Comparative genomics, using the model organism approach, has provided powerful insights into the structure and evolution of whole genomes. Unfortunately, only a small fraction of Earth's biodiversity will have its genome sequenced in the foreseeable future. Most wild organisms have radically different life histories and evolutionary genomics than current model systems. A novel technique is needed to expand comparative genomics to a wider range of organisms. Here, we describe a novel approach using an anonymous DNA microarray platform that gathers genomic samples of sequence variation from any organism. Oligonucleotide probe sequences placed on a custom 44 K array were 25 bp long and designed using a simple set of criteria to maximize their complexity and dispersion in sequence probability space. Using whole genomic samples from three known genomes (mouse, rat and human) and one unknown (Gonystylus bancanus), we demonstrate and validate its power, reliability, transitivity and sensitivity. Using two separate statistical analyses, a large numbers of genomic 'indicator' probes were discovered. The construction of a genomic signature database based upon this technique would allow virtual comparisons and simple queries could generate optimal subsets of markers to be used in large-scale assays, using simple downstream techniques. Biologists from a wide range of fields, studying almost any organism, could efficiently perform genomic comparisons, at potentially any phylogenetic level after performing a small number of standardized DNA microarray hybridizations. Possibilities for refining and expanding the approach are discussed.

译文

使用模式生物方法的比较基因组学为整个基因组的结构和进化提供了有力的见解。不幸的是,在可预见的将来,地球生物多样性中只有一小部分将对其基因组进行测序。大多数野生生物的生活史和进化基因组学与当前的模型系统完全不同。需要一种新技术来将比较基因组学扩展到更广泛的生物体。在这里,我们描述了一种使用匿名DNA微阵列平台的新颖方法,该平台收集来自任何生物的序列变异的基因组样本。放置在定制的44 K阵列上的寡核苷酸探针序列长25 bp,并使用一组简单的标准进行设计,以最大程度地提高其在序列概率空间中的复杂性和分散性。使用来自三个已知基因组 (小鼠,大鼠和人类) 和一个未知基因组 (Gonystylus bancanus) 的全基因组样本,我们证明并验证了其功能,可靠性,传递性和敏感性。使用两个单独的统计分析,发现了大量的基因组 “指标” 探针。基于该技术的基因组签名数据库的构建将允许虚拟比较,并且简单的查询可以使用简单的下游技术生成用于大规模测定的最佳标记子集。来自广泛领域的生物学家,研究几乎任何生物,可以在进行少量标准化DNA微阵列杂交后,在潜在的任何系统发育水平上有效地进行基因组比较。讨论了改进和扩展该方法的可能性。

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