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

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.

Figure 1.

AED CDF for TAIR10 annotations compared with human RefSeq annotations. AED can be used to assess how well an annotation set agrees with its associated evidence. When plotted as a cumulative AED distribution, multiple annotation sets can be visualized on the same plot. Here, we have included the AED CDF for the TAIR10 (orange line) annotation of Arabidopsis and the human RefSeq (purple line) annotations of human for purposes of comparison.

Figure 2.

MAKER-P de novo annotation and update of TAIR10 annotations. AED CDF curves are shown for MAKER-P run as a de novo plant annotation engine (green curve) and when used to update the existing TAIR10 gene annotation data set (blue curve), bringing it into better agreement with the evidence. Both MAKER-P data sets improve upon the existing TAIR10 annotations (orange curve).

Figure 3.

MAKER-P improvements in AED are distributed across the entire TAIR10 data set. The cumulative AED distributions for the TAIR10 representative transcripts are broken down by the TAIR star rating system. Note the excellent agreement between the TAIR10 manually curated evidence classifications and MAKER’s automatic AED-based quality-control scheme. The dotted lines denote the AED curves for the MAKER-P-updated TAIR10 annotations.

Figure 4.

MAKER-P run times on the entire maize V2 genome assembly versus the number of processors used. Increasing the number of processors given to MAKER-P decreases the run time. Run time is less than 4 h using fewer than 500 CPUs, decreasing to less than 3 h with 1,092 CPUs.

Figure 5.

MAKER-P annotations can be easily visualized using WebApollo. This view from WebApollo shows the original TAIR10 AT5G03540 gene transcripts (orange), the MAKER-P de novo gene annotation at that locus (blue), and the MAKER-P-updated AT5G03540 gene transcripts (green). A subset of the mRNA-Seq and EST/cDNA data are shown in beige.