The Babesia bovis gene and promoter model: an update from full-length EST analysis.
The Babesia bovis gene and promoter model: an update from full-length EST analysis.
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牛巴贝斯虫基因和启动子模型：全长 EST 分析的更新。
DOI：
10.1186/1471-2164-15-678
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发表时间：
2014-08-13
期刊：
影响因子：
4.4
通讯作者：
Igarashi I
中科院分区：
文献类型：
--
作者：
Yamagishi J;Wakaguri H;Yokoyama N;Yamashita R;Suzuki Y;Xuan X;Igarashi I
牛巴贝虫是一种顶复门寄生虫，可引起感染牛的巴贝虫病。病原体的基因组包含有希望的信息，可以促进控制感染的方法的发展。尽管B.牛的基因是可获得的，但注释的基因模型在实验验证之前不是高度可靠的。因此，我们验证了预先提出的B的基因模型。bovis的，并扩展了相关的注释实验获得的全长表达序列标签（EST）的基础上。从体外培养的裂殖子中，使用桑格方法从两端对12，286个含有全长cDNA的克隆进行测序，并组装6，787个全长cDNA。然后对这些序列进行聚类，构建了2，115个全长cDNA序列的非冗余参考数据集。将预先提出的基因模型与我们的数据集进行比较，发现了310个相同的基因，342个几乎相同的基因，1，054个具有潜在结构不一致性的基因和409个新基因。5'非翻译区（UTR）的中位长度为152 nt。随后，我们通过检测5'EST鉴定了4，086个转录起始位点（TSS）和2，023个转录活性区（TAR）。我们将ATGGGG和CCCCAT位点鉴定为分布在距离TSS约50 bp的TAR中的共有基序。此外，我们发现ACACA，TGTGT，和TATAT网站，这是定期分布在大约150 bp的循环TSS周围。此外，在哺乳动物启动子区没有观察到相关的周期性分布。本研究中的观察结果表明，综合生物信息学和实验数据用于改进基因组注释的实用性。特别是，全长cDNA与TSS的一个碱基分辨率，使启动子序列中的共识基序的识别，并证明了明确的分布所确定的基序。这些观察允许的模型启动子组合物的说明，这支持顶复门寄生虫和哺乳动物之间的转录调控框架的差异。本文的在线版本（doi：10.1186/1471-2164-15-678）包含补充材料，可供授权用户使用。
Babesia bovis is an apicomplexan parasite that causes babesiosis in infected cattle. Genomes of pathogens contain promising information that can facilitate the development of methods for controlling infections. Although the genome of B. bovis is publically available, annotated gene models are not highly reliable prior to experimental validation. Therefore, we validated a preproposed gene model of B. bovis and extended the associated annotations on the basis of experimentally obtained full-length expressed sequence tags (ESTs). From in vitro cultured merozoites, 12,286 clones harboring full-length cDNAs were sequenced from both ends using the Sanger method, and 6,787 full-length cDNAs were assembled. These were then clustered, and a nonredundant referential data set of 2,115 full-length cDNA sequences was constructed. The comparison of the preproposed gene model with our data set identified 310 identical genes, 342 almost identical genes, 1,054 genes with potential structural inconsistencies, and 409 novel genes. The median length of 5' untranslated regions (UTRs) was 152 nt. Subsequently, we identified 4,086 transcription start sites (TSSs) and 2,023 transcriptionally active regions (TARs) by examining 5' ESTs. We identified ATGGGG and CCCCAT sites as consensus motifs in TARs that were distributed around -50 bp from TSSs. In addition, we found ACACA, TGTGT, and TATAT sites, which were distributed periodically around TSSs in cycles of approximately 150 bp. Moreover, related periodical distributions were not observed in mammalian promoter regions. The observations in this study indicate the utility of integrated bioinformatics and experimental data for improving genome annotations. In particular, full-length cDNAs with one-base resolution for TSSs enabled the identification of consensus motifs in promoter sequences and demonstrated clear distributions of identified motifs. These observations allowed the illustration of a model promoter composition, which supports the differences in transcriptional regulation frameworks between apicomplexan parasites and mammals. The online version of this article (doi:10.1186/1471-2164-15-678) contains supplementary material, which is available to authorized users.
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