De Novo Assembly of a High-Quality Reference Genome for the Horned Lark (Eremophila alpestris)
The Horned Lark (Eremophila alpestris) is a small songbird that exhibits remarkable geographic variation in appearance and habitat across an expansive distribution. While E. alpestris has been the focus of many ecological and evolutionary studies, we still lack a highly contiguous genome assembly fo...
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Oxford University Press
2020
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ftdoajarticles:oai:doaj.org/article:223e5f5b95bb4a3db34eb5b0952ea7db 2023-05-15T16:06:20+02:00 De Novo Assembly of a High-Quality Reference Genome for the Horned Lark (Eremophila alpestris) Nicholas A. Mason Paulo Pulgarin Carlos Daniel Cadena Irby J. Lovette 2020-02-01T00:00:00Z https://doi.org/10.1534/g3.119.400846 https://doaj.org/article/223e5f5b95bb4a3db34eb5b0952ea7db EN eng Oxford University Press http://g3journal.org/lookup/doi/10.1534/g3.119.400846 https://doaj.org/toc/2160-1836 2160-1836 doi:10.1534/g3.119.400846 https://doaj.org/article/223e5f5b95bb4a3db34eb5b0952ea7db G3: Genes, Genomes, Genetics, Vol 10, Iss 2, Pp 475-478 (2020) alaudidae allpaths-lg eremophila alpestris genome assembly horned lark Genetics QH426-470 article 2020 ftdoajarticles https://doi.org/10.1534/g3.119.400846 2022-12-31T06:57:21Z The Horned Lark (Eremophila alpestris) is a small songbird that exhibits remarkable geographic variation in appearance and habitat across an expansive distribution. While E. alpestris has been the focus of many ecological and evolutionary studies, we still lack a highly contiguous genome assembly for the Horned Lark and related taxa (Alaudidae). Here, we present CLO_EAlp_1.0, a highly contiguous assembly for E. alpestris generated from a blood sample of a wild, male bird captured in the Altiplano Cundiboyacense of Colombia. By combining short-insert and mate-pair libraries with the ALLPATHS-LG genome assembly pipeline, we generated a 1.04 Gb assembly comprised of 2713 scaffolds, with a largest scaffold size of 31.81 Mb, a scaffold N50 of 9.42 Mb, and a scaffold L50 of 30. These scaffolds were assembled from 23685 contigs, with a largest contig size of 1.69 Mb, a contig N50 of 193.81 kb, and a contig L50 of 1429. Our assembly pipeline also produced a single mitochondrial DNA contig of 14.00 kb. After polishing the genome, we identified 94.5% of single-copy gene orthologs from an Aves data set and 97.7% of single-copy gene orthologs from a vertebrata data set, which further demonstrates the high quality of our assembly. We anticipate that this genomic resource will be useful to the broader ornithological community and those interested in studying the evolutionary history and ecological interactions of larks, which comprise a widespread, yet understudied lineage of songbirds. Article in Journal/Newspaper Eremophila alpestris Directory of Open Access Journals: DOAJ Articles The Altiplano ENVELOPE(163.917,163.917,-78.133,-78.133) G3 Genes|Genomes|Genetics 10 2 475 478 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
alaudidae allpaths-lg eremophila alpestris genome assembly horned lark Genetics QH426-470 |
spellingShingle |
alaudidae allpaths-lg eremophila alpestris genome assembly horned lark Genetics QH426-470 Nicholas A. Mason Paulo Pulgarin Carlos Daniel Cadena Irby J. Lovette De Novo Assembly of a High-Quality Reference Genome for the Horned Lark (Eremophila alpestris) |
topic_facet |
alaudidae allpaths-lg eremophila alpestris genome assembly horned lark Genetics QH426-470 |
description |
The Horned Lark (Eremophila alpestris) is a small songbird that exhibits remarkable geographic variation in appearance and habitat across an expansive distribution. While E. alpestris has been the focus of many ecological and evolutionary studies, we still lack a highly contiguous genome assembly for the Horned Lark and related taxa (Alaudidae). Here, we present CLO_EAlp_1.0, a highly contiguous assembly for E. alpestris generated from a blood sample of a wild, male bird captured in the Altiplano Cundiboyacense of Colombia. By combining short-insert and mate-pair libraries with the ALLPATHS-LG genome assembly pipeline, we generated a 1.04 Gb assembly comprised of 2713 scaffolds, with a largest scaffold size of 31.81 Mb, a scaffold N50 of 9.42 Mb, and a scaffold L50 of 30. These scaffolds were assembled from 23685 contigs, with a largest contig size of 1.69 Mb, a contig N50 of 193.81 kb, and a contig L50 of 1429. Our assembly pipeline also produced a single mitochondrial DNA contig of 14.00 kb. After polishing the genome, we identified 94.5% of single-copy gene orthologs from an Aves data set and 97.7% of single-copy gene orthologs from a vertebrata data set, which further demonstrates the high quality of our assembly. We anticipate that this genomic resource will be useful to the broader ornithological community and those interested in studying the evolutionary history and ecological interactions of larks, which comprise a widespread, yet understudied lineage of songbirds. |
format |
Article in Journal/Newspaper |
author |
Nicholas A. Mason Paulo Pulgarin Carlos Daniel Cadena Irby J. Lovette |
author_facet |
Nicholas A. Mason Paulo Pulgarin Carlos Daniel Cadena Irby J. Lovette |
author_sort |
Nicholas A. Mason |
title |
De Novo Assembly of a High-Quality Reference Genome for the Horned Lark (Eremophila alpestris) |
title_short |
De Novo Assembly of a High-Quality Reference Genome for the Horned Lark (Eremophila alpestris) |
title_full |
De Novo Assembly of a High-Quality Reference Genome for the Horned Lark (Eremophila alpestris) |
title_fullStr |
De Novo Assembly of a High-Quality Reference Genome for the Horned Lark (Eremophila alpestris) |
title_full_unstemmed |
De Novo Assembly of a High-Quality Reference Genome for the Horned Lark (Eremophila alpestris) |
title_sort |
de novo assembly of a high-quality reference genome for the horned lark (eremophila alpestris) |
publisher |
Oxford University Press |
publishDate |
2020 |
url |
https://doi.org/10.1534/g3.119.400846 https://doaj.org/article/223e5f5b95bb4a3db34eb5b0952ea7db |
long_lat |
ENVELOPE(163.917,163.917,-78.133,-78.133) |
geographic |
The Altiplano |
geographic_facet |
The Altiplano |
genre |
Eremophila alpestris |
genre_facet |
Eremophila alpestris |
op_source |
G3: Genes, Genomes, Genetics, Vol 10, Iss 2, Pp 475-478 (2020) |
op_relation |
http://g3journal.org/lookup/doi/10.1534/g3.119.400846 https://doaj.org/toc/2160-1836 2160-1836 doi:10.1534/g3.119.400846 https://doaj.org/article/223e5f5b95bb4a3db34eb5b0952ea7db |
op_doi |
https://doi.org/10.1534/g3.119.400846 |
container_title |
G3 Genes|Genomes|Genetics |
container_volume |
10 |
container_issue |
2 |
container_start_page |
475 |
op_container_end_page |
478 |
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1766402223834660864 |