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Free Content A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation

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Summary

As part of a larger project to sequence the Populus genome and generate genomic resources for this emerging model tree, we constructed a physical map of the Populus genome, representing one of the few such maps of an undomesticated, highly heterozygous plant species. The physical map, consisting of 2802 contigs, was constructed from fingerprinted bacterial artificial chromosome (BAC) clones. The map represents approximately 9.4-fold coverage of the Populus genome, which has been estimated from the genome sequence assembly to be 485 ± 10 Mb in size. BAC ends were sequenced to assist long-range assembly of whole-genome shotgun sequence scaffolds and to anchor the physical map to the genome sequence. Simple sequence repeat-based markers were derived from the end sequences and used to initiate integration of the BAC and genetic maps. A total of 2411 physical map contigs, representing 97% of all clones assigned to contigs, were aligned to the sequence assembly (JGI Populus trichocarpa, version 1.0). These alignments represent a total coverage of 384 Mb (79%) of the entire poplar sequence assembly and 295 Mb (96%) of linkage group sequence assemblies. A striking result of the physical map contig alignments to the sequence assembly was the co-localization of multiple contigs across numerous regions of the 19 linkage groups. Targeted sequencing of BAC clones and genetic analysis in a small number of representative regions showed that these co-aligning contigs represent distinct haplotypes in the heterozygous individual sequenced, and revealed the nature of these haplotype sequence differences.
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Keywords: BAC end sequences; Populus trichocarpa; genome integration; haplotype diversity; physical map; poplar genomics

Document Type: Research Article

Affiliations: 1: Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada, 2: Genome Sciences Centre, 100-570 West 7th Avenue, Vancouver, BC V5Z 4S6, Canada, 3: Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA, 4: US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA, 5: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA, 6: Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA, 7: Department of Forest Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada, and

Publication date: June 1, 2007

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