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 Anna-Liisa, Smailus Duane E, Stott Jeffery M, Tsai Miranda, Wye Natasja H, Yang George S, Zhuang Jun, Holt Robert A, Putnam Nicholas H, Vrebalov Julia, Giovannoni 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
Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
Plant J. 2007 Jun;50(6):1063-78. doi: 10.1111/j.1365-313X.2007.03112.x. Epub 2007 May 3.
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.
作为对毛果杨基因组进行测序及为这种新兴模式树种生成基因组资源的更大项目的一部分，我们构建了毛果杨基因组的物理图谱，这是未驯化的、高度杂合植物物种中为数不多的此类图谱之一。该物理图谱由2802个重叠群组成，是从经指纹识别的细菌人工染色体（BAC）克隆构建而来。该图谱代表了毛果杨基因组约9.4倍的覆盖率，根据基因组序列组装估计，毛果杨基因组大小为485±10 Mb。对BAC末端进行测序，以协助全基因组鸟枪法序列支架的长距离组装，并将物理图谱锚定到基因组序列上。基于简单序列重复的标记是从末端序列衍生而来，并用于启动BAC图谱和遗传图谱的整合。共有2411个物理图谱重叠群（占所有分配到重叠群的克隆的97%）与序列组装（JGI毛果杨，版本1.0）进行了比对。这些比对代表了整个杨树序列组装384 Mb（79%）和连锁群序列组装295 Mb（96%）的总覆盖率。物理图谱重叠群与序列组装比对的一个显著结果是，在19个连锁群的众多区域中多个重叠群共定位。对BAC克隆进行靶向测序以及在少数代表性区域进行遗传分析表明，这些共比对的重叠群代表了所测序的杂合个体中的不同单倍型，并揭示了这些单倍型序列差异的性质。
