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...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2023-03-01
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| Series: | PLoS Genetics |
| Online Access: | https://doi.org/10.1371/journal.pgen.1010468 |
| _version_ | 1797850280841183232 |
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| author | Sichong Peng Anna R Dahlgren Callum G Donnelly Erin N Hales Jessica L Petersen Rebecca R Bellone Ted Kalbfleisch Carrie J Finno |
| author_facet | Sichong Peng Anna R Dahlgren Callum G Donnelly Erin N Hales Jessica L Petersen Rebecca R Bellone Ted Kalbfleisch Carrie J Finno |
| author_sort | Sichong Peng |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-09T18:58:59Z |
| format | Article |
| id | doaj.art-1876f7e0d619444dac57309eeaae8585 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-04-09T18:58:59Z |
| publishDate | 2023-03-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-1876f7e0d619444dac57309eeaae85852023-04-09T05:31:58ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042023-03-01193e101046810.1371/journal.pgen.1010468Functional annotation of the animal genomes: An integrated annotation resource for the horse.Sichong PengAnna R DahlgrenCallum G DonnellyErin N HalesJessica L PetersenRebecca R BelloneTed KalbfleischCarrie J FinnoThe 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.https://doi.org/10.1371/journal.pgen.1010468 |
| spellingShingle | Sichong Peng Anna R Dahlgren Callum G Donnelly Erin N Hales Jessica L Petersen Rebecca R Bellone Ted Kalbfleisch Carrie J Finno Functional annotation of the animal genomes: An integrated annotation resource for the horse. PLoS Genetics |
| 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 |
| url | https://doi.org/10.1371/journal.pgen.1010468 |
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