MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations1[W][OPEN]

By Michael Campbell, Meiyee Law, Carson Holt, J. Stein, G. Moghe, D. Hufnagel, Jikai Lei, Rujira Achawanantakun, Dian Jiao, Carolyn J. Lawrence-Dill and 6 more. Plant Physiology, 2013

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MAKER-P annotates the entire Arabidopsis and maize genomes in less than 3 h with comparable quality to the current TAIR10 and maize V2 annotation builds. We have optimized and extended the widely used annotation engine MAKER in order to better support plant genome annotation efforts. New features include better parallelization for large repeat-rich plant genomes, noncoding RNA annotation capabilities, and support for pseudogene identification. We have benchmarked the resulting software tool kit, MAKER-P, using the Arabidopsis (Arabidopsis thaliana) and maize (Zea mays) genomes. Here, we demonstrate the ability of the MAKER-P tool kit to automatically update, extend, and revise the Arabidopsis annotations in light of newly available data and to annotate pseudogenes and noncoding RNAs absent from The Arabidopsis Informatics Resource 10 build. Our results demonstrate that MAKER-P can be used to manage and improve the annotations of even Arabidopsis, perhaps the best-annotated plant genome. We have also installed and benchmarked MAKER-P on the Texas Advanced Computing Center. We show that this public resource can de novo annotate the entire Arabidopsis and maize genomes in less than 3 h and produce annotations of comparable quality to those of the current The Arabidopsis Information Resource 10 and maize V2 annotation builds.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/eaf252e51499a878d9c31b922bca7414221a626d

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Citations in the corpus

Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline (2019, methodology): “Finally, protein-coding sequences were removed using the ProtExcluder package [73].”
Genome Annotation and Curation Using MAKER and MAKER-P (2014, methodology): “…update existing annotations in the light of new experimental evidence and for quality control of gene models produced by other annotation pipelines (Campbell et al., 2013; Law et al., 2014) MAKER and MAKER-P are both highly parallelized applications with support for the Message Passing Interface…”
Araport11: a complete reannotation of the Arabidopsis thaliana reference genome (2016, methodology): “…generated in this study, 2) the EST, full-length cDNAs and RNA-seq data including non-control and additional ecotype samples generated by MAKER-P (Campbell et al. 2014) and 3) UniRef90 protein sequences for ten plant species (see “Novel transcribed regions” in Methods) aligned to TAIR10 genome…”