An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids.
An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids.
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DOI：
10.1186/s12859-016-1428-4
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发表时间：
2017-01-11
影响因子：
3
通讯作者：
Bellgard MI
中科院分区：
文献类型：
--
作者：
Barrero RA;Napier KR;Cunnington J;Liefting L;Keenan S;Frampton RA;Szabo T;Bulman S;Hunter A;Ward L;Whattam M;Bellgard MI
检测和防止外来病毒和类病毒进入边境对保护世界各地的植物产业贸易至关重要。现有的入境后检疫筛查协议依赖于耗时的生物学指标和/或需要了解感染病毒病原体的分子分析。植物已经发展出识别和应对病毒感染的能力，这种酶可以将病毒序列裂解成特定的小RNA产物。许多研究报告了广泛的小RNA的使用，包括参与不同生物途径的几种DICER酶的产物大小。在这里，我们通过使用特定的小RNA子集来优化病毒序列的组装。我们对澳大利亚和新西兰的检疫温室设施中的21种植物的小RNA片段进行了测序。对几种新组装工具进行基准测试后，得到了使用KMER为19的黑桃，以产生最佳的组装结果。我们还发现，使用21-25个核苷酸的小RNA进行从头组装可以导致病毒序列和植物寄主序列的嵌合组装。这种非特异性组件可以通过使用21-22个核苷酸或24个核苷酸的小RNA亚集来解析。在21个样本中，我们鉴定了与13个样本中的18个病毒和3个类病毒具有序列相似性的重叠群。大多数病毒只使用21-22nT长的病毒衍生siRNAs(ViRNAs)组装，除了一种柑橘内源副病毒病毒使用24nt长的viRNAs更有效地组装。这项研究中发现的所有三个类病毒都是使用21-22个核苷酸或24个核苷酸的病毒RNA完全组装的。优化的分析工作流程是在Yabi基于网络的分析环境中定制的。我们提出了一个完全自动化的病毒监测和诊断网络生物信息学工具包，为病毒病原体的发现和诊断提供了一个灵活的、用户友好的、健壮的和可扩展的界面。我们已经实施了一个自动化病毒监测和诊断(VSD)生物信息学工具包，该工具包可以产生改进的病毒和类病毒序列组合。VSD工具包提供了几个适用于不同病毒病原体的优化和可重复使用的工作流程。我们预计，这一资源将有助于监测和诊断植物、昆虫和无脊椎动物中的病毒病原体。本文的在线版本(doi：10.1186/s12859-0161428-4)包含补充材料，授权用户可以使用。
Detection and preventing entry of exotic viruses and viroids at the border is critical for protecting plant industries trade worldwide. Existing post entry quarantine screening protocols rely on time-consuming biological indicators and/or molecular assays that require knowledge of infecting viral pathogens. Plants have developed the ability to recognise and respond to viral infections through Dicer-like enzymes that cleave viral sequences into specific small RNA products. Many studies reported the use of a broad range of small RNAs encompassing the product sizes of several Dicer enzymes involved in distinct biological pathways. Here we optimise the assembly of viral sequences by using specific small RNA subsets. We sequenced the small RNA fractions of 21 plants held at quarantine glasshouse facilities in Australia and New Zealand. Benchmarking of several de novo assembler tools yielded SPAdes using a kmer of 19 to produce the best assembly outcomes. We also found that de novo assembly using 21–25 nt small RNAs can result in chimeric assemblies of viral sequences and plant host sequences. Such non-specific assemblies can be resolved by using 21–22 nt or 24 nt small RNAs subsets. Among the 21 selected samples, we identified contigs with sequence similarity to 18 viruses and 3 viroids in 13 samples. Most of the viruses were assembled using only 21–22 nt long virus-derived siRNAs (viRNAs), except for one Citrus endogenous pararetrovirus that was more efficiently assembled using 24 nt long viRNAs. All three viroids found in this study were fully assembled using either 21–22 nt or 24 nt viRNAs. Optimised analysis workflows were customised within the Yabi web-based analytical environment. We present a fully automated viral surveillance and diagnosis web-based bioinformatics toolkit that provides a flexible, user-friendly, robust and scalable interface for the discovery and diagnosis of viral pathogens. We have implemented an automated viral surveillance and diagnosis (VSD) bioinformatics toolkit that produces improved viruses and viroid sequence assemblies. The VSD toolkit provides several optimised and reusable workflows applicable to distinct viral pathogens. We envisage that this resource will facilitate the surveillance and diagnosis viral pathogens in plants, insects and invertebrates. The online version of this article (doi:10.1186/s12859-016-1428-4) contains supplementary material, which is available to authorized users.