Profiling the malaria genome: a gene survey of three species of malaria parasite with comparison to other apicomplexan species
Profiling the malaria genome: a gene survey of three species of malaria parasite with comparison to other apicomplexan species
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DOI：
10.1016/s0166-6851(01)00371-1
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发表时间：
2001-12-01
影响因子：
1.5
通讯作者：
Dame, JB
中科院分区：
文献类型：
--
作者：
Carlton, JMR;Muller, R;Dame, JB
我们已经进行了第一次比较试点基因发现分析约25 000随机基因组和表达序列标签（EST）从三个物种的疟原虫，感染剂，导致疟疾。共有5482基因组调查序列（GSS）和5582 EST产生绿豆核酸酶（MBN）和cDNA文库，分别为ANKA线的啮齿类疟原虫？berghei，和10 874 GSS产生自间日疟原虫的萨尔瓦多I和贝伦系的MBN文库，间日疟原虫是地理上分布最广的人类疟疾病原体。这些标签与GenBank中存在的2438个恶性疟原虫序列一起用于进行首过组装和转录重建，并创建非冗余共有序列数据集。这些数据集与公共蛋白质数据库进行了比较，并根据序列相似性鉴定了1000多种推定的新疟原虫蛋白质。先前表征的疟原虫基因的同源物也被鉴定，使公共数据库中间日疟原虫和伯氏疟原虫序列的数量增加至少10倍。与Apicomplexa其他物种的比较研究确定了可能具有治疗或诊断价值的有趣同源物。基因预测程序Phat用于预测所有三个数据集中蛋白质的可能开放阅读框。预测的和非冗余的BLAST匹配的蛋白质提交到InterPro，一个集成的数据库的蛋白质结构域，签名和家庭，功能分类。因此，为每个物种创建了部分预测蛋白质组。疟原虫蛋白编码序列的首次比较分析为进一步研究这一重要病原体的生物学提供了宝贵的资源。(C)2001 Elsevier Science B.V.保留所有权利。
We have undertaken the first comparative pilot gene discovery analysis of approximately 25 000 random genomic and expressed sequence tags (ESTs) from three species of Plasmodium, the infectious agent that causes malaria. A total of 5482 genome survey sequences (GSSs) and 5582 ESTs were generated from mung bean nuclease (MBN) and cDNA libraries, respectively, of the ANKA line of the rodent malaria parasite Plasmodium? berghei, and 10 874 GSSs generated from MBN libraries of the Salvador I and Belem lines of Plasmodium vivax, the most geographically wide-spread human malaria pathogen. These tags. together with 2438 Plasmodium falciparum sequences present in GenBank, were used to perform first-pass assembly and transcript reconstruction, and non-redundant consensus sequence datasets created. The datasets were compared against public protein databases and more than 1000 putative new Plasmodium proteins identified based on sequence similarity. Homologs of previously characterized Plasmodium genes were also identified, increasing the number of P. vivax and P. berghei sequences in public databases at least 10-fold. Comparative studies with other species of Apicomplexa identified interesting homologs of possible therapeutic or diagnostic value. A gene prediction program, Phat, was used to predict probable open reading frames for proteins in all three datasets. Predicted and non-redundant BLAST-matched proteins were submitted to InterPro, an integrated database of protein domains, signatures and families, for functional classification. Thus a partial predicted proteome was created for each species. This first comparative analysis of Plasmodium protein coding sequences represents a valuable resource for further studies on the biology of this important pathogen. (C) 2001 Elsevier Science B.V. All rights reserved.