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.

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

“…TreeBest software was used to construct consensus phylogenetic gene trees incorporating five different tree-building methods: two were maximum-likelihood methods based on either protein alignment (WAG model) or codon alignment (phymal HKY model), and three were neighbor-joining methods that used p distance, dN distance or dS distance within codon alignments. The pipeline was run on the MAKER-P 136 annotations for ten Oryza species and L. perrieri (Table 1). Also included were annotations of three outgroup species, Arabidopsis thaliana (version TAIR10) 137 , Sorghum bicolor (version Sbi1.4) 138 and B. distachyon (version Brachy1.2) 139 , loaded from Gramene v40 Ensembl core databases 140 .…”

Improved maize reference genome with single-molecule technologies

“…The scripts, parameters, and intermediate files of each transposable element superfamily are available at https://github.com/mcstitzer/maize_v4_TE_annotation. The MAKER P pipeline was used to annotate protein coding genes 46 , integrat ing ab initio prediction with publicly available evidence from full length cDNA 47 , de novo assembled transcripts from short read mRNA sequencing (mRNA seq) 48 , isoform sequencing (Iso Seq) full length transcripts 14 , and proteins from other species. The gene models were filtered to remove transposons and low confidence predictions.…”

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

“…Protein coding genes were annotated using the MAKER‐P v.2.3 annotation pipeline (Campbell et al ., 2014). Within the pipeline, the repeat elements were masked using the RepeatMasker (www.repeatmasker.org, v. 3.3.0).…”