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A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation
Author(s) -
Kelleher Colin T.,
Chiu Readman,
Shin Heesun,
Bosdet Ian E.,
Krzywinski Martin I.,
Fjell Chris D.,
Wilkin Jennifer,
Yin TongMing,
DiFazio Stephen P.,
Ali Johar,
Asano Jennifer K.,
Chan Susanna,
Cloutier Alison,
Girn Noreen,
Leach Stephen,
Lee Darlene,
Mathewson Carrie A.,
Olson Teika,
O’Connor Katie,
Prabhu AnnaLiisa,
Smailus Duane E.,
Stott Jeffery M.,
Tsai Miranda,
Wye Natasja H.,
Yang George S.,
Zhuang Jun,
Holt Robert A.,
Putnam Nicholas H.,
Vrebalov Julia,
Giovani James J.,
Grimwood Jane,
Schmutz Jeremy,
Rokhsar Daniel,
Jones Steven J.M.,
Marra Marco A.,
Tuskan Gerald A.,
Bohlmann Jörg,
Ellis Brian E.,
Ritland Kermit,
Douglas Carl J.,
Schein Jacqueline E.
Publication year - 2007
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/j.1365-313x.2007.03112.x
Subject(s) - contig , genome , genetics , biology , shotgun sequencing , whole genome sequencing , sequence assembly , reference genome , sequence (biology) , genome project , sequence tagged site , haplotype , populus trichocarpa , computational biology , gene mapping , chromosome , gene , allele , gene expression , transcriptome
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.