Double triage to identify poorly annotated genes in maize: The missing link in community curation
Double triage to identify poorly annotated genes in maize: The missing link in community curation
Abstract The sophistication of gene prediction algorithms and the abundance of RNA-based evidence for the maize genome may suggest that manual curation of gene models is no longer necessary. However, quality metrics generated by the MAKER-P gene annotation pipeline identified 17,225 of 130,330 (13%) protein-coding transcripts in the B73 Reference Genome V4 gene set with models of low concordance to available biological evidence. Working with eight graduate students, we used the Apollo annotation editor to curate 86 transcript models flagged by quality metrics and a complimentary method using the Gramene gene tree visualizer. All of the triaged models had significant errors – including missing or extra exons, non-canonical splice sites, and incorrect UTRs. A correct transcript model existed for about 60% of genes (or transcripts) flagged by quality metrics; we attribute this to the convention of elevating the transcript with the longest coding sequence (CDS) to the canonical, or first, position. The remaining 40% of flagged genes resulted in novel annotations and represent a manual curation space of about 10% of the maize genome (~4,000 protein-coding genes). MAKER-P metrics have a specificity of 100%, and a sensitivity of 85%; the gene tree visualizer has a specificity of 100%. Together with the Apollo graphical editor, our double triage provides an infrastructure to support the community curation of eukaryotic genomes by scientists, students, and potentially even citizen scientists.
Qiao Pengfei、Wasikowski Rachael、Ghiban Cornel、Olson Andrew C.、Ware Doreen C.、Marco Cristina F.、Khangura Rajdeep S.、Wu Hao、Hsu Fei-Man、Stitzer Michelle C.、Micklos David A.、Barone Lindsay C.、Chougule Kapeel、Wang Liya C.、Muna Demitri、Sapkota Sirjan、Zhan Junpeng、Tello-Ruiz Marcela K.
Plant Biology Section, School of Integrative Plant Sciences, Cornell UniversityDepartment of Biological Sciences, University of ToledoDNA Learning Center, Cold Spring Harbor LaboratoryPlant Biology Program, Cold Spring Harbor LaboratoryPlant Biology Program, Cold Spring Harbor Laboratory||USDA, Agricultural Research ServiceDNA Learning Center, Cold Spring Harbor LaboratoryDepartment of Biochemistry, Purdue UniversityGenetics, Development & Cell Biology Department, Iowa State UniversityGraduate School of Frontier Sciences, University of TokyoDepartment of Plant Sciences and Center for Population Biology, University of CaliforniaDNA Learning Center, Cold Spring Harbor LaboratoryDNA Learning Center, Cold Spring Harbor LaboratoryPlant Biology Program, Cold Spring Harbor LaboratoryPlant Biology Program, Cold Spring Harbor LaboratoryPlant Biology Program, Cold Spring Harbor LaboratoryDepartment of Plant and Environmental Sciences, Clemson UniversitySchool of Plant Sciences, University of Arizona||Donald Danforth Plant Science CenterPlant Biology Program, Cold Spring Harbor Laboratory||Department of Biological Sciences, State University of New York at Old Westbury
遗传学生物科学研究方法、生物科学研究技术植物学
Qiao Pengfei,Wasikowski Rachael,Ghiban Cornel,Olson Andrew C.,Ware Doreen C.,Marco Cristina F.,Khangura Rajdeep S.,Wu Hao,Hsu Fei-Man,Stitzer Michelle C.,Micklos David A.,Barone Lindsay C.,Chougule Kapeel,Wang Liya C.,Muna Demitri,Sapkota Sirjan,Zhan Junpeng,Tello-Ruiz Marcela K..Double triage to identify poorly annotated genes in maize: The missing link in community curation[EB/OL].(2025-03-28)[2025-04-28].https://www.biorxiv.org/content/10.1101/654848.点此复制
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