pathway analysis. This information provides a primary visual schema allowing us to understand the dynamics of the regulatory gene network responding to salt stress in Populus.
authors.affiliation: Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, People's Republic of China. jingnasi@bjfu.edu.cn.
authors.forename: Jingna
authors.initials: J
authors.lastname: Si
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, People's Republic of China.
authors.forename: Xiyang
authors.initials: X
authors.lastname: Zhao
authors.affiliation: Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, People's Republic of China.
authors.forename: Xinyin
authors.initials: X
authors.lastname: Zhao
authors.affiliation: Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, People's Republic of China.
authors.forename: Rongling
authors.initials: R
authors.lastname: Wu
mesh_terms: D002874:Chromosome Mapping / Q000379:methods; D003198:Computer Simulation; D030541:Databases, Genetic; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics / Q000379:methods; D008957:Models, Genetic; D010940:Plant Proteins / Q000235:genetics*; D032107:Populus / Q000235:genetics*; D055051:Salt-Tolerant Plants / Q000235:genetics*
chemical_list: D010940:Plant Proteins