AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences.
AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences.
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DOI：
10.1038/srep21077
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发表时间：
2016-02-15
影响因子：
4.6
通讯作者：
Boch J
中科院分区：
文献类型：
--
作者：
Grau J;Reschke M;Erkes A;Streubel J;Morgan RD;Wilson GG;Koebnik R;Boch J
转录激活子样效应子(TALE)是由植物病原菌黄单胞菌产生的毒力因子，在植物细胞内起基因激活剂的作用。虽然单个故事对传染性的贡献已经被证明，但大多数故事的具体作用以及整个故事在黄单胞菌中的多样性。是未知的。故事有一个高度重复的DNA结合域，这是出了名的难以测序。在这里，我们描述了一种改进的方法，通过使用PacBio测序来表征TALL基因。我们介绍了“AnnoTALE”，这是一套应用程序，用于分析和注释Xanthomonas基因组中的故事基因，并将类似的故事分类。在这些分类的基础上，我们提出了黄单胞菌故事的统一命名，揭示了指向相关功能的相似性。这一新的分类使我们能够比较相关的故事，并确定导致故事特殊性进化的碱基替换。
Transcription activator-like effectors (TALEs) are virulence factors, produced by the bacterial plant-pathogen Xanthomonas, that function as gene activators inside plant cells. Although the contribution of individual TALEs to infectivity has been shown, the specific roles of most TALEs, and the overall TALE diversity in Xanthomonas spp. is not known. TALEs possess a highly repetitive DNA-binding domain, which is notoriously difficult to sequence. Here, we describe an improved method for characterizing TALE genes by the use of PacBio sequencing. We present ‘AnnoTALE’, a suite of applications for the analysis and annotation of TALE genes from Xanthomonas genomes, and for grouping similar TALEs into classes. Based on these classes, we propose a unified nomenclature for Xanthomonas TALEs that reveals similarities pointing to related functionalities. This new classification enables us to compare related TALEs and to identify base substitutions responsible for the evolution of TALE specificities.