ArticlePlant physiology2014
MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations.
Article in Plant physiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 272 papers.
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272 citing papers in PubMed.
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- A pangenome of maize provides genetic insights into drought resistance.Nature genetics · 2025Article
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- Comprehensive review of multiomics applications and remediation of plant heavy metal toxicity.Stress biology · 2025Review
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- Chromosome-level haplotype-resolved genome assembly provides insights into the highly heterozygous genome of Italian ryegrass (Lolium multiflorum Lam.).The plant genome · 2025Article
- A comparison of 27 Arabidopsis thaliana genomes and the path toward an unbiased characterization of genetic polymorphism.Nature genetics · 2025Article
- A phased chromosome-level genome of the annelid tubeworm Galeolaria caespitosa.The Journal of heredity · 2025Article
- The chromosome-level genome of Hemerocallis middendorffii provides new insights into the floral scents and color biosynthesis in Chinese native daylily.BMC plant biology · 2025Article
- Plastomic studies inform the mechanisms of edaphic adaptation in North American species in the tribe Thelypodieae (Brassicaceae).American journal of botany · 2025Article
- Evidence for evolution of a new sex chromosome within the haploid-dominant Marchantiales plant lineage.Journal of integrative plant biology · 2025Article
212 more citing papers are in PubMed but not listed here.
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Authors and funding
16 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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