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Title: MAKER-P: a tool-kit for the creation, management, and quality control of plant genome annotations

item CAMPBELL, MICHAEL - University Of Utah
item LAW, MEIYEE - University Of Utah
item HOLT, CARSON - Ontario Cancer Institute
item STEIN, JOSHUA - Cold Spring Harbor Laboratory
item MOGHE, GAURAV - Michigan State University
item HUNAGEL, DAVID - Michigan State University
item LEI, JIKAI - Michigan State University
item ACHAWANANTAKUN, RUJIRA - Michigan State University
item Lawrence, Carolyn
item Ware, Doreen
item SHIU, SHIN-HAN - Michigan State University
item CHILDS, KEVIN - Michigan State University
item SUN, YANNI - Michigan State University
item JIANG, NING - Michigan State University
item YANDELL, MARK - University Of Utah

Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/3/2013
Publication Date: 2/1/2014
Citation: Campbell, M.S., Law, M., Holt, C., Stein, J., Moghe, G., Hunagel, D., Lei, J., Achawanantakun, R., Lawrence, C.J., Ware, D., Shiu, S., Childs, K.L., Sun, Y., Jiang, N., Yandell, M. 2014. MAKER-P: a tool-kit for the creation, management, and quality control of plant genome annotations. Plant Physiology. 164(2):513-24.

Interpretive Summary: Genomic information can only be used to improve plants if the genes are identified and characterized. A first step in this process is to specify regions of the genomes containing genes. Without those regions annotated, it is impossible to predict and test gene function. The tool described here accurately predicts genic regions of plant genomes and enables those annotations to be computed rapidly.

Technical Abstract: We have optimized and extended the widely used annotation-engine MAKER for use on plant genomes. We have benchmarked the resulting software, MAKER-P, using the A. thaliana genome and the TAIR10 gene models. Here we demonstrate the ability of the MAKER-P toolkit to generate de novo repeat databases, automatically update, extend, and revise the A. thaliana annotations in light of newly available RNA-Seq data and to annotate pseudogenes and ncRNAs absent from the TAIR10 build. Our results demonstrate that MAKER-P can be used to manage and improve the annotations of even A. thaliana, perhaps the best-annotated plant genome. We have also produced a massively parallel version of MAKER-P that is available for use as an iPlant Atmosphere image at the Texas Advanced Computing Center (TACC). Using this resource we show that MAKER-P can be used to annotate plant genomes and to make the results available online to the community within hours.