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
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: | 16 Jul 2021 19:52 |
| PMCID: | PMC4280997 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/30926 |
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