Yu Qingyi, Tong Eric, Skelton Rachel L, Bowers John E, Jones Meghan R, Murray Jan E, Hou Shaobin, Guan Peizhu, Acob Ricelle A, Luo Ming-Cheng, Moore Paul H, Alam Maqsudul, Paterson Andrew H, Ming Ray
Cellular and Molecular Biology Research Unit, Hawaii Agriculture Research Center, Aiea, HI 96701, USA.
BMC Genomics. 2009 Aug 7;10:371. doi: 10.1186/1471-2164-10-371.
Papaya is a major fruit crop in tropical and subtropical regions worldwide and has primitive sex chromosomes controlling sex determination in this trioecious species. The papaya genome was recently sequenced because of its agricultural importance, unique biological features, and successful application of transgenic papaya for resistance to papaya ringspot virus. As a part of the genome sequencing project, we constructed a BAC-based physical map using a high information-content fingerprinting approach to assist whole genome shotgun sequence assembly.
The physical map consists of 963 contigs, representing 9.4x genome equivalents, and was integrated with the genetic map and genome sequence using BAC end sequences and a sequence-tagged high-density genetic map. The estimated genome coverage of the physical map is about 95.8%, while 72.4% of the genome was aligned to the genetic map. A total of 1,181 high quality overgo (overlapping oligonucleotide) probes representing conserved sequences in Arabidopsis and genetically mapped loci in Brassica were anchored on the physical map, which provides a foundation for comparative genomics in the Brassicales. The integrated genetic and physical map aligned with the genome sequence revealed recombination hotspots as well as regions suppressed for recombination across the genome, particularly on the recently evolved sex chromosomes. Suppression of recombination spread to the adjacent region of the male specific region of the Y chromosome (MSY), and recombination rates were recovered gradually and then exceeded the genome average. Recombination hotspots were observed at about 10 Mb away on both sides of the MSY, showing 7-fold increase compared with the genome wide average, demonstrating the dynamics of recombination of the sex chromosomes.
A BAC-based physical map of papaya was constructed and integrated with the genetic map and genome sequence. The integrated map facilitated the draft genome assembly, and is a valuable resource for comparative genomics and map-based cloning of agronomically and economically important genes and for sex chromosome research.
番木瓜是全球热带和亚热带地区的主要水果作物，在这种雌雄异株的物种中具有控制性别决定的原始性染色体。由于其农业重要性、独特的生物学特性以及转基因番木瓜在抗番木瓜环斑病毒方面的成功应用，番木瓜基因组最近已被测序。作为基因组测序项目的一部分，我们采用高信息含量指纹图谱方法构建了基于细菌人工染色体（BAC）的物理图谱，以协助全基因组鸟枪法序列组装。
该物理图谱由963个重叠群组成，代表9.4倍基因组当量，并使用BAC末端序列和序列标签高密度遗传图谱与遗传图谱和基因组序列整合。物理图谱估计的基因组覆盖率约为95.8%，而72.4%的基因组与遗传图谱对齐。共有1181个高质量的重叠寡核苷酸（overgo）探针，代表拟南芥中的保守序列和芸苔属中的遗传定位位点，被锚定在物理图谱上，这为十字花目植物的比较基因组学提供了基础。与基因组序列对齐的整合遗传图谱和物理图谱揭示了全基因组范围内的重组热点以及重组受到抑制的区域，特别是在最近进化的性染色体上。重组抑制扩展到Y染色体雄性特异性区域（MSY）的相邻区域，重组率逐渐恢复，然后超过基因组平均值。在MSY两侧约10 Mb处观察到重组热点，与全基因组平均水平相比增加了7倍，证明了性染色体重组的动态变化。
构建了基于BAC的番木瓜物理图谱，并与遗传图谱和基因组序列整合。整合图谱促进了基因组草图组装，是比较基因组学以及基于图谱克隆农艺和经济上重要基因以及进行性染色体研究的宝贵资源。
