A quick guide for student-driven community genome annotation

Abstract

High quality gene models are necessary to expand the molecular and genetic tools available for a target organism, but these are available for only a handful of model organisms that have undergone extensive curation and experimental validation over the course of many years. The majority of gene models present in biological databases today have been identified in draft genome assemblies using automated annotation pipelines that are frequently based on orthologs from distantly related model organisms and usually have minor or major errors. Manual curation is time consuming and often requires substantial expertise, but is instrumental in improving gene model structure and identification. Manual annotation may seem to be a daunting and cost-prohibitive task for small research communities but involving undergraduates in community genome annotation consortiums can be mutually beneficial for both education and improved genomic resources. We outline a workflow for efficient manual annotation driven by a team of primarily undergraduate annotators. This model can be scaled to large teams and includes quality control processes through incremental evaluation. Moreover, it gives students an opportunity to increase their understanding of genome biology and to participate in scientific research in collaboration with peers and senior researchers at multiple institutions.

Diaci v3.0: Chromosome-level assembly,de novotranscriptome and manual annotation ofDiaphorina citri,insect vector of Huanglongbing

“…Implementation of rigorous and consistent annotation practices across a virtual team of highly diverse annotators required project management tools and regular video conferences followed by extensive documentation that was continuously updated in response to user feedback. Standard operating procedures have been reported in as a guide for other annotation communities [14] to implement similar programs.…”

“…Curated genes represent manually refined models based on evidence from orthology and expression data using Apollo annotation editor [9]. Curation was performed by distributed groups based on curated workflow previously described in Hosmani et al [14]. Detailed reports of curated gene families in pathways of interest are described in the following sections and supplementary notes.…”

“…All publicly available RNA-Seq datasets were mapped as quantitative tracks. Manual curation was performed following the workflow previously described in [14] and modifications to the workflow, if any, are described in the individual pathway reports. Official gene set 3 (OGSv3) consists of predicted gene models from the MAKER annotation pipeline and manually curated genes from the Apollo annotation editor.…”

Facilitating Growth through Frustration: Using Genomics Research in a Course-Based Undergraduate Research Experience

“…Thousands of student investigators have annotated regions of previously unstudied Drosophila genomes, which are then used in meta-analyses to address a particular scientific question (28,29). A similar approach can be used to investigate any organism for which an assembled genome exists (30), allowing undergraduates to contribute meaningfully to scientific knowledge (31). Thus, GEP provides a dynamic approach to resolving the dual challenges of engaging large numbers of students in research and analyzing large amounts of data (32).…”

G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation

“…Gene annotation builds on what students are learning about gene structure, while requiring them to grapple with multiple lines of evidence to establish defendable gene models. Student annotation projects thus are mutually beneficial for researchers and for students, enabling unique science and providing a multi-faceted learning experience for students [6,7,8,9,10].…”