Manual annotation of Drosophila genes: a Genomics Education Partnership protocol.
Manual annotation of Drosophila genes: a Genomics Education Partnership protocol.
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DOI：
10.12688/f1000research.126839.3
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发表时间：
2022
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注释多个物种的基因组使我们能够分析它们基因的进化。虽然许多真核基因组组装已经包括计算基因预测，但这些预测可以受益于通过手动基因注释进行的审查和改进。基因组学教育伙伴关系（GEP; https：//thegep.org/）开发了一种蛋白质编码基因的结构注释协议，使本科生和教师研究人员能够创建高质量的基因注释，可用于后续的科学研究。例如，GEP的教职员工已经利用该协议，让本科生参与27种果蝇中胰岛素信号通路相关基因的比较注释，使用D。黑腹果蝇作为参考基因组。学生使用多条计算和经验证据构建基因模型，包括表达数据（例如，RNA-Seq）、序列相似性（例如，BLAST和多序列比对）和计算基因预测。质量控制措施要求每个基因由至少两名独立工作的学生进行注释，然后由更有经验的学生对提交的基因模型进行核对。本文提供了一个注释协议的概述，并介绍了如何解决学生提交的基因模型的差异，以产生一个最终的，高质量的基因集适合于随后的分析。该协议可以适用于其他科学问题（例如，果蝇Muller F元件的扩增）和物种（例如，寄生蜂），为本科生提供更多机会参与基因组学研究。这些学生注释的努力可以大大提高基因注释的质量在公开可用的基因组数据库。
Annotating the genomes of multiple species allows us to analyze the evolution of their genes. While many eukaryotic genome assemblies already include computational gene predictions, these predictions can benefit from review and refinement through manual gene annotation. The Genomics Education Partnership (GEP; https://thegep.org/) developed a structural annotation protocol for protein-coding genes that enables undergraduate student and faculty researchers to create high-quality gene annotations that can be utilized in subsequent scientific investigations. For example, this protocol has been utilized by the GEP faculty to engage undergraduate students in the comparative annotation of genes involved in the insulin signaling pathway in 27 Drosophila species, using D. melanogaster as the reference genome. Students construct gene models using multiple lines of computational and empirical evidence including expression data (e.g., RNA-Seq), sequence similarity (e.g., BLAST and multiple sequence alignment), and computational gene predictions. Quality control measures require each gene be annotated by at least two students working independently, followed by reconciliation of the submitted gene models by a more experienced student. This article provides an overview of the annotation protocol and describes how discrepancies in student submitted gene models are resolved to produce a final, high-quality gene set suitable for subsequent analyses. The protocol can be adapted to other scientific questions (e.g., expansion of the Drosophila Muller F element) and species (e.g., parasitoid wasps) to provide additional opportunities for undergraduate students to participate in genomics research. These student annotation efforts can substantially improve the quality of gene annotations in publicly available genomic databases.