Progression of the canonical reference malaria parasite genome from 2002–2019
Progression of the canonical reference malaria parasite genome from 2002–2019
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2002-2019 年典型参考疟疾寄生虫基因组的进展
DOI：
10.12688/wellcomeopenres.15194.2
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发表时间：
2019
影响因子：
--
通讯作者：
M. Berriman
中科院分区：
文献类型：
--
作者：
U. Böhme;T. Otto;M. Sanders;C. Newbold;M. Berriman
在这里，我们描述了恶性疟原虫参考基因组的序列和注释自2002年发表以来发生了变化的方式。作为世界上造成死亡人数最多的疟疾物种，丰富的注释和序列的准确性是恶性疟原虫研究界的重要资源，也是解释随后测序物种基因组的基础。在2002年发表时，超过60%的预测基因具有未知的功能。截至2019年3月，这一数字已大幅下降至33%。这种减少是由于纳入了后来经过实验表征的基因，以及与其他具有已知功能的基因具有显著相似性的基因。此外，基因的结构注释也得到了显著的改进；自2002年以来，27%的基因结构发生了变化，包括外显子-内含子边界的变化、外显子的添加或缺失以及基因的添加或缺失。序列也有了显著的改进。除了纠正了大量的单碱基和插入或缺失错误外，7号和8号染色体亚端粒之间的一个重大错配也得到了纠正。随着已测序分离株的数量持续快速增长，单一的参考基因组将不足以解释种内序列多样性。因此，我们在本出版物中描述了恶性疟原虫的种群参考基因组，称为Pfref1。此引用将使社区能够映射到当前程序集中不存在的区域。恶性疟原虫3D7将继续保持，并进行持续的管理，以确保注释质量的持续改进。
Here we describe the ways in which the sequence and annotation of the Plasmodium falciparum reference genome has changed since its publication in 2002. As the malaria species responsible for the most deaths worldwide, the richness of annotation and accuracy of the sequence are important resources for the P. falciparum research community as well as the basis for interpreting the genomes of subsequently sequenced species. At the time of publication in 2002 over 60% of predicted genes had unknown functions. As of March 2019, this number has been significantly decreased to 33%. The reduction is due to the inclusion of genes that were subsequently characterised experimentally and genes with significant similarity to others with known functions. In addition, the structural annotation of genes has been significantly refined; 27% of gene structures have been changed since 2002, comprising changes in exon-intron boundaries, addition or deletion of exons and the addition or deletion of genes. The sequence has also undergone significant improvements. In addition to the correction of a large number of single-base and insertion or deletion errors, a major miss-assembly between the subtelomeres of chromosome 7 and 8 has been corrected. As the number of sequenced isolates continues to grow rapidly, a single reference genome will not be an adequate basis for interpreting intra-species sequence diversity. We therefore describe in this publication a population reference genome of P. falciparum, called Pfref1. This reference will enable the community to map to regions that are not present in the current assembly. P. falciparum 3D7 will continue to be maintained, with ongoing curation ensuring continual improvements in annotation quality.
影响因子：
14.9
作者：
The Gene Ontology Consortium
通讯作者：
The Gene Ontology Consortium