cDNA sequences reveal considerable gene prediction inaccuracy in the Plasmodium falciparum genome.
cDNA sequences reveal considerable gene prediction inaccuracy in the Plasmodium falciparum genome.
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DOI：
10.1186/1471-2164-8-255
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发表时间：
2007-07-27
期刊：
影响因子：
4.4
通讯作者：
Su XZ
中科院分区：
文献类型：
--
作者：
Lu F;Jiang H;Ding J;Mu J;Valenzuela JG;Ribeiro JM;Su XZ
恶性疟原虫基因组的完成是疟疾研究的一个里程碑。基因组序列允许发展全基因组的方法，如微阵列和蛋白质组学，这将极大地促进我们对寄生虫生物学的理解，并加速新药和疫苗的开发。然而，这些全基因组分析的设计和应用需要关于基因预测和基因组注释的准确信息。不幸的是，寄生虫基因组数据库中的基因大多是使用计算机软件识别的，这些软件可能会做出一些错误的预测。我们的目标是获得基因序列，以检验基因预测的准确性。利用SMART文库构建技术构建了恶性疟原虫混合血液期的基因文库，获得了17332个高质量的表达序列标签，其中包括2198个来自引物行走实验的表达序列标签。当我们的EST与公共数据库中的EST组装时，我们的序列标签的组装产生了2548个重叠群和2671个单体，而当我们的EST与EST组装时，产生了5220个重叠群和5910个单体。将所有组装的EST/重叠群与预测的CDS和PlamoDB数据库中的基因组序列进行比较，发现356个基因的预测编码序列完全被EST覆盖，其中85个基因(23.6%)的内含子预测错误。仔细的自动软件和人工比对发现了另外308个基因的内含子与预测的不同，发现了152个新的内含子，182个内含子的大小或位置与预测的不同。还检测到选择性剪接转录本和反义转录本。将cdna与预测的基因进行匹配也发现了沉默的染色体区域，主要位于端粒以下区域。我们的数据表明，当前数据库中大约24%的基因被错误预测，尽管其中一些错误可能代表选择性剪接的转录本，并且比目前预测的更多的基因具有一个或多个额外的内含子。因此，有必要用实验数据对寄生虫基因组进行注释，尽管由于基因组的高AT性质，从这种寄生虫中获得完整的cDNA序列将是一项艰巨的任务。这项研究为基因组注释提供了有价值的信息，这将是功能分析的关键。
The completion of the Plasmodium falciparum genome represents a milestone in malaria research. The genome sequence allows for the development of genome-wide approaches such as microarray and proteomics that will greatly facilitate our understanding of the parasite biology and accelerate new drug and vaccine development. Designing and application of these genome-wide assays, however, requires accurate information on gene prediction and genome annotation. Unfortunately, the genes in the parasite genome databases were mostly identified using computer software that could make some erroneous predictions. We aimed to obtain cDNA sequences to examine the accuracy of gene prediction in silico. We constructed cDNA libraries from mixed blood stages of P. falciparum parasite using the SMART cDNA library construction technique and generated 17332 high-quality expressed sequence tags (EST), including 2198 from primer-walking experiments. Assembly of our sequence tags produced 2548 contigs and 2671 singletons versus 5220 contigs and 5910 singletons when our EST were assembled with EST in public databases. Comparison of all the assembled EST/contigs with predicted CDS and genomic sequences in the PlasmoDB database identified 356 genes with predicted coding sequences fully covered by EST, including 85 genes (23.6%) with introns incorrectly predicted. Careful automatic software and manual alignments found an additional 308 genes that have introns different from those predicted, with 152 new introns discovered and 182 introns with sizes or locations different from those predicted. Alternative spliced and antisense transcripts were also detected. Matching cDNA to predicted genes also revealed silent chromosomal regions, mostly at subtelomere regions. Our data indicated that approximately 24% of the genes in the current databases were predicted incorrectly, although some of these inaccuracies could represent alternatively spliced transcripts, and that more genes than currently predicted have one or more additional introns. It is therefore necessary to annotate the parasite genome with experimental data, although obtaining complete cDNA sequences from this parasite will be a formidable task due to the high AT nature of the genome. This study provides valuable information for genome annotation that will be critical for functional analyses.
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作者：
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