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Functional annotation of the animal genomes: An integrated annotation resource for the horse
The genomic sequence of the horse has been available since 2009, providing critical resources for discovering important genomic variants regarding both animal health and population structures. However, to fully understand the functional implications of these variants, detailed annotation of the hors...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10013926/ https://www.ncbi.nlm.nih.gov/pubmed/36862752 http://dx.doi.org/10.1371/journal.pgen.1010468 |
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author | Peng, Sichong Dahlgren, Anna R. Donnelly, Callum G. Hales, Erin N. Petersen, Jessica L. Bellone, Rebecca R. Kalbfleisch, Ted Finno, Carrie J. |
author_facet | Peng, Sichong Dahlgren, Anna R. Donnelly, Callum G. Hales, Erin N. Petersen, Jessica L. Bellone, Rebecca R. Kalbfleisch, Ted Finno, Carrie J. |
author_sort | Peng, Sichong |
collection | PubMed |
description | The genomic sequence of the horse has been available since 2009, providing critical resources for discovering important genomic variants regarding both animal health and population structures. However, to fully understand the functional implications of these variants, detailed annotation of the horse genome is required. Due to the limited availability of functional data for the equine genome, as well as the technical limitations of short-read RNA-seq, existing annotation of the equine genome contains limited information about important aspects of gene regulation, such as alternate isoforms and regulatory elements, which are either not transcribed or transcribed at a very low level. To solve above problems, the Functional Annotation of the Animal Genomes (FAANG) project proposed a systemic approach to tissue collection, phenotyping, and data generation, adopting the blueprint laid out by the Encyclopedia of DNA Elements (ENCODE) project. Here we detail the first comprehensive overview of gene expression and regulation in the horse, presenting 39,625 novel transcripts, 84,613 candidate cis-regulatory elements (CRE) and their target genes, 332,115 open chromatin regions genome wide across a diverse set of tissues. We showed substantial concordance between chromatin accessibility, chromatin states in different genic features and gene expression. This comprehensive and expanded set of genomics resources will provide the equine research community ample opportunities for studies of complex traits in the horse. |
format | Online Article Text |
id | pubmed-10013926 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-100139262023-03-15 Functional annotation of the animal genomes: An integrated annotation resource for the horse Peng, Sichong Dahlgren, Anna R. Donnelly, Callum G. Hales, Erin N. Petersen, Jessica L. Bellone, Rebecca R. Kalbfleisch, Ted Finno, Carrie J. PLoS Genet Research Article The genomic sequence of the horse has been available since 2009, providing critical resources for discovering important genomic variants regarding both animal health and population structures. However, to fully understand the functional implications of these variants, detailed annotation of the horse genome is required. Due to the limited availability of functional data for the equine genome, as well as the technical limitations of short-read RNA-seq, existing annotation of the equine genome contains limited information about important aspects of gene regulation, such as alternate isoforms and regulatory elements, which are either not transcribed or transcribed at a very low level. To solve above problems, the Functional Annotation of the Animal Genomes (FAANG) project proposed a systemic approach to tissue collection, phenotyping, and data generation, adopting the blueprint laid out by the Encyclopedia of DNA Elements (ENCODE) project. Here we detail the first comprehensive overview of gene expression and regulation in the horse, presenting 39,625 novel transcripts, 84,613 candidate cis-regulatory elements (CRE) and their target genes, 332,115 open chromatin regions genome wide across a diverse set of tissues. We showed substantial concordance between chromatin accessibility, chromatin states in different genic features and gene expression. This comprehensive and expanded set of genomics resources will provide the equine research community ample opportunities for studies of complex traits in the horse. Public Library of Science 2023-03-02 /pmc/articles/PMC10013926/ /pubmed/36862752 http://dx.doi.org/10.1371/journal.pgen.1010468 Text en © 2023 Peng et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Peng, Sichong Dahlgren, Anna R. Donnelly, Callum G. Hales, Erin N. Petersen, Jessica L. Bellone, Rebecca R. Kalbfleisch, Ted Finno, Carrie J. Functional annotation of the animal genomes: An integrated annotation resource for the horse |
title | Functional annotation of the animal genomes: An integrated annotation resource for the horse |
title_full | Functional annotation of the animal genomes: An integrated annotation resource for the horse |
title_fullStr | Functional annotation of the animal genomes: An integrated annotation resource for the horse |
title_full_unstemmed | Functional annotation of the animal genomes: An integrated annotation resource for the horse |
title_short | Functional annotation of the animal genomes: An integrated annotation resource for the horse |
title_sort | functional annotation of the animal genomes: an integrated annotation resource for the horse |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10013926/ https://www.ncbi.nlm.nih.gov/pubmed/36862752 http://dx.doi.org/10.1371/journal.pgen.1010468 |
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