Abstract
Populus has become a model for genomics research in woody perennial plants due to the release of its genome sequence and the important roles it has been playing in research areas related to alternative energy and climate change. Over the past five years, enormous advances have been made in both experimental and computational genomics in Populus. In the area of Populus
experimental genomics, traditional genetic approaches have been advanced to the genome scale with resolution to the gene and/or single nucleotide level on the one hand, and on the other hand, the modern �omics� approaches have been successfully applied to analyses of gene functions, including transcriptome profiling using microarrays as well as the next-generation DNA sequencing technology, proteome analysis using matrix assisted laser desorption ionization timeof-flight mass spectrometry, and metabolome characterization using gas chromatography/timeof-flight mass spectrometry. In the area of Populus computational genomics, significant progress has been made in sequence-based discovery of predicted gene function, comparative analysis of
gene families, development of online genomic databases, and studies of the evolutionary dynamics at both the gene and genome level. While exciting achievements have been obtained in Populus genomics, several challenges need to be addressed in the future: 1) better annotation of the Populus genome; 2) robust technology for large-scale gene expression analysis; 3) an
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.
