The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

Science. 2006 Sep 15;313(5793):1596-604. doi: 10.1126/science.1128691.


We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Arabidopsis / genetics
  • Chromosome Mapping
  • Computational Biology
  • Evolution, Molecular
  • Expressed Sequence Tags
  • Gene Duplication*
  • Gene Expression
  • Genes, Plant
  • Genome, Plant*
  • Oligonucleotide Array Sequence Analysis
  • Phylogeny
  • Plant Proteins / chemistry
  • Plant Proteins / genetics
  • Polymorphism, Single Nucleotide
  • Populus / genetics*
  • Populus / growth & development
  • Populus / metabolism
  • Protein Structure, Tertiary
  • RNA, Plant / analysis
  • RNA, Untranslated / analysis
  • Sequence Analysis, DNA*


  • Plant Proteins
  • RNA, Plant
  • RNA, Untranslated