Arner Erik, Kindlund Ellen, Nilsson Daniel, Farzana Fatima, Ferella Marcela, Tammi Martti T, Andersson Björn
Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
BMC Genomics. 2007 Oct 26;8:391. doi: 10.1186/1471-2164-8-391.
Repeats are present in all genomes, and often have important functions. However, in large genome sequencing projects, many repetitive regions remain uncharacterized. The genome of the protozoan parasite Trypanosoma cruzi consists of more than 50% repeats. These repeats include surface molecule genes, and several other gene families. In the T. cruzi genome sequencing project, it was clear that not all copies of repetitive genes were present in the assembly, due to collapse of nearly identical repeats. However, at the time of publication of the T. cruzi genome, it was not clear to what extent this had occurred.
We have developed a pipeline to estimate the genomic repeat content, where shotgun reads are aligned to the genomic sequence and the gene copy number is estimated using the average shotgun coverage. This method was applied to the genome of T. cruzi and copy numbers of all protein coding sequences and pseudogenes were estimated. The 22,640 results were stored in a database available online. 18% of all protein coding sequences and pseudogenes were estimated to exist in 14 or more copies in the T. cruzi CL Brener genome. The average coverage of the annotated protein coding sequences and pseudogenes indicate a total gene copy number, including allelic gene variants, of over 40,000.
Our results indicate that the number of protein coding sequences and pseudogenes in the T. cruzi genome may be twice the previous estimate. We have constructed a database of the T. cruzi gene repeat data that is available as a resource to the community. The main purpose of the database is to enable biologists interested in repeated, unfinished regions to closely examine and resolve these regions themselves using all available shotgun data, instead of having to rely on annotated consensus sequences that often are erroneous and possibly misleading. Five repetitive genes were studied in more detail, in order to illustrate how the database can be used to analyze and extract information about gene repeats with different characteristics in Trypanosoma cruzi.
重复序列存在于所有基因组中，且通常具有重要功能。然而，在大型基因组测序项目中，许多重复区域仍未得到表征。原生动物寄生虫克氏锥虫的基因组中重复序列占比超过50%。这些重复序列包括表面分子基因以及其他几个基因家族。在克氏锥虫基因组测序项目中，由于几乎相同的重复序列发生塌陷，很明显并非所有重复基因的拷贝都存在于组装结果中。然而，在克氏锥虫基因组发表时，尚不清楚这种情况发生的程度。
我们开发了一种用于估计基因组重复序列含量的流程，即将鸟枪法测序读段与基因组序列进行比对，并使用平均鸟枪法覆盖度来估计基因拷贝数。该方法应用于克氏锥虫基因组，估计了所有蛋白质编码序列和假基因的拷贝数。22640个结果存储在一个在线数据库中。据估计，在克氏锥虫CL Brener基因组中，18%的蛋白质编码序列和假基因以14个或更多拷贝存在。注释的蛋白质编码序列和假基因的平均覆盖度表明，包括等位基因变体在内的总基因拷贝数超过40000个。
我们的结果表明，克氏锥虫基因组中蛋白质编码序列和假基因的数量可能是先前估计值的两倍。我们构建了一个克氏锥虫基因重复数据数据库，作为一种资源供学界使用。该数据库的主要目的是使对重复、未完成区域感兴趣的生物学家能够利用所有可用的鸟枪法数据自行仔细研究和解析这些区域，而不必依赖通常有误且可能具有误导性的注释一致序列。为了说明如何利用该数据库分析和提取克氏锥虫中具有不同特征的基因重复信息，我们对五个重复基因进行了更详细的研究。
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