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The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).
Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).ORCID iD: 0000-0002-7906-6891
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2006 (English)In: Science, ISSN 1095-9203, Vol. 313, no 5793, 1596-604 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2006. Vol. 313, no 5793, 1596-604 p.
Keyword [en]
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/genetics, Polymorphism; Single Nucleotide, Populus/*genetics/growth & development/metabolism, Protein Structure; Tertiary, RNA; Plant/analysis, RNA; Untranslated/analysis, Sequence Analysis; DNA
URN: urn:nbn:se:umu:diva-14206DOI: 10.1126/science.1128691PubMedID: 16973872OAI: diva2:153877
Available from: 2007-05-24 Created: 2007-05-24 Last updated: 2015-04-29Bibliographically approved

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Jansson, StefanKarlsson, JanSandberg, Göran
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Department of Plant PhysiologyUmeå Plant Science Centre (UPSC)

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