MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

Michael S Campbell,Doreen Ware,Dian Jiao,Jikai Lei,Meiyee Law,Mark Yandell,Rujira Achawanantakun,Kevin L Childs,David E Hufnagel,Ning Jiang,Yanni Sun,Gaurav D Moghe,Shin-Han Shiu,Carolyn J Lawrence,Joshua C Stein,Carson Holt

doi:10.1104/pp.113.230144

Abstract

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.

Highlights

We have optimized and extended the widely used annotation engine MAKER in order to better support plant genome annotation efforts
The resulting software is available for download, and a MAKER-P module is installed at the Texas Advanced Computing Center (TACC) using the iPlant Cyberinfrastructure (Goff et al, 2011)
Using a massively parallel version of MAKER-P on the TACC, we show that MAKER-P can de novo annotate the Arabidopsis and maize genomes in less than 3 h and that the resulting annotations are of comparable quality to the current The Arabidopsis Information Resource 10 (TAIR10) and maize V2 annotation builds

Summary

Introduction

We have optimized and extended the widely used annotation engine MAKER in order to better support plant genome annotation efforts. A major challenge for these researchers is the generation and dissemination of high-quality gene structure annotations for downstream applications This is especially true for plant genomics researchers, given that plant genomes can be difficult targets for annotation: they are unusually rich in transposable elements (Feschotte et al, 2002; Schnable et al, 2009; Kejnovsky et al, 2012), have high. To achieve these goals, we have optimized and extended an established genome annotation engine, MAKER (Holt and Yandell, 2011), for the plant genome research community. The resulting software is available for download, and a MAKER-P module is installed at the Texas Advanced Computing Center (TACC) using the iPlant Cyberinfrastructure (Goff et al, 2011)

Methods

Results

Conclusion