Boffelli Dario, Weer Claire V, Weng Li, Lewis Keith D, Shoukry Malak I, Pachter Lior, Keys David N, Rubin Edward M
US Dept. of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.
Genome Res. 2004 Dec;14(12):2406-11. doi: 10.1101/gr.3199704. Epub 2004 Nov 15.
Analysis of sequence variation among members of a single species offers a potential approach to identify functional DNA elements responsible for biological features unique to that species. Due to its high rate of allelic polymorphism and ease of genetic manipulability, we chose the sea squirt, Ciona intestinalis, to explore intraspecies sequence comparisons for genome annotation. A large number of C. intestinalis specimens were collected from four continents, and a set of genomic intervals were amplified, resequenced, and analyzed to determine the mutation rates at each nucleotide in the sequence. We found that regions with low mutation rates efficiently demarcated functionally constrained sequences: these include a set of noncoding elements, which we showed in C. intestinalis transgenic assays to act as tissue-specific enhancers, as well as the location of coding sequences. This illustrates that comparisons of multiple members of a species can be used for genome annotation, suggesting a path for the annotation of the sequenced genomes of organisms occupying uncharacterized phylogenetic branches of the animal kingdom. It also raises the possibility that the resequencing of a large number of Homo sapiens individuals might be used to annotate the human genome and identify sequences defining traits unique to our species.
对单一物种成员间的序列变异进行分析，为识别负责该物种独特生物学特征的功能性DNA元件提供了一种潜在方法。由于其等位基因多态性率高且易于进行基因操作，我们选择海鞘（Ciona intestinalis）来探索种内序列比较以进行基因组注释。从四大洲收集了大量的肠鳃纲海鞘标本，并对一组基因组区间进行扩增、重测序和分析，以确定序列中每个核苷酸的突变率。我们发现，低突变率区域有效地划分了功能受限序列：这些序列包括一组非编码元件，我们在肠鳃纲海鞘转基因试验中证明它们可作为组织特异性增强子，以及编码序列的位置。这表明对一个物种的多个成员进行比较可用于基因组注释，为注释处于动物王国未表征系统发育分支的生物体的测序基因组指明了一条道路。这也增加了一种可能性，即对大量人类个体进行重测序可能用于注释人类基因组并识别定义我们物种独特性状的序列。
