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Mammalian genome : official journal of the International Mammalian Genome Society2023; 34(3); 418-436; doi: 10.1007/s00335-023-10008-1

AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes.

Abstract: Current genome sequencing technologies have made it possible to generate highly contiguous genome assemblies for non-model animal species. Despite advances in genome assembly methods, there is still room for improvement in the delineation of specific gene features in the genomes. Here we present genome visualization and annotation tools to support seven livestock species (bovine, chicken, goat, horse, pig, sheep, and water buffalo), available in a new resource called AgAnimalGenomes. In addition to supporting the manual refinement of gene models, these browsers provide visualization tracks for hundreds of RNAseq experiments, as well as data generated by the Functional Annotation of Animal Genomes (FAANG) Consortium. For species with predicted gene sets from both Ensembl and RefSeq, the browsers provide special tracks showing the thousands of protein-coding genes that disagree across the two gene sources, serving as a valuable resource to alert researchers to gene model issues that may affect data interpretation. We describe the data and search methods available in the new genome browsers and how to use the provided tools to edit and create new gene models.
© 2023. The Author(s).
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Publication Date: 2023-07-17 PubMed ID: 37460664PubMed Central: PMC10382368DOI: 10.1007/s00335-023-10008-1Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • U.S. Gov't
  • Non-P.H.S.

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research paper introduces a new resource, AgAnimalGenomes, which consists of genome visualization and annotation tools designed to analyse and refine gene models for seven different livestock species. It serves as an important platform for the resolution of gene model conflicts and can help in better data interpretation.

AgAnimalGenomes and its Role

  • The study is centered around a new resource known as AgAnimalGenomes. This platform is a collection of genome visualization and annotation tools that cover seven livestock species—bovine, chicken, goat, horse, pig, sheep, and water buffalo.
  • Even with advancements in genome sequencing, there exist gaps when it comes to identifying and interpreting specific gene features. AgAnimalGenomes aims to mitigate these gaps by allowing for manual gene model refinement.
  • In addition to enabling gene model enhancement, AgAnimalGenomes also acts as a visualization platform for the users. It includes hundreds of visualization tracks that represent RNAseq experiments. This means users can visually refer to these experiments for their assistance.

Functional Annotation of Animal Genomes (FAANG) Consortium

  • The data generated by the Functional Annotation of Animal Genomes Consortium (FAANG) is included in AgAnimalGenomes. The scope of FAANG involves annotating the areas of all animal genomes that dictate the structure and function of RNA and proteins, as per the study’s findings.
  • The inclusion of FAANG’s data in AgAnimalGenomes would significantly contribute to the comprehensive and valuable insights of gene models and structures.

Alerting Researchers to Gene Model Issues

  • For species that have predicted gene sets from both Ensembl and RefSeq, AgAnimalGenomes provides special tracks that highlight the inconsistencies between the two gene sources.
  • This feature is of great value to the researchers as it alerts them to gene model issues that could potentially affect the interpretation of their data. It’s effectively like a safeguard against errors in research studies caused by conflicting gene model data.

Use and Functionality of AgAnimalGenomes

  • The authors of the study also describe the different search methods available within the AgAnimalGenomes. This allows users to leverage the functionalities better and refine their search results.
  • Users can harness the tools provided in AgAnimalGenomes to edit and create new gene models, thereby empowering researchers to generate fresh insights or correct existing gene models to enhance scientific studies and data interpretation.

Cite This Article

APA
Triant DA, Walsh AT, Hartley GA, Petry B, Stegemiller MR, Nelson BM, McKendrick MM, Fuller EP, Cockett NE, Koltes JE, McKay SD, Green JA, Murdoch BM, Hagen DE, Elsik CG. (2023). AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes. Mamm Genome, 34(3), 418-436. https://doi.org/10.1007/s00335-023-10008-1

Publication

Mammalian genome : official journal of the International Mammalian Genome Society
ISSN: 1432-1777
NlmUniqueID: 9100916
Country: United States
Language: English
Volume: 34
Issue: 3
Pages: 418-436

Researcher Affiliations

Triant, Deborah A
  • Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
Walsh, Amy T
  • Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
Hartley, Gabrielle A
  • Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA.
Petry, Bruna
  • Department of Animal Science, Iowa State University, Ames, IA, 50011, USA.
Stegemiller, Morgan R
  • Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, 83844, USA.
Nelson, Benjamin M
  • Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
McKendrick, Makenna M
  • Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, 74078, USA.
Fuller, Emily P
  • Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA.
Cockett, Noelle E
  • Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, 84322, USA.
Koltes, James E
  • Department of Animal Science, Iowa State University, Ames, IA, 50011, USA.
McKay, Stephanie D
  • Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, 05405, USA.
Green, Jonathan A
  • Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
Murdoch, Brenda M
  • Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, 83844, USA.
Hagen, Darren E
  • Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, 74078, USA.
Elsik, Christine G
  • Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA. elsikc@missouri.edu.
  • Division of Plant Science & Technology, University of Missouri, Columbia, MO, 65211, USA. elsikc@missouri.edu.
  • Institute for Data Science & Informatics, University of Missouri, Columbia, MO, 65211, USA. elsikc@missouri.edu.

MeSH Terms

  • Animals
  • Cattle
  • Swine
  • Horses / genetics
  • Sheep / genetics
  • Animals, Domestic / genetics
  • Molecular Sequence Annotation
  • Databases, Genetic
  • Genome / genetics
  • Chromosome Mapping
  • Goats / genetics

Conflict of Interest Statement

The authors have no relevant financial or non-financial interests to disclose.

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Citations

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