The genome of black cottonwood, Populus trichocarpa, was sequenced and assembled using a whole-genome shotgun approach, resulting in a draft genome of approximately 485 Mb. The genome contains over 45,000 putative protein-coding genes, with a whole-genome duplication event identified, resulting in approximately 8,000 pairs of duplicated genes. A second, older duplication event is coincident with the divergence of Populus and Arabidopsis. Populus has more protein-coding genes than Arabidopsis, with an average of 1.4-1.6 homologs per Arabidopsis gene. The relative frequency of protein domains in the two genomes is similar, with Populus showing overrepresented genes related to disease resistance, meristem development, metabolite transport, and lignocellulosic wall biosynthesis. The genome of Populus trichocarpa was compared to other sequenced plant genomes, revealing a large-scale genome history shared with Salix. The genome duplication in Populus is estimated to have occurred around 8-13 million years ago, but the fossil record suggests a divergence of Populus and Salix lineages 60-65 million years ago. This indicates that the molecular clock in Populus is slower than in Arabidopsis. The genome duplication in Populus is referred to as the "salicoid" duplication event, while the older duplication shared with Arabidopsis is called the "eurosid" duplication event. The Populus genome contains a large number of protein-coding genes, with a significant portion of these genes involved in lignocellulosic wall formation, secondary metabolism, and disease resistance. The genome also contains a variety of non-coding RNAs, including tRNAs, snRNAs, and snoRNAs. The genome of Populus has a higher number of tRNA genes compared to Arabidopsis, and the number of snRNA genes is similar, though some are overrepresented in Populus. The genome of Populus trichocarpa also contains a large number of gene families, including those involved in cellulose biosynthesis, hemicellulose biosynthesis, and lignin biosynthesis. The genome contains a variety of genes involved in secondary metabolism, including those involved in the production of phenolic esters, phenolic glycosides, and condensed tannins. The genome also contains a variety of genes involved in disease resistance, including those encoding NBS-LRR proteins, which are involved in recognizing pathogen-associated molecular patterns. The genome of Populus trichocarpa also contains a variety of genes involved in membrane transport, including those involved in the transport of nutrients, water, and secondary metabolites. The genome contains a large number of transporter genes, including those involved in the transport of amino acids, auxins, and gibberellins. The genome also contains a variety of genes involvedThe genome of black cottonwood, Populus trichocarpa, was sequenced and assembled using a whole-genome shotgun approach, resulting in a draft genome of approximately 485 Mb. The genome contains over 45,000 putative protein-coding genes, with a whole-genome duplication event identified, resulting in approximately 8,000 pairs of duplicated genes. A second, older duplication event is coincident with the divergence of Populus and Arabidopsis. Populus has more protein-coding genes than Arabidopsis, with an average of 1.4-1.6 homologs per Arabidopsis gene. The relative frequency of protein domains in the two genomes is similar, with Populus showing overrepresented genes related to disease resistance, meristem development, metabolite transport, and lignocellulosic wall biosynthesis. The genome of Populus trichocarpa was compared to other sequenced plant genomes, revealing a large-scale genome history shared with Salix. The genome duplication in Populus is estimated to have occurred around 8-13 million years ago, but the fossil record suggests a divergence of Populus and Salix lineages 60-65 million years ago. This indicates that the molecular clock in Populus is slower than in Arabidopsis. The genome duplication in Populus is referred to as the "salicoid" duplication event, while the older duplication shared with Arabidopsis is called the "eurosid" duplication event. The Populus genome contains a large number of protein-coding genes, with a significant portion of these genes involved in lignocellulosic wall formation, secondary metabolism, and disease resistance. The genome also contains a variety of non-coding RNAs, including tRNAs, snRNAs, and snoRNAs. The genome of Populus has a higher number of tRNA genes compared to Arabidopsis, and the number of snRNA genes is similar, though some are overrepresented in Populus. The genome of Populus trichocarpa also contains a large number of gene families, including those involved in cellulose biosynthesis, hemicellulose biosynthesis, and lignin biosynthesis. The genome contains a variety of genes involved in secondary metabolism, including those involved in the production of phenolic esters, phenolic glycosides, and condensed tannins. The genome also contains a variety of genes involved in disease resistance, including those encoding NBS-LRR proteins, which are involved in recognizing pathogen-associated molecular patterns. The genome of Populus trichocarpa also contains a variety of genes involved in membrane transport, including those involved in the transport of nutrients, water, and secondary metabolites. The genome contains a large number of transporter genes, including those involved in the transport of amino acids, auxins, and gibberellins. The genome also contains a variety of genes involved