Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA.
BMC Genomics. 2011 Sep 9;12:447. doi: 10.1186/1471-2164-12-447.
A robust bacterial artificial chromosome (BAC)-based physical map is essential for many aspects of genomics research, including an understanding of chromosome evolution, high-resolution genome mapping, marker-assisted breeding, positional cloning of genes, and quantitative trait analysis. To facilitate turkey genetics research and better understand avian genome evolution, a BAC-based integrated physical, genetic, and comparative map was developed for this important agricultural species.
The turkey genome physical map was constructed based on 74,013 BAC fingerprints (11.9 × coverage) from two independent libraries, and it was integrated with the turkey genetic map and chicken genome sequence using over 41,400 BAC assignments identified by 3,499 overgo hybridization probes along with > 43,000 BAC end sequences. The physical-comparative map consists of 74 BAC contigs, with an average contig size of 13.6 Mb. All but four of the turkey chromosomes were spanned on this map by three or fewer contigs, with 14 chromosomes spanned by a single contig and nine chromosomes spanned by two contigs. This map predicts 20 to 27 major rearrangements distinguishing turkey and chicken chromosomes, despite up to 40 million years of separate evolution between the two species. These data elucidate the chromosomal evolutionary pattern within the Phasianidae that led to the modern turkey and chicken karyotypes. The predominant rearrangement mode involves intra-chromosomal inversions, and there is a clear bias for these to result in centromere locations at or near telomeres in turkey chromosomes, in comparison to interstitial centromeres in the orthologous chicken chromosomes.
The BAC-based turkey-chicken comparative map provides novel insights into the evolution of avian genomes, a framework for assembly of turkey whole genome shotgun sequencing data, and tools for enhanced genetic improvement of these important agricultural and model species.
对于基因组学研究的许多方面，包括理解染色体进化、高分辨率基因组作图、标记辅助育种、基因的定位克隆和数量性状分析，一个强大的基于细菌人工染色体 (BAC) 的物理图谱是必不可少的。为了促进火鸡遗传学研究，并更好地了解鸟类基因组进化，为这个重要的农业物种开发了基于 BAC 的综合物理、遗传和比较图谱。
火鸡基因组物理图谱是基于两个独立文库中的 74013 个 BAC 指纹（覆盖率为 11.9×）构建的，该图谱与火鸡遗传图谱和鸡基因组序列整合在一起，使用超过 41400 个 BAC 分配，这些分配是由 3499 个过度杂交探针识别的，超过 43000 个 BAC 末端序列。物理-比较图谱由 74 个 BAC 连续图谱组成，平均图谱大小为 13.6 Mb。除了四个图谱之外，这个图谱上的火鸡染色体都由三个或更少的连续图谱覆盖，其中 14 个染色体由一个连续图谱覆盖，9 个染色体由两个连续图谱覆盖。该图谱预测了 20 到 27 个主要的重排，区分了火鸡和鸡的染色体，尽管这两个物种已经分开进化了 4000 万年。这些数据阐明了导致现代火鸡和鸡染色体的雀形目内的染色体进化模式。主要的重排模式涉及染色体内部倒位，并且在火鸡染色体中，着丝粒位于或靠近端粒的位置，而在同源鸡染色体中，着丝粒位于染色体的中间位置，这明显存在偏向性。
基于 BAC 的火鸡-鸡比较图谱为鸟类基因组的进化提供了新的见解，为组装火鸡全基因组霰弹测序数据提供了一个框架，并为这些重要的农业和模式物种的遗传改良提供了工具。
