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A Chromosome-Level Genome Assembly of the Reed Warbler (Acrocephalus scirpaceus)

The reed warbler (Acrocephalus scirpaceus) is a long-distance migrant passerine with a wide distribution across Eurasia. This species has fascinated researchers for decades, especially its role as host of a brood parasite, and its capacity for rapid phenotypic change in the face of climate change. C...

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Autores principales: Sætre, Camilla Lo Cascio, Eroukhmanoff, Fabrice, Rönkä, Katja, Kluen, Edward, Thorogood, Rose, Torrance, James, Tracey, Alan, Chow, William, Pelan, Sarah, Howe, Kerstin, Jakobsen, Kjetill S, Tørresen, Ole K
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8459166/
https://www.ncbi.nlm.nih.gov/pubmed/34499122
http://dx.doi.org/10.1093/gbe/evab212
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author Sætre, Camilla Lo Cascio
Eroukhmanoff, Fabrice
Rönkä, Katja
Kluen, Edward
Thorogood, Rose
Torrance, James
Tracey, Alan
Chow, William
Pelan, Sarah
Howe, Kerstin
Jakobsen, Kjetill S
Tørresen, Ole K
author_facet Sætre, Camilla Lo Cascio
Eroukhmanoff, Fabrice
Rönkä, Katja
Kluen, Edward
Thorogood, Rose
Torrance, James
Tracey, Alan
Chow, William
Pelan, Sarah
Howe, Kerstin
Jakobsen, Kjetill S
Tørresen, Ole K
author_sort Sætre, Camilla Lo Cascio
collection PubMed
description The reed warbler (Acrocephalus scirpaceus) is a long-distance migrant passerine with a wide distribution across Eurasia. This species has fascinated researchers for decades, especially its role as host of a brood parasite, and its capacity for rapid phenotypic change in the face of climate change. Currently, it is expanding its range northwards in Europe, and is altering its migratory behavior in certain areas. Thus, there is great potential to discover signs of recent evolution and its impact on the genomic composition of the reed warbler. Here, we present a high-quality reference genome for the reed warbler, based on PacBio, 10×, and Hi-C sequencing. The genome has an assembly size of 1,075,083,815 bp with a scaffold N50 of 74,438,198 bp and a contig N50 of 12,742,779 bp. BUSCO analysis using aves_odb10 as a model showed that 95.7% of BUSCO genes were complete. We found unequivocal evidence of two separate macrochromosomal fusions in the reed warbler genome, in addition to the previously identified fusion between chromosome Z and a part of chromosome 4A in the Sylvioidea superfamily. We annotated 14,645 protein-coding genes, and a BUSCO analysis of the protein sequences indicated 97.5% completeness. This reference genome will serve as an important resource, and will provide new insights into the genomic effects of evolutionary drivers such as coevolution, range expansion, and adaptations to climate change, as well as chromosomal rearrangements in birds.
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spelling pubmed-84591662021-09-23 A Chromosome-Level Genome Assembly of the Reed Warbler (Acrocephalus scirpaceus) Sætre, Camilla Lo Cascio Eroukhmanoff, Fabrice Rönkä, Katja Kluen, Edward Thorogood, Rose Torrance, James Tracey, Alan Chow, William Pelan, Sarah Howe, Kerstin Jakobsen, Kjetill S Tørresen, Ole K Genome Biol Evol Genome Report The reed warbler (Acrocephalus scirpaceus) is a long-distance migrant passerine with a wide distribution across Eurasia. This species has fascinated researchers for decades, especially its role as host of a brood parasite, and its capacity for rapid phenotypic change in the face of climate change. Currently, it is expanding its range northwards in Europe, and is altering its migratory behavior in certain areas. Thus, there is great potential to discover signs of recent evolution and its impact on the genomic composition of the reed warbler. Here, we present a high-quality reference genome for the reed warbler, based on PacBio, 10×, and Hi-C sequencing. The genome has an assembly size of 1,075,083,815 bp with a scaffold N50 of 74,438,198 bp and a contig N50 of 12,742,779 bp. BUSCO analysis using aves_odb10 as a model showed that 95.7% of BUSCO genes were complete. We found unequivocal evidence of two separate macrochromosomal fusions in the reed warbler genome, in addition to the previously identified fusion between chromosome Z and a part of chromosome 4A in the Sylvioidea superfamily. We annotated 14,645 protein-coding genes, and a BUSCO analysis of the protein sequences indicated 97.5% completeness. This reference genome will serve as an important resource, and will provide new insights into the genomic effects of evolutionary drivers such as coevolution, range expansion, and adaptations to climate change, as well as chromosomal rearrangements in birds. Oxford University Press 2021-09-09 /pmc/articles/PMC8459166/ /pubmed/34499122 http://dx.doi.org/10.1093/gbe/evab212 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Genome Report
Sætre, Camilla Lo Cascio
Eroukhmanoff, Fabrice
Rönkä, Katja
Kluen, Edward
Thorogood, Rose
Torrance, James
Tracey, Alan
Chow, William
Pelan, Sarah
Howe, Kerstin
Jakobsen, Kjetill S
Tørresen, Ole K
A Chromosome-Level Genome Assembly of the Reed Warbler (Acrocephalus scirpaceus)
title A Chromosome-Level Genome Assembly of the Reed Warbler (Acrocephalus scirpaceus)
title_full A Chromosome-Level Genome Assembly of the Reed Warbler (Acrocephalus scirpaceus)
title_fullStr A Chromosome-Level Genome Assembly of the Reed Warbler (Acrocephalus scirpaceus)
title_full_unstemmed A Chromosome-Level Genome Assembly of the Reed Warbler (Acrocephalus scirpaceus)
title_short A Chromosome-Level Genome Assembly of the Reed Warbler (Acrocephalus scirpaceus)
title_sort chromosome-level genome assembly of the reed warbler (acrocephalus scirpaceus)
topic Genome Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8459166/
https://www.ncbi.nlm.nih.gov/pubmed/34499122
http://dx.doi.org/10.1093/gbe/evab212
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