Cargando…

New genome assembly of the barn owl (Tyto alba alba)

New genomic tools open doors to study ecology, evolution, and population genomics of wild animals. For the Barn owl species complex, a cosmopolitan nocturnal raptor, a very fragmented draft genome was assembled for the American species (Tyto furcata pratincola) (Jarvis et al. 2014). To improve the g...

Descripción completa

Detalles Bibliográficos
Autores principales: Ducrest, Anne‐Lyse, Neuenschwander, Samuel, Schmid‐Siegert, Emanuel, Pagni, Marco, Train, Clément, Dylus, David, Nevers, Yannis, Warwick Vesztrocy, Alex, San‐Jose, Luis M., Dupasquier, Mélanie, Dessimoz, Christophe, Xenarios, Ioannis, Roulin, Alexandre, Goudet, Jérôme
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7069322/
https://www.ncbi.nlm.nih.gov/pubmed/32184981
http://dx.doi.org/10.1002/ece3.5991
_version_ 1783505757457612800
author Ducrest, Anne‐Lyse
Neuenschwander, Samuel
Schmid‐Siegert, Emanuel
Pagni, Marco
Train, Clément
Dylus, David
Nevers, Yannis
Warwick Vesztrocy, Alex
San‐Jose, Luis M.
Dupasquier, Mélanie
Dessimoz, Christophe
Xenarios, Ioannis
Roulin, Alexandre
Goudet, Jérôme
author_facet Ducrest, Anne‐Lyse
Neuenschwander, Samuel
Schmid‐Siegert, Emanuel
Pagni, Marco
Train, Clément
Dylus, David
Nevers, Yannis
Warwick Vesztrocy, Alex
San‐Jose, Luis M.
Dupasquier, Mélanie
Dessimoz, Christophe
Xenarios, Ioannis
Roulin, Alexandre
Goudet, Jérôme
author_sort Ducrest, Anne‐Lyse
collection PubMed
description New genomic tools open doors to study ecology, evolution, and population genomics of wild animals. For the Barn owl species complex, a cosmopolitan nocturnal raptor, a very fragmented draft genome was assembled for the American species (Tyto furcata pratincola) (Jarvis et al. 2014). To improve the genome, we assembled de novo Illumina and Pacific Biosciences (PacBio) long reads sequences of its European counterpart (Tyto alba alba). This genome assembly of 1.219 Gbp comprises 21,509 scaffolds and results in a N50 of 4,615,526 bp. BUSCO (Universal Single‐Copy Orthologs) analysis revealed an assembly completeness of 94.8% with only 1.8% of the genes missing out of 4,915 avian orthologs searched, a proportion similar to that found in the genomes of the zebra finch (Taeniopygia guttata) or the collared flycatcher (Ficedula albicollis). By mapping the reads of the female American barn owl to the male European barn owl reads, we detected several structural variants and identified 70 Mbp of the Z chromosome. The barn owl scaffolds were further mapped to the chromosomes of the zebra finch. In addition, the completeness of the European barn owl genome is demonstrated with 94 of 128 proteins missing in the chicken genome retrieved in the European barn owl transcripts. This improved genome will help future barn owl population genomic investigations.
format Online
Article
Text
id pubmed-7069322
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher John Wiley and Sons Inc.
record_format MEDLINE/PubMed
spelling pubmed-70693222020-03-17 New genome assembly of the barn owl (Tyto alba alba) Ducrest, Anne‐Lyse Neuenschwander, Samuel Schmid‐Siegert, Emanuel Pagni, Marco Train, Clément Dylus, David Nevers, Yannis Warwick Vesztrocy, Alex San‐Jose, Luis M. Dupasquier, Mélanie Dessimoz, Christophe Xenarios, Ioannis Roulin, Alexandre Goudet, Jérôme Ecol Evol Original Research New genomic tools open doors to study ecology, evolution, and population genomics of wild animals. For the Barn owl species complex, a cosmopolitan nocturnal raptor, a very fragmented draft genome was assembled for the American species (Tyto furcata pratincola) (Jarvis et al. 2014). To improve the genome, we assembled de novo Illumina and Pacific Biosciences (PacBio) long reads sequences of its European counterpart (Tyto alba alba). This genome assembly of 1.219 Gbp comprises 21,509 scaffolds and results in a N50 of 4,615,526 bp. BUSCO (Universal Single‐Copy Orthologs) analysis revealed an assembly completeness of 94.8% with only 1.8% of the genes missing out of 4,915 avian orthologs searched, a proportion similar to that found in the genomes of the zebra finch (Taeniopygia guttata) or the collared flycatcher (Ficedula albicollis). By mapping the reads of the female American barn owl to the male European barn owl reads, we detected several structural variants and identified 70 Mbp of the Z chromosome. The barn owl scaffolds were further mapped to the chromosomes of the zebra finch. In addition, the completeness of the European barn owl genome is demonstrated with 94 of 128 proteins missing in the chicken genome retrieved in the European barn owl transcripts. This improved genome will help future barn owl population genomic investigations. John Wiley and Sons Inc. 2020-02-19 /pmc/articles/PMC7069322/ /pubmed/32184981 http://dx.doi.org/10.1002/ece3.5991 Text en © 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Research
Ducrest, Anne‐Lyse
Neuenschwander, Samuel
Schmid‐Siegert, Emanuel
Pagni, Marco
Train, Clément
Dylus, David
Nevers, Yannis
Warwick Vesztrocy, Alex
San‐Jose, Luis M.
Dupasquier, Mélanie
Dessimoz, Christophe
Xenarios, Ioannis
Roulin, Alexandre
Goudet, Jérôme
New genome assembly of the barn owl (Tyto alba alba)
title New genome assembly of the barn owl (Tyto alba alba)
title_full New genome assembly of the barn owl (Tyto alba alba)
title_fullStr New genome assembly of the barn owl (Tyto alba alba)
title_full_unstemmed New genome assembly of the barn owl (Tyto alba alba)
title_short New genome assembly of the barn owl (Tyto alba alba)
title_sort new genome assembly of the barn owl (tyto alba alba)
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7069322/
https://www.ncbi.nlm.nih.gov/pubmed/32184981
http://dx.doi.org/10.1002/ece3.5991
work_keys_str_mv AT ducrestannelyse newgenomeassemblyofthebarnowltytoalbaalba
AT neuenschwandersamuel newgenomeassemblyofthebarnowltytoalbaalba
AT schmidsiegertemanuel newgenomeassemblyofthebarnowltytoalbaalba
AT pagnimarco newgenomeassemblyofthebarnowltytoalbaalba
AT trainclement newgenomeassemblyofthebarnowltytoalbaalba
AT dylusdavid newgenomeassemblyofthebarnowltytoalbaalba
AT neversyannis newgenomeassemblyofthebarnowltytoalbaalba
AT warwickvesztrocyalex newgenomeassemblyofthebarnowltytoalbaalba
AT sanjoseluism newgenomeassemblyofthebarnowltytoalbaalba
AT dupasquiermelanie newgenomeassemblyofthebarnowltytoalbaalba
AT dessimozchristophe newgenomeassemblyofthebarnowltytoalbaalba
AT xenariosioannis newgenomeassemblyofthebarnowltytoalbaalba
AT roulinalexandre newgenomeassemblyofthebarnowltytoalbaalba
AT goudetjerome newgenomeassemblyofthebarnowltytoalbaalba