Título:
Rapid genome functional annotation pipeline anchored to the house sparrow (Passer domesticus, Linnaeus 1758) genome reannotation
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Autor:
Magallanes-Alba, Melisa Eliana
Baricalla, Agustın
Rego, Natalia
Brun, Antonio
Karasov, William H
Caviedes-Vidal, Enrique
Baricalla, Agustın
Rego, Natalia
Brun, Antonio
Karasov, William H
Caviedes-Vidal, Enrique
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Tipo de documento:
Artículo
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Palabras clave:
Gene annotation
RNA-Seq
Annotation pipeline
Intestine
Birds
Passer domesticus
RNA-Seq
Annotation pipeline
Intestine
Birds
Passer domesticus
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Año de publicación:
2023
Contenido:
Resumen:
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 50- and 30-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.
Descripción:
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Oxford
EN:
Biology Methods and Protocols, 2023, 8(1): bpad013.
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Citación:
Magallanes-Alba, M, Baricalla, A, Natalia, R [y otros autores]. "Rapid genome functional annotation pipeline anchored to the house sparrow (Passer domesticus, Linnaeus 1758) genome reannotation". Biology Methods and Protocols. [en línea] 2023, 8(1): bpad013. 7 h. DOI: 10.1093/biomethods/bpad013.
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2396-8923
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Licencia:
Licencia Creative Commons Atribución - No Comercial (CC - By-NC 4.0)
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| Ficheros | Descripción | Tamaño | Formato | ||
|---|---|---|---|---|---|
| 10.1093.biomethods.bpad013.pdf | — | 706.07 KB | Adobe PDF |