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Rapid genome functional annotation pipeline anchored to the house sparrow (Passer domesticus, Linnaeus 1758) genome reannotation

The house sparrow (Passer domesticus) is a valuable avian model for studying evolutionary genetics, development, neurobiology, physiology, behavior, and ecology, both in laboratory and field-based settings. The current annotation of the P. domesticus genome available at the Ensembl Rapid Release sit...

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Autores principales: Magallanes-Alba, Melisa Eliana, Baricalla, Agustín, Rego, Natalia, Brun, Antonio, Karasov, William H, Caviedes-Vidal, Enrique
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10373626/
https://www.ncbi.nlm.nih.gov/pubmed/37521110
http://dx.doi.org/10.1093/biomethods/bpad013
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author Magallanes-Alba, Melisa Eliana
Baricalla, Agustín
Rego, Natalia
Brun, Antonio
Karasov, William H
Caviedes-Vidal, Enrique
author_facet Magallanes-Alba, Melisa Eliana
Baricalla, Agustín
Rego, Natalia
Brun, Antonio
Karasov, William H
Caviedes-Vidal, Enrique
author_sort Magallanes-Alba, Melisa Eliana
collection PubMed
description The house sparrow (Passer domesticus) is a valuable avian model for studying evolutionary genetics, development, neurobiology, physiology, behavior, and ecology, both in laboratory and field-based settings. The current annotation of the P. domesticus genome available at the Ensembl Rapid Release site is primarily focused on gene set building and lacks functional information. In this study, we present the first comprehensive functional reannotation of the P. domesticus genome using intestinal Illumina RNA sequencing (RNA-Seq) libraries. Our revised annotation provides an expanded view of the genome, encompassing 38592 transcripts compared to the current 23574 transcripts in Ensembl. We also predicted 14717 protein-coding genes, achieving 96.4% completeness for Passeriformes lineage BUSCOs. A substantial improvement in this reannotation is the accurate delineation of untranslated region (UTR) sequences. We identified 82.7% and 93.8% of the transcripts containing 5′- and 3′-UTRs, respectively. These UTR annotations are crucial for understanding post-transcriptional regulatory processes. Our findings underscore the advantages of incorporating additional specific RNA-Seq data into genome annotation, particularly when leveraging fast and efficient data processing capabilities. This functional reannotation enhances our understanding of the P. domesticus genome, providing valuable resources for future investigations in various research fields.
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spelling pubmed-103736262023-07-28 Rapid genome functional annotation pipeline anchored to the house sparrow (Passer domesticus, Linnaeus 1758) genome reannotation Magallanes-Alba, Melisa Eliana Baricalla, Agustín Rego, Natalia Brun, Antonio Karasov, William H Caviedes-Vidal, Enrique Biol Methods Protoc Methods Article The house sparrow (Passer domesticus) is a valuable avian model for studying evolutionary genetics, development, neurobiology, physiology, behavior, and ecology, both in laboratory and field-based settings. The current annotation of the P. domesticus genome available at the Ensembl Rapid Release site is primarily focused on gene set building and lacks functional information. In this study, we present the first comprehensive functional reannotation of the P. domesticus genome using intestinal Illumina RNA sequencing (RNA-Seq) libraries. Our revised annotation provides an expanded view of the genome, encompassing 38592 transcripts compared to the current 23574 transcripts in Ensembl. We also predicted 14717 protein-coding genes, achieving 96.4% completeness for Passeriformes lineage BUSCOs. A substantial improvement in this reannotation is the accurate delineation of untranslated region (UTR) sequences. We identified 82.7% and 93.8% of the transcripts containing 5′- and 3′-UTRs, respectively. These UTR annotations are crucial for understanding post-transcriptional regulatory processes. Our findings underscore the advantages of incorporating additional specific RNA-Seq data into genome annotation, particularly when leveraging fast and efficient data processing capabilities. This functional reannotation enhances our understanding of the P. domesticus genome, providing valuable resources for future investigations in various research fields. Oxford University Press 2023-07-07 /pmc/articles/PMC10373626/ /pubmed/37521110 http://dx.doi.org/10.1093/biomethods/bpad013 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Methods Article
Magallanes-Alba, Melisa Eliana
Baricalla, Agustín
Rego, Natalia
Brun, Antonio
Karasov, William H
Caviedes-Vidal, Enrique
Rapid genome functional annotation pipeline anchored to the house sparrow (Passer domesticus, Linnaeus 1758) genome reannotation
title Rapid genome functional annotation pipeline anchored to the house sparrow (Passer domesticus, Linnaeus 1758) genome reannotation
title_full Rapid genome functional annotation pipeline anchored to the house sparrow (Passer domesticus, Linnaeus 1758) genome reannotation
title_fullStr Rapid genome functional annotation pipeline anchored to the house sparrow (Passer domesticus, Linnaeus 1758) genome reannotation
title_full_unstemmed Rapid genome functional annotation pipeline anchored to the house sparrow (Passer domesticus, Linnaeus 1758) genome reannotation
title_short Rapid genome functional annotation pipeline anchored to the house sparrow (Passer domesticus, Linnaeus 1758) genome reannotation
title_sort rapid genome functional annotation pipeline anchored to the house sparrow (passer domesticus, linnaeus 1758) genome reannotation
topic Methods Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10373626/
https://www.ncbi.nlm.nih.gov/pubmed/37521110
http://dx.doi.org/10.1093/biomethods/bpad013
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