A pan-genomic approach to genome databases using maize as a model system

Research in the past decade has demonstrated that a single reference genome is not representative of a species’ diversity. MaizeGDB introduces a pan-genomic approach to hosting genomic data, leveraging the large number of diverse maize genomes and their associated datasets to quickly and efficiently...

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Autores principales: Woodhouse, Margaret R., Cannon, Ethalinda K., Portwood, John L., Harper, Lisa C., Gardiner, Jack M., Schaeffer, Mary L., Andorf, Carson M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Database
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8377966/
https://www.ncbi.nlm.nih.gov/pubmed/34416864
http://dx.doi.org/10.1186/s12870-021-03173-5
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author Woodhouse, Margaret R.
Cannon, Ethalinda K.
Portwood, John L.
Harper, Lisa C.
Gardiner, Jack M.
Schaeffer, Mary L.
Andorf, Carson M.
author_facet Woodhouse, Margaret R.
Cannon, Ethalinda K.
Portwood, John L.
Harper, Lisa C.
Gardiner, Jack M.
Schaeffer, Mary L.
Andorf, Carson M.
author_sort Woodhouse, Margaret R.
collection PubMed
description Research in the past decade has demonstrated that a single reference genome is not representative of a species’ diversity. MaizeGDB introduces a pan-genomic approach to hosting genomic data, leveraging the large number of diverse maize genomes and their associated datasets to quickly and efficiently connect genomes, gene models, expression, epigenome, sequence variation, structural variation, transposable elements, and diversity data across genomes so that researchers can easily track the structural and functional differences of a locus and its orthologs across maize. We believe our framework is unique and provides a template for any genomic database poised to host large-scale pan-genomic data. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-021-03173-5.
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spelling pubmed-83779662021-08-23 A pan-genomic approach to genome databases using maize as a model system Woodhouse, Margaret R. Cannon, Ethalinda K. Portwood, John L. Harper, Lisa C. Gardiner, Jack M. Schaeffer, Mary L. Andorf, Carson M. BMC Plant Biol Database Research in the past decade has demonstrated that a single reference genome is not representative of a species’ diversity. MaizeGDB introduces a pan-genomic approach to hosting genomic data, leveraging the large number of diverse maize genomes and their associated datasets to quickly and efficiently connect genomes, gene models, expression, epigenome, sequence variation, structural variation, transposable elements, and diversity data across genomes so that researchers can easily track the structural and functional differences of a locus and its orthologs across maize. We believe our framework is unique and provides a template for any genomic database poised to host large-scale pan-genomic data. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-021-03173-5. BioMed Central 2021-08-20 /pmc/articles/PMC8377966/ /pubmed/34416864 http://dx.doi.org/10.1186/s12870-021-03173-5 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Database
Woodhouse, Margaret R.
Cannon, Ethalinda K.
Portwood, John L.
Harper, Lisa C.
Gardiner, Jack M.
Schaeffer, Mary L.
Andorf, Carson M.
A pan-genomic approach to genome databases using maize as a model system
title A pan-genomic approach to genome databases using maize as a model system
title_full A pan-genomic approach to genome databases using maize as a model system
title_fullStr A pan-genomic approach to genome databases using maize as a model system
title_full_unstemmed A pan-genomic approach to genome databases using maize as a model system
title_short A pan-genomic approach to genome databases using maize as a model system
title_sort pan-genomic approach to genome databases using maize as a model system
topic Database
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8377966/
https://www.ncbi.nlm.nih.gov/pubmed/34416864
http://dx.doi.org/10.1186/s12870-021-03173-5
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