Gene discovery in the Apicomplexa as revealed by EST sequencing and assembly of a comparative gene database
Gene discovery in the Apicomplexa as revealed by EST sequencing and assembly of a comparative gene database
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DOI：
10.1101/gr.693203
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发表时间：
2003-03-01
期刊：
影响因子：
7
通讯作者：
Sibley, LD
中科院分区：
文献类型：
--
作者：
Li, L;Brunk, BP;Sibley, LD
为了发现基因，对顶复门内几种重要寄生虫进行了大规模 EST 测序项目。其中包括几种具有医学重要性的寄生虫（恶性疟原虫、弓形虫）和其他具有兽医重要性的寄生虫（柔嫩艾美耳球虫、神经肉孢子虫和犬新孢子虫）。分析中纳入了存入 dbEST/GenBank 的总共 55,192 个 EST。所得序列已聚集成非冗余基因组件，并存入支持各种序列和文本搜索的关系数据库中。该数据库已用于使用 BLAST 相似性比较与公共蛋白质数据库来比较基因组装，以识别推定基因。在这些新条目中，相似的 15%-20% 代表保守截止值 p < 10(-9) 的推定同源物，从而识别出许多可能与其他经过充分研究的生物体共享共同功能的保守基因。基因组装还用于鉴定菌株多态性、检查阶段特异性表达并鉴定基因家族。鉴定出一类有趣的基因，这些基因仅限于该门的成员，并且不为植物、动物或真菌所共有。这些基因可能介导顶复合体成员的新生物学特征，因此为生物学研究和可能的治疗靶点提供了巨大的潜力。
Large-scale EST sequencing projects for several important parasites within the phylum Apicomplexa were undertaken for the purpose of gene discovery. Included were several parasites of medical importance (Plasmodium falciparum, Toxoplasma gondii) and others of veterinary importance (Eimeria tenella, Sarcocystis neurona, and Neospora caninum). A total of 55,192 ESTs, deposited into dbEST/GenBank, were included in the analyses. The resulting sequences have been clustered into nonredundant gene assemblies and deposited into a relational database that supports a variety of sequence and text searches. This database has been used to compare the gene assemblies using BLAST similarity comparisons to the public protein databases to identify putative genes. Of these new entries, similar to15%-20% represent putative homologs with a conservative cutoff of p < 10(-9), thus identifying many conserved genes that are likely to share common functions with other well-studied organisms. Gene assemblies were also used to identify strain polymorphisms, examine stage-specific expression, and identify gene families. An interesting class of genes that are confined to members of this phylum and not shared by plants, animals, or fungi, was identified. These genes likely mediate the novel biological features of members of the Apicomplexa and hence offer great potential for biological investigation and as possible therapeutic targets.