A Reference Genome Assembly for the Spotted Flycatcher (Muscicapa striata)

The spotted flycatcher (Muscicapa striata) forms with the Mediterranean flycatcher (Muscicapa tyrrhenica) a newly recognized species pair of trans-Saharan migratory passerines. These flycatchers present a nested peripatric distribution, a pattern especially unusual among high dispersal species that...

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Autores principales: Baudrin, Gaspard, Pons, Jean-Marc, Bed’Hom, Bertrand, Gil, Lisa, Boyer, Roxane, Dusabyinema, Yves, Jiguet, Frédéric, Fuchs, Jérôme
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Genome Resource
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10402868/
https://www.ncbi.nlm.nih.gov/pubmed/37506263
http://dx.doi.org/10.1093/gbe/evad140
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author Baudrin, Gaspard
Pons, Jean-Marc
Bed’Hom, Bertrand
Gil, Lisa
Boyer, Roxane
Dusabyinema, Yves
Jiguet, Frédéric
Fuchs, Jérôme
author_facet Baudrin, Gaspard
Pons, Jean-Marc
Bed’Hom, Bertrand
Gil, Lisa
Boyer, Roxane
Dusabyinema, Yves
Jiguet, Frédéric
Fuchs, Jérôme
author_sort Baudrin, Gaspard
collection PubMed
description The spotted flycatcher (Muscicapa striata) forms with the Mediterranean flycatcher (Muscicapa tyrrhenica) a newly recognized species pair of trans-Saharan migratory passerines. These flycatchers present a nested peripatric distribution, a pattern especially unusual among high dispersal species that questions the eco-evolutionary factors involved during the speciation process. Here, we present a genome assembly for M. striata assembled using a combination of Nanopore and Illumina sequences. The final assembly is 1.08 Gb long and consists of 4,779 contigs with an N50 of 3.2 Mb. The completeness of our M. striata genome assembly is supported by the number of BUSCO (95%) and ultraconserved element (UCE) (4889/5041; 97.0%) loci retrieved. This assembly showed high synteny with the Ficedula albicollis reference genome, the closest species for which a chromosome-scale reference genome is available. Several inversions were identified and will need to be investigated at the family level.
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spelling pubmed-104028682023-08-05 A Reference Genome Assembly for the Spotted Flycatcher (Muscicapa striata) Baudrin, Gaspard Pons, Jean-Marc Bed’Hom, Bertrand Gil, Lisa Boyer, Roxane Dusabyinema, Yves Jiguet, Frédéric Fuchs, Jérôme Genome Biol Evol Genome Resource The spotted flycatcher (Muscicapa striata) forms with the Mediterranean flycatcher (Muscicapa tyrrhenica) a newly recognized species pair of trans-Saharan migratory passerines. These flycatchers present a nested peripatric distribution, a pattern especially unusual among high dispersal species that questions the eco-evolutionary factors involved during the speciation process. Here, we present a genome assembly for M. striata assembled using a combination of Nanopore and Illumina sequences. The final assembly is 1.08 Gb long and consists of 4,779 contigs with an N50 of 3.2 Mb. The completeness of our M. striata genome assembly is supported by the number of BUSCO (95%) and ultraconserved element (UCE) (4889/5041; 97.0%) loci retrieved. This assembly showed high synteny with the Ficedula albicollis reference genome, the closest species for which a chromosome-scale reference genome is available. Several inversions were identified and will need to be investigated at the family level. Oxford University Press 2023-07-28 /pmc/articles/PMC10402868/ /pubmed/37506263 http://dx.doi.org/10.1093/gbe/evad140 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. 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 Genome Resource
Baudrin, Gaspard
Pons, Jean-Marc
Bed’Hom, Bertrand
Gil, Lisa
Boyer, Roxane
Dusabyinema, Yves
Jiguet, Frédéric
Fuchs, Jérôme
A Reference Genome Assembly for the Spotted Flycatcher (Muscicapa striata)
title A Reference Genome Assembly for the Spotted Flycatcher (Muscicapa striata)
title_full A Reference Genome Assembly for the Spotted Flycatcher (Muscicapa striata)
title_fullStr A Reference Genome Assembly for the Spotted Flycatcher (Muscicapa striata)
title_full_unstemmed A Reference Genome Assembly for the Spotted Flycatcher (Muscicapa striata)
title_short A Reference Genome Assembly for the Spotted Flycatcher (Muscicapa striata)
title_sort reference genome assembly for the spotted flycatcher (muscicapa striata)
topic Genome Resource
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10402868/
https://www.ncbi.nlm.nih.gov/pubmed/37506263
http://dx.doi.org/10.1093/gbe/evad140
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