Double triage to identify poorly annotated genes in maize: The missing link in community curation

Autoři: Marcela K. Tello-Ruiz aff001;  Cristina F. Marco aff003;  Fei-Man Hsu aff004;  Rajdeep S. Khangura aff005;  Pengfei Qiao aff006;  Sirjan Sapkota aff007;  Michelle C. Stitzer aff008;  Rachael Wasikowski aff009;  Hao Wu aff010;  Junpeng Zhan aff011;  Kapeel Chougule aff001;  Lindsay C. Barone aff003;  Cornel Ghiban aff003;  Demitri Muna aff001;  Andrew C. Olson aff001;  Liya Wang aff001;  Doreen Ware aff001;  David A. Micklos aff003
Působiště autorů: Plant Biology Program, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America aff001;  Department of Biological Sciences, State University of New York at Old Westbury, Old Westbury, New York, United States of America aff002;  DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America aff003;  Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan aff004;  Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America aff005;  Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, New York, United States of America aff006;  Department of Plant and Environmental Sciences, Clemson University, Clemson, South Carolina, United States of America aff007;  Department of Plant Sciences and Center for Population Biology, University of California Davis, Davis, California, United States of America aff008;  Department of Biological Sciences, University of Toledo, Toledo, Ohio, United States of America aff009;  Genetics, Development & Cell Biology Department, Iowa State University, Ames, Iowa, United States of America aff010;  School of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America aff011;  Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America aff012;  USDA, Agricultural Research Service, Washington, D.C., United States of America aff013
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article


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.

Klíčová slova:

Functional genomics – Genome annotation – Invertebrate genomics – Maize – Phylogenetic analysis – Plant genomics – Sequence alignment


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2019 Číslo 10
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