Assessment and improvement of the Plasmodium yoelii yoelii genome annotation through comparative analysis.
Assessment and improvement of the Plasmodium yoelii yoelii genome annotation through comparative analysis.
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DOI：
10.1093/bioinformatics/btn140
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发表时间：
2008-07-01
期刊：
影响因子：
--
通讯作者：
Peng X
中科院分区：
文献类型：
--
作者：
Vaughan A;Chiu SY;Ramasamy G;Li L;Gardner MJ;Tarun AS;Kappe SH;Peng X
动机：约氏疟原虫（一种啮齿动物疟原虫模型）基因组的测序极大地促进了针对疟疾的新药物和候选疫苗的开发研究。不幸的是，只有初步的基因模型在部分测序的基因组上进行了注释，主要是通过计算机基因预测，并且自 2002 年以来注释没有重大改进。 结果：在此，我们报告基于对一组全面的 cDNA 序列和蛋白质组数据的详细分析，对基因组注释的准确性进行了系统评估。我们发现当前注释的覆盖范围往往偏向于寄生虫生命周期的血液阶段中表达的基因。根据我们的蛋白质组分析，我们估计我们生成的大约 15% 的肝脏阶段蛋白质组数据在当前注释中不存在。通过比较分析，我们鉴定并手动整理了另外 510 个约氏疟原虫基因，这些基因在恶性疟原虫基因组中具有明确的直系同源物，但在当前注释中不存在或注释不正确。这项研究表明，当前约氏疟原虫基因组注释的改进应重点关注在血液阶段以外的阶段表达的基因。比较分析对于这种重新注释至关重要。添加新注释的基因将有助于使用约氏疟原虫作为研究人类疟疾的模型系统。联系方式：xinxia.peng@sbri.org； stefan.kappe@sbri.org 补充信息：补充数据可在生物信息学在线获取。
Motivation: The sequencing of the Plasmodium yoelii genome, a model rodent malaria parasite, has greatly facilitated research for the development of new drug and vaccine candidates against malaria. Unfortunately, only preliminary gene models were annotated on the partially sequenced genome, mostly by in silico gene prediction, and there has been no major improvement of the annotation since 2002. Results: Here we report on a systematic assessment of the accuracy of the genome annotation based on a detailed analysis of a comprehensive set of cDNA sequences and proteomics data. We found that the coverage of the current annotation tends to be biased toward genes expressed in the blood stages of the parasite life cycle. Based on our proteomic analysis, we estimate that about 15% of the liver stage proteome data we have generated is absent from the current annotation. Through comparative analysis we identified and manually curated a further 510 P. yoelii genes which have clear orthologs in the P. falciparum genome, but were not present or incorrectly annotated in the current annotation. This study suggests that improvements of the current P. yoelii genome annotation should focus on genes expressed in stages other than blood stages. Comparative analysis will be critically helpful for this re-annotation. The addition of newly annotated genes will facilitate the use of P. yoelii as a model system for studying human malaria. Contact: xinxia.peng@sbri.org; stefan.kappe@sbri.org Supplementary information: Supplementary data are available at Bioinformatics online.
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