An Overview of Best Practices for Transposable Element Identification, Classification, and Annotation in Eukaryotic Genomes.
An Overview of Best Practices for Transposable Element Identification, Classification, and Annotation in Eukaryotic Genomes.
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DOI：
10.1007/978-1-0716-2883-6_1
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发表时间：
2023
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转座因子对真核生物基因组结构、功能和进化的影响越来越广泛。大量的基因组学、转录组学和蛋白质组学数据为基本上将任何非模型真核生物物种转变为研究生物体生物学的任何和所有方面的新兴模型提供了基础，最终塑造了生物医学、环境和生物多样性研究的未来方向。然而，移动的基因组组分的鉴定和注释仍然落后于宿主基因注释所接受的标准。为了实现为每个基因组计划提供除了标准基因和转录组数据集之外的其mobilome组分的全面描述的目标，TE鉴定、分类和注释的每个步骤都应专注于改进TE边界指定，降低鉴定错误率，并提供关于TE插入的类型和完整性的准确信息。在这里，我们为在非模型生物的从头组装中生成TE模型提供了实用的建议，提供了一步一步的指导，以指导经验不足的TE注释者通过一些常用的TE分析管道，并接受工具改进的建议，这些建议可以由感兴趣的开发人员实施。
Transposable elements (TEs) exert an increasingly diverse spectrum of influences on eukaryotic genome structure, function, and evolution. A deluge of genomic, transcriptomic and proteomic data provides the foundation for turning essentially any non-model eukaryotic species into an emerging model to study any and all aspects of organismal biology, ultimately shaping future directions for biomedical, environmental and biodiversity research. However, identification and annotation of the mobile genome component still lags behind the standards accepted for host gene annotation. To achieve the objective of providing every genome project with a comprehensive description of its mobilome component in addition to the standard genic and transcriptomic datasets, each step of TE identification, classification and annotation should be focused on improving TE boundary designation, reducing identification error rates, and providing accurate information on the type and integrity of TE insertions. Here, we offer practical advice for generating TE models in de novo assemblies for non-model organisms, provide step-by-step instructions to guide inexperienced TE annotators through some of the commonly utilized TE analysis pipelines, and entertain suggestions for tool improvement which could be implemented by interested developers.