Mun Jeong-Hwan, Kwon Soo-Jin, Yang Tae-Jin, Kim Hye-Sun, Choi Beom-Soon, Baek Seunghoon, Kim Jung Sun, Jin Mina, Kim Jin A, Lim Myung-Ho, Lee Soo In, Kim Ho-Il, Kim Hyungtae, Lim Yong Pyo, Park Beom-Seok
Brassica Genomics Team, National Institute of Agricultural Biotechnology, Rural Development Administration, 225 Seodun-dong, Gwonseon-gu, Suwon 441-707, South Korea.
BMC Genomics. 2008 Jun 12;9:280. doi: 10.1186/1471-2164-9-280.
The genus Brassica includes the most extensively cultivated vegetable crops worldwide. Investigation of the Brassica genome presents excellent challenges to study plant genome evolution and divergence of gene function associated with polyploidy and genome hybridization. A physical map of the B. rapa genome is a fundamental tool for analysis of Brassica "A" genome structure. Integration of a physical map with an existing genetic map by linking genetic markers and BAC clones in the sequencing pipeline provides a crucial resource for the ongoing genome sequencing effort and assembly of whole genome sequences.
A genome-wide physical map of the B. rapa genome was constructed by the capillary electrophoresis-based fingerprinting of 67,468 Bacterial Artificial Chromosome (BAC) clones using the five restriction enzyme SNaPshot technique. The clones were assembled into contigs by means of FPC v8.5.3. After contig validation and manual editing, the resulting contig assembly consists of 1,428 contigs and is estimated to span 717 Mb in physical length. This map provides 242 anchored contigs on 10 linkage groups to be served as seed points from which to continue bidirectional chromosome extension for genome sequencing.
The map reported here is the first physical map for Brassica "A" genome based on the High Information Content Fingerprinting (HICF) technique. This physical map will serve as a fundamental genomic resource for accelerating genome sequencing, assembly of BAC sequences, and comparative genomics between Brassica genomes. The current build of the B. rapa physical map is available at the B. rapa Genome Project website for the user community.
芸苔属包含全球种植最为广泛的蔬菜作物。对芸苔属基因组的研究为探讨植物基因组进化以及与多倍体和基因组杂交相关的基因功能差异带来了巨大挑战。白菜型油菜基因组的物理图谱是分析芸苔属“A”基因组结构的基础工具。通过在测序流程中将遗传标记与细菌人工染色体（BAC）克隆相连接，从而将物理图谱与现有的遗传图谱整合起来，这为正在进行的基因组测序工作和全基因组序列组装提供了关键资源。
利用五种限制性内切酶的SNaPshot技术，通过毛细管电泳对67,468个细菌人工染色体（BAC）克隆进行指纹识别，构建了白菜型油菜基因组的全基因组物理图谱。这些克隆通过FPC v8.5.3软件组装成重叠群。经过重叠群验证和人工编辑后，最终的重叠群组装由1428个重叠群组成，估计物理长度跨越717 Mb。该图谱在10个连锁群上提供了242个锚定重叠群，作为种子点用于基因组测序的双向染色体延伸。
本文报道的图谱是基于高信息含量指纹识别（HICF）技术构建的首个芸苔属“A”基因组物理图谱。该物理图谱将作为一种基础基因组资源，用于加速基因组测序、BAC序列组装以及芸苔属基因组之间的比较基因组学研究。白菜型油菜物理图谱的当前版本可在白菜型油菜基因组计划网站上供用户群体使用。
