Automated update, revision and quality control of the Zea mays genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes

Law, M., Childs, K. L., Campbell, M. S., Stein, J. C., Holt, C., Panchy, N., Lei, J., Jao, D., Andorf, C. M., Lawrence, C. J., Ware, D., Shiu, S. H., Sun, Y., Jiang, N., Yandell, M. (November 2014) Automated update, revision and quality control of the Zea mays genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes. Plant Physiology. ISSN 0032-0889

URL: http://www.ncbi.nlm.nih.gov/pubmed/25384563
DOI: 10.1104/pp.114.245027

Abstract

The large size and relative complexity of many plant genomes makes creation, quality control, and dissemination of high quality gene-structure annotations challenging. In response we have developed MAKER-P, a fast and easy-to-use genome annotation engine for plants. Here we report the use of MAKER-P to update and revise the Zea mays B73 RefGen_v3 annotation build (5b+) in less than three hours using the iPlant Cyberinfrastructure. MAKER-P identified and annotated 4,466 additional, well-supported protein-coding genes not present in the 5b+ annotation build; added additional untranslated regions (UTR) to 1,393 5b+ gene models, identified 2,647 5b+ gene models that lack any supporting evidence (despite the use of a large and diverse evidence datasets), identified 102,370 pseudogene fragments, and created an additional 2,522 non-coding gene annotations. We also describe a method for de novo training of MAKER-P for annotation of novel grass genomes. Collectively these results lead to the 6a maize genome annotation and demonstrate the utility of MAKER-P for rapid annotation, management, and quality control of grasses and other difficult-to-annotate plant genomes.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes > genome annotation
organism description > plant
CSHL Authors:
Communities: CSHL labs > Ware lab
Depositing User: Matt Covey
Date: 10 November 2014
Date Deposited: 21 Nov 2014 17:11
Last Modified: 21 Nov 2014 17:11
Related URLs:
URI: http://repository.cshl.edu/id/eprint/30926

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