Poplar genomics: State of the science

Recent advances in Populus genomics have greatly expanded its popularity as a reference for fundamental as well as applied research in woody plants. In this review, we provide an overview of the state-of-the-science in Populus genomics research, including experimental and computational genomics. We have surveyed and summarized the following: 1) pioneering as well as more recent reports of genetics- and genomics-based investigations in Populus, 2) the positive impact of technological improvements, 3) findings from phylogenetic analyses of gene families, and 4) genomic databases. In the area of Populus experimental genomics, genetic approaches have been advanced to the genome scale with resolution to the gene and/or single nucleotide level. On the other hand, the modern "omics" approaches have been successfully applied to analysis of gene function, such as transcriptome profiling using microarrays as well as the next-generation DNA sequencing technology, and characterization of proteome and metabolome using modern instruments. In the area of Populus computational genomics, significant progresses have been made in sequence-based discovery of predicted gene function, comparative analysis of gene families, development of genomic databases, and studies of the evolutionary dynamics at both the gene and genome level. While significant advancements have been achieved in Populus genome-based science, several challenges need to be addressed, such as 1) better annotation of the Populus genome, 2) robust technology for large-scale molecular profiling, 3) efficient system for genome-wide mutagenesis, and 4) high-performance computational pipelines to keep up with the pace of the rapid accumulation of data and to integrate "omics" data into functional systems biology platforms.