ArticlePlant physiology2015
Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes.
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Article in Plant physiology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30citing papers in PubMed
3.3field-weighted citation impact, top 7% of its field
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Who cites it
30 citing papers in PubMed, 51 citations in OpenAlex.
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- Complex genetic architecture underlying the plasticity of maize agronomic traits.Plant communications · 2023Article
- A comparative genomics examination of desiccation tolerance and sensitivity in two sister grass species.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Comprehensive transcriptome characterization of Grus japonensis using PacBio SMRT and Illumina sequencing.Scientific reports · 2021Article
- De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes.Science (New York, N.Y.) · 2021Article
- Sequence of the supernumerary B chromosome of maize provides insight into its drive mechanism and evolution.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn.Nature communications · 2021Article
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- Genomic prediction applied to multiple traits and environments in second season maize hybrids.Heredity · 2020Article
- MaizeMine: A Data Mining Warehouse for the Maize Genetics and Genomics Database.Frontiers in plant science · 2020Article
- Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae.Scientific reports · 2019Article
- The complexity of alternative splicing and landscape of tissue-specific expression in lotus (Nelumbo nucifera) unveiled by Illumina- and single-molecule real-time-based RNA-sequencing.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry.GigaScience · 2019Article
- Double triage to identify poorly annotated genes in maize: The missing link in community curation.PloS one · 2019Article
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- Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes.Nature genetics · 2018Article
- The maize W22 genome provides a foundation for functional genomics and transposon biology.Nature genetics · 2018Article
- An improved assembly and annotation of the melon (Cucumis melo L.) reference genome.Scientific reports · 2018Article
- A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa.BMC bioinformatics · 2017Article
- Article
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Authors and funding
16 authors at 8 institutions in 3 countries.
MeiYee LawThe Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.).
Kevin L ChildsThe Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.).
Michael S CampbellThe Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.).
Joshua C SteinThe Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.).
Andrew J OlsonThe Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.).
Carson HoltThe Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.).
Nicholas PanchyThe Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.).
Jikai LeiThe Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.).
Dian JiaoThe Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.).
Carson M AndorfThe Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.).
Carolyn J LawrenceThe Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.).
Doreen WareThe Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.).
Shin-Han ShiuThe Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.).
Yanni SunThe Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.).
Ning JiangThe Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.).
Mark YandellThe Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.) myandell@genetics.utah.edu.
University of Utah · USCold Spring Harbor Laboratory · USInstitute of Human Genetics · PLUnited States Department of Agriculture · USMichigan State University · USOntario Institute for Cancer Research · CAStar Center · USTexas Advanced Computing Center
Funding
No grant is acknowledged in the PubMed record.
Abstract
The large size and relative complexity of many plant genomes make creation, quality control, and dissemination of high-quality gene structure annotations challenging. In response, we have developed MAKER-P, a fast and easy-to-use genome annotation engine for plants. Here, we report the use of MAKER-P to update and revise the maize (Zea mays) B73 RefGen_v3 annotation build (5b+) in less than 3 h using the iPlant Cyberinfrastructure. MAKER-P identified and annotated 4,466 additional, well-supported protein-coding genes not present in the 5b+ annotation build, added additional untranslated regions to 1,393 5b+ gene models, identified 2,647 5b+ gene models that lack any supporting evidence (despite the use of large and diverse evidence data sets), identified 104,215 pseudogene fragments, and created an additional 2,522 noncoding gene annotations. We also describe a method for de novo training of MAKER-P for the annotation of newly sequenced grass genomes. Collectively, these results lead to the 6a maize genome annotation and demonstrate the utility of MAKER-P for rapid annotation, management, and quality control of grasses and other difficult-to-annotate plant genomes.
Indexed as
Databases, GeneticExonsGenes, PlantGenome, PlantIntronsModels, GeneticMolecular Sequence AnnotationPseudogenesQuality ControlRNA, UntranslatedZea maysRNA, Untranslated
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